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User Manual - PENN

1. window Tunctior v This opens the processing parameter editor see also chapter 5 1 The following extra buttons are available 1 Undo last value change Can be used to undo multiple changes amp Status parameter display The button turns green when activated dpp 123 Change processed dataset dimensionality parameter PPARMOD W Collapse expand all parameter sections gy Search for specified parameter Changed parameters are automatically saved 1D Display 117 How to Set Acquisition Parameters r Click the AcquPars tab eda examid 1H 1 1 Chio guest Sel Spectrum ProcPars AcquPars Title PulseProg Peaks Integrals Sample structure Fid ACU oln s e Hlgl ial YF Experiment PULPROts Current pulse pr At mod Acquisition modi TD size of fid NS Number of Scar DS Murmber of durntr TOU Loop count for t YF Width 12 0160 Spectral width w Ti gt This opens the acquisition parameter editor see also chapter 5 1 The following extra buttons are available 1 Undo last value change Can be used to undo multiple changes Tl Show pulse program parameters ased s Status parameter display The button turns green when activated dpa g Set probehead solvent dependant parameters getprosol rss Set nuclei and routing edasp 123 Change raw dataset dimensionality parameter PARMODE W Collapse expand all parameter sections Sear
2. Figure 12 12 How to Display the Next Previous Name Expno To compare a series of spectra you can interactively increment or decrement the dataset name or expno A dataset name is incremented according to the ICON NMR naming convention of increasing extensions e g name 001 name 002 etc r Click one of the following button button turns green E Show the previous name expno procno of the last dataset E Show the previous name expno procno of the last dataset Ei Set the increment options Clicking this button will open the following dialog where you can choose to increment the procno expno or name set the expno increment and switch individual scaling on off How to Scan Rows Columns Click the following button it turns green and move the mouse in the data field LT to scan rows in the 2D spectrum 232 2D Interactive Manipulation Click the following button it turns green and move the mouse in the data field 4 to scan columns in the 2D spectrum Click the following button it turns green and move the mouse in the data field lf to scan rows and columns in the 2D spectrum To scale up the displayed row column r Click the left mouse button or turn the mouse wheel up To scale down the displayed row column r Click the middle mouse button or turn the mouse wheel down How to Grab a Row Column You can grab a row or column 1 e keep it displayed in the data window as fol lows 1 Scan rows or columns
3. 110 How to Reopen a Dataset in a Second Third etc Window 110 How to Rescale or Shift one Dataset in Multiple windows 111 8 3 Changing the Display of a 1D Spectrum or FID 112 How to Change the Vertical Scaling of the FID or Spectrum 112 How to Smoothly Change the Vertical Scaling of the FID Spectrum 112 How to Change the Horizontal Scaling of the FID or Spectrum 112 How to Shift a Spectral Region to the Left or to the Right 114 How to Shift the Spectrum Up or Down 0000 114 Sd Usma the ODi eaer eed od hoe erie head eet ees 115 How to Display the Spectrum 0 ccc ee ees 115 How to Set Processing Parameters 0 00 cece eee eens 116 How to Set Acquisition Parameters 0 0 0 cece eee eee 117 Howto Edit Me TG reirei ae eee ered edie weet eee 118 How to Edit the Pulse Program 20 cc cece eee eee 119 How to Display the Peak list 2 0 0 ee eee 119 How to Display the Integral list 0 0 0 0 00000 128 How to view Sample Information 0 0 0 0 cee ee eee 135 How to Open the Jmol Molecule Structure Viewer 136 Chapter 9 8 5 8 6 8 7 8 8 Howto Display the PID srie ewe lca aw Se kee ea hee a eee oe SA LD Display OPUS c2s03stanw ese ean e Stan eassae ata dao ees ould How to Toggle between Hertz and ppm Axis Units How to Switch on off th
4. General Control amp Function Keys You may assign your own commands to functions keys Here is an example of how to do that 1 Open the file cmdt ab_user prop located in the subdirectory userde fined of the user properties directory to locate this directory enter hist and look for the entry User properties directory The file cmdtab_user prop 1s initially empty and can be filled with your own command definitions 2 Insert e g the following lines into the file _f3 Sem F 3etrl Sft FSalt sok f5 Shait _f5ctrl Sreb _f5alt Spopt 3 Restart TOPSPIN Now when you hit the F3 key the command em will be executed In the same way Ctrl F3 Alt F3 F5 Ctr1 F5 and A1lt F5 will execute the com mands ft pk halt reb and popt respectively You can assign any com mand macro AU program or Python program to any function keys Only the keys Alt F4 F6 Ctr1 F6 and Alt F6 are currently fixed Their function cannot be changed 2 8 How to Open Multiple TOPSPIN Interfaces TOPSPIN allows you to open multiple User Interfaces This is for example useful to run an acquisition in one interface and process data in another To open an addi tion interface enter the command newtop on the command line or click Window New Topspin To open yet another interface enter newtop in the first or in the second interface The display in each interface is completely independent from the others As such you can display different dat
5. Home select the first peak End select the last peak Shift Home select current and first peak and all in between Shift End select current and last peak and all in between Note that these keys only work when the cursor focus is in the data window Table properties Various properties of the peak table can be configured To do that 1 Right click an entry to open the popup menu see Fig 8 4 2 Click Table properties 1D Display 125 3 In the appearing dialog box with 3 tabs Columns Allows you to select the columns to be displayed set the column width and the number of fraction digits Furthermore you can switch on off scientific notation of values for each column individually Colours Allows you to set various colours of the table Spacings Allows you to set various spacings of the table 126 1D Display Table properties Region Type index F1 WF 1 ppm WF 14 Hz Intensity abs Kk OO LI intensity rel Column properties Column width Fraction digits Scientific notation Figure 8 5 When you move the cursor over the peak list the active peak will by default be highlighted in blue see peak 3 in Fig 8 6 If the correlated spectrum is also dis played a vertical line moves along showing corresponding position in the spec trum see Fig 8 6 1D Display 127 examid_1H 1 1 Cbio guest 1 Epp Intensity
6. Table 12 1 shows the list of integrals based on the regions defined in Fig 12 8 226 2D Interactive Manipulation SIFI rowl row2 rowl ppm row2ppm_ Abs Int Integral SLF2 coll col2 coll ppm col2 ppm 1 1024 666 689 50 14583 46 43132 9 2529e 008 882 42 1024 510 522 6 04420 5 89291 2 1024 597 632 61 28934 55 71759 1 1135e 009 1062 1024 520 533 5 91452 5 74162 3 1024 652 692 52 46739 45 96701 3 7699e 007 35 953 1024 566 579 5 31659 5 15089 4 1024 683 721 47 35995 41 32388 1 0072e 009 960 57 1024 589 605 5 02122 4 81230 5 1024 683 721 47 35995 41 32388 1 064e 009 1014 7 1024 589 605 5 02122 4 81230 6 1024 683 721 47 35995 41 32388 5 6725e 007 54 097 1024 589 605 5 02122 4 81230 7 1024 502 543 76 61168 70 11130 1 2637e 009 1205 2 1024 637 649 4 38726 4 23598 8 1024 502 543 76 61168 70 11130 1 2911le 009 1231 3 1024 637 649 4 38726 4 23598 Table 12 1 a Alternatively you can define a reference integral and integrate the defined regions of the same or of a different dataset relative to this integral For this purpose the I button offers the following menu items e Integrate current regions rel to reference You will be prompted for the reference integral number and value o List integral values The output list will now show an additional column with the normalized integral values e Define current dataset as reference You will be prompted for the reference integral number and value 2D Interactiv
7. 0 0 ee ees 232 How to Show the Next Previous Row or Column 233 How to Move the Selected Dataset Up Down in the Dataset List 233 How to Extract a Row Column 0 0c ccc ee ees 234 How to Copy Contour Levels from First to Other Spectra 234 How to Switch on off 2D contour display 000 235 How to Position the Baseline of the Row Column 235 124 2Dnt ractive Calibratiom sise 04 40 gene oe bathe eer ite 235 How to Switch to 2D Calibration mode 0 0 0000 ee 235 How to Perform 2D Calibration 0 00 ccc eee ees 236 12 5 2D Chemical Shift Distance Measurement 231 How to Measure a 2D Chemical Shift Distance 257 Chapter 13 Data Window Handling ccc cece cece ccc ccccees 239 E Mata WindOw s a3 un 28 che uk ade i oto E oe eos hee ae 239 How to Move a Data Window 0 0 ccc eee eens 240 How to Resize a Data Window 0c cece ee ees 240 How to Select activate a Data Window 0000 241 How to Open a New empty Data Window 000 242 How to Arrange Data Windows 0 ccc cee eee eens 242 How to Iconify minimize a Data Window 0000 244 How to De iconify a Data Window 000 cece ee eens 245 How to Maximize a Data Window 0 cece eens 245 How to Restore the Size and Position o
8. 00 0 eee 316 How to Configure the Tab Bar 0 0 ccc ee nes 316 How to Configure the Right click Menu Function 317 Chapter 20 How to Change Colors of Data Objects on the Screen 317 How to Change Colors of Data Objects on the Printer 318 How to Change Colors of the Lock Display 318 How to Create a New Data Window Color Scheme 318 How to Read a Different Data Window Color Scheme 319 How to Change Peak and Integral table Colour Spacings 319 How to Create Thick Lines on the Screen 000 321 How to Create Thick Lines on the Printer 0 321 How to Change All Fonts of the Topspin Interface 321 How to Change the Font of the TOPSPIN menu 322 How to Change the Font of the Tab bar 323 How to Change the Font of Dialog Boxes 040 324 How to Change the Font of the Browser 000 00 ee 324 How to Change the Font of the Command Line 325 How to Change the Font of the Status Line 325 How to Auto Archive existing CxpnOS 00 ccc eee eee 323 192 Command Line FPreferenG S ceesre iots ee Geran a 326 How to Resize the Command Line 0 00 ce eee eee 326 How to Set the Minimum and Maximum Command Line Size 327 19 3 Disabling Enabling Toolbar Bu
9. 2 In the appearing dialog box Enter the exact values for the region limits 3 Click OK to define the selected region How to Select Deselect Integral Regions To select deselect all displayed integral regions c Click the button button 1D Interactive Manipulation 189 To select a single integral region 1 Right click in the integral region 2 Choose Select Deselect from the popup menu To select the next integral region t Click the button To select the previous integral region t Click the button To select multiple integral regions 1 Click the button button to select all integrals 2 Deselect the integral that are not to be selected Selected integral regions are indicated by a color filled integral label In the Fig 11 4 the five left most regions are selected the region around 6 ppm is currently being deselected examid 1H 1 1 Chio guest House Sensitivity 1 0 6 04 ppm 3020 776 Hz Calibrate Mormalize Lastscal Delete Figure 11 4 Note that 190 1D Interactive Manipulation e Ifno integral is selected the next and previous integral button select the first or last integral respectively e the select all integrals button remains green while all or multiple integrals are selected This indicated a selection mode How to Read Integral Regions from Disk You can read integrals regions from disk which have been st
10. 3 2 1 3 2 2 3 2 3 TOPSPIN command log By default the history protocol feature is switched on This means all TOPSPIN commands will be protocolled and can be examined by entering hist on the com mand line If for some reason history is switched off you can switch it on as follows 1 Click Options Preferences click Miscellaneous 2 Check the entry Record commands in protocol file 3 Click OK TOPSPIN spooler report TOPSPIN reports all queued delayed and cron jobs in the so called spooler report file The spooler report stores all jobs since TOPSPIN installation and can become very large Therefore it should be cleaned from time to time To do that 1 Enter the command spooler 2 Click Tools gt Show spooler report 3 Mark the entries to be deleted 4 Right click in the dialog and choose Delete 5 Close the Spooler report Note that the spooler report can also be opened from Spooler field if enabled in the Acquisition Status Bar by right clicking the word Spooler and choosing Show spooler report TOPSPIN command dataserver and network log A full protocol including not only TOPSPIN commands but also dataserver and net work traffic is show by the command ptrace This opens the following dialog Trouble Shooting 49 window 2 ptrace TopSpin Log File Tracer i 0 x File Time Message a 2 13 15 36 16 135 TOPSPINVersion 1 3 5 12 13 15 36 16145 history registratio
11. Print preview Table properties Figure 8 8 Here you can choose from the following options tS Show spectrum In correlated spectrum to open a new data window showing the full correlated spectrum us Expand spectrum In current window to change the current data window to spectrum display showing the re gion around the selected integral t5 Expand spectrum In correlated window to open a new data window showing the region around the selected inte gral lower part of Fig 8 7 Note that clicking the marked entry in the right click popup menu is equivalent to pressing of the Enter key Export Import Entries of the Integral List Entries of the integral list can easily be exported to Excel or any other program as follows 1 For multiple integrals 1D Display 131 Select the desired entries while pressing the Ctrl or Shift key 2 Right click an entry to open the popup menu see Fig 8 8 3 Click one of the following menu items e Copy Copy the selected integral s entry to the Clipboard Equivalent to clicking Edit gt Copy or hitting Ctr1 c Copied integrals can easily be pasted in any other application such as Excel e Export Export selected integrals Check the box in the lower left corner to export the selected integrals only or uncheck it to export the entire list Then click Export Calibrate Integrals to Compare Spectra Integrals from the current and other spectra can be calibrated with
12. Put focus into TOPSPIN window a Close the lock display window Note that an external lock display window is independent from the TOPSPIN win dow You can for example minimizes TOPSPIN while keeping the lock display open The lock display can also be opened by double clicking the lock field in the acqui sition status bar see par 15 4 The lock process can be started by entering Lock on the command line This com mand is described in the Acquisition Reference manual 15 8 BSMS Control Panel The BSMS control panel allows shimming locking sample handling and helium level measurement To open this panel r Enter bsmsdisp on the command line The BSMS Control Suite window will appear see Fig 15 9 212 Acquisition ESMS Control Suite Main Lock Sample amp Level Shim Autoshitn Service AUTO Phaze Power ain Lock Lock Phaze Power Gain SAMPLE LIFT SPIN SHIM a Previous Actual Absolute Step Difference Step Stepsize tot Q1 1 yur jar 1 10 100 Tes qeg 6 O Figure 15 9 The individual functions BSMS control panel are described in detail in the Acqui sition Reference manual Acquisition 273 15 9 Interactive Parameter Adjustment GS Several parameters can be adjusted interactively while observing the acquired FID To start this r Enter gs on the command line A split window will appear showing e the FID display see Fig 15 10 e the GS para
13. r Click the Sample tab edsamn examid_1h 1 1 Bio guest moek Spectrum ProcPars AcquPars Title PulseProg Peaks Integrals ample Structure Fid Accu Sample Description Sample ID Origin Concentration Date Prepared Butter Contact Comment Figure 8 11 This table can be used to fill out any sample information you want to store with 136 1D Display the dataset The table can easily be modified or extended with the following func tions To select an item double click it F Save the sample information table with the dataset E Save the sample information table as default w Reload the original table discarding any changes Add a new item to the table You will be prompted for an identification name and the desired number of lines Remove the selected item from the table Move the selected item one place up in the table 4 Move the selected item one place down in the table How to Open the Jmol Molecule Structure Viewer n Click the Structure tab jmo1 examid 1H 1 1 Cobio guest 1 Spectrum ProcPars AcquPars Title PuleeProg Peaks Integrals Sample Structure F Lr File Edit Display wiew Toole Macros Plugins Help OBES ORS omo ee N cyclasporina pa cyclosporina Orme Gre Figure 8 12 1D Display 137 opens the Jmol molecule structure viewer TOPSPIN 2 1 contains Jmol version 10 This has the foll
14. 4 Select the desired color in the appearing dialog box and click OK 5 Click Apply How to Create a New Data Window Color Scheme To create a new data window color scheme 1 Click Options Preferences set 2 Change any color of the objects Spectrum Spectrum title Spectrum cursor or Spectrum parameters 3 Click Apply 4 Click Spectrum in the left part of the User preferences box 5 Click the button Save as to the right of the object Save spectral window colors as a new color scheme User Preferences 319 and enter a new name in the appearing dialog box 6 Click OK How to Read a Different Data Window Color Scheme 1 Click Options Preferences set 2 Click Spectrum in the left part of the User preferences box 3 Click in the list box to the right of the object Change spectral window color scheme and select an element from the appearing list 4 Click OK TOPSPIN is delivered wit two colors schemes e light default a white background with black axes e dark a dark blue background with a white axes How to Change Peak and Integral table Colour Spacings 1 Click Options Preferences set 2 Click Miscellaneous in the left part of the User preferences box 3 Click in the list box to the right of the object Table colors see Fig 19 4 for simple tables like peaks solvents nuclei tables Tree table colors 320 User Preferences for nested lists like the integral table Table propertie
15. Figure 19 3 2 In the appearing dialog see Fig 19 3 select the desired action 3 Click OK 19 1 3 Changing Colors How to Change Colors of Data Objects on the Screen The color of various objects in a data window on the screen like 1 2 and 3 4 spectrum axis parameters etc can be changed To set these colors 1 Click Options Preferences set 2 Click Spectrum in the left part of the User preferences box 3 Click the Change button to the right of the object you want to change e g Color of 1st10O spectrum a Change 4 Select the desired color in the appearing dialog box and click OK 5 Click Apply 318 User Preferences How to Change Colors of Data Objects on the Printer The color of data objects on the printer is independent from the color of the cor responding object on the screen To set print colors 1 Click Options Preferences set 2 Click Printer in the left part of the User Preferences box 3 Click the Change button to the right of the object you want to change e g Color of title jie Change 4 Select the desired color in the appearing dialog box and click OK 5 Click Apply How to Change Colors of the Lock Display The colors of lock display objects can be changed as follows 1 Click Options Preferences set 2 Click Lock display in the left part of the User preferences box 3 Click the Change button to the right of the object you want to change e g Color 2 ia Change
16. How to Use the 1D Processing Dialog 1D data processing often involves the same sequence of steps which can easily be performed as follows 1 Click Processing Process Plot Current data 2 In the appearing dialog see Fig 1 1 a Enable the desired processing plotting steps b Set the parameter LB for exponential multiplication c Select the desired LAYOUT for plotting d Click OK Data Processing 95 N proci d Press OF to process J plot the selected dataset using the enabled options The command procid y will process data without this dialog using the last settings Exponential Multiply Cert LB Hz Fourier Transform Tt Auto Phasing tapk Set Spectrum Reterence sre Auto Baseline Correction abs Plot autoplot Figure 6 1 How to Use the Processing Guide in Automatic mode The Processing Guide in automatic mode guides you through the entire process ing sequence of data selection processing printing and archiving with minimum user interaction 1 Click Processing Processing Guide The Processing Guide window will appear as an integral part of the current data window see Fig 6 2 96 Data Processing MMF Data Processing Guide 7 Open Data Set a Advanced EG Window Function e Peak an cking Fourier Transtorrn e Integration gt Phase Correction Plot Print E O ppm Axis Calibration J
17. Manuals Programming Manuals Processing and analysis commands require certain parameters to be set correctly Most commands in the Processing or Analysis menu like wm and ft f open a dia log box showing the available options and required parameters for that command Other commands such as em ft start processing immediately Before you use them you must set their parameters from the parameter editor To do that enter edp or click the ProcPars Tab of the data window If you are a new or occasional user we recommend you to process your data with the TOPSPIN Processing Guide This will guide you through the typical sequence of processing steps To start the Processing Guide click Processing Processing Guide In Automatic mode the Processing Guide will simply execute each processing command when you click the corresponding button This requires the processing parameters to be set correctly In interactive mode Automatic mode unchecked the Processing Guide will at each step open a dialog box offering you the available options and required parameters For example the phase correc tion button offers various automatic algorithms as well as an option to enter inter active phasing mode A simple way to process 1D data is the following 1 Click Processing Process Plot Current data 2 In the appearing dialog see Fig 1 1 a Enable the desired processing plotting steps b Set the parameter LB for Exponential multiplicat
18. Peaks Integrals Molecule Fid 5 Figure 13 4 244 Data Window Handling To arrange data windows side by side see Fig 13 5 w Click Window Arrange Side by Side Figure 13 5 To cascade data windows see Fig 13 6 c Click Window Cascade Figure 13 6 Note that you can instruct TOPSPIN to open new data windows cascaded rather than maximized as well configure cascaded windows command set Window set tings see also chapter 4 3 How to Iconify minimize a Data Window r Click the button in the windows title bar Data Window Handling 245 Or r Click Window Iconify all to iconify all windows How to De iconify a Data Window r Click the button or double click the title bar How to Maximize a Data Window us Click the Ol button or double click the title bar The window will cover the entire data area Note that a maximized window can not be moved of resized but can be restored in size and position 1conified or closed How to Restore the Size and Position of a Data Window r Click the button or double click the title bar Note that this is only possible if the title bar contains the button This is only the case after the window has been maximized or iconified How to Close a Data Window To close the active data window r Click File gt Close Crt1 w or rs Click the x button in the windows title bar To close any data win
19. Save digital as analog fitered data O Save other file Required parameters processed data as new PROCHO Figure 4 19 2 Select an option and if applicable a file type 3 Click OK to execute the option The six options correspond to the following command line commands 74 Dataset Handling e wrpa copies the current data to a new data name or expno e tozip convert a dataset of any dimension to ZIP format e tojdx convert a 1D or 2D dataset to JCAMP DX format e totxt convert a 1D or 2D dataset text format e wpar write parameter set e convdta save digitally filtered data as analog filtered data e wrp wra genfid wmisc write various files How to Save an Entire Dataset 1 Click File Save Ctr1 s 2 Select the option Copy dataset to a new destination wrpa and click OK 3 Specify the dataset variables and click OK How to Save Processed Data 1 Click File Save Ctr1 s 2 Select the option Save other file 3 Select File type Processed data as new procno wrp and click OK 4 Enter a processing number procno and click OK How to Save Acquisition Data Click File gt Save Ctr1 s Select the option Save other file Select File type Acqu data as new expno wra and click OK mW N m Enter a experiment number expno and click OK How to Save Processed Data as Pseudo Raw Data 1 Click File Save Ctrl1 s 2 Select the option
20. The ID is an arbitray name Editor ID Full path Remove Save Cancel 4 Click Save to save the changes If no editor is specified here the TOPSPIN internal editor is used It the file being edited is read only the TOPSPIN internal viewer is used How to Configure the Tab Bar The default Tab bar at the top of the data window consist of Tabs to switch be tween various dataset objects like Spectrum Parameters Title etc You can how ever configure the Tab bar to contain Tabs for interactive data manipulation like phase correction integration etc These Tabs have the same function as the cor responding buttons in the upper tool bar see chapter 11 and 12 but are easier to access You can configure the Tab bar as follows 1 Click Options Preferences Click Spectrum in the left part of the User preferences box Click the Change button to the right of the object Tabbed pane layout Check the desired Tabs uncheck the others Click OK nN Aa Ww N User Preferences 317 How to Configure the Right click Menu Function Right clicking a pull down or popup menu can perform various actions This can be configured as follows 1 Right click an empty part of the menubar and choose Define Right Click Action from the popup menu Define right click action on a menu tem O Mo action when right button clicked O Display help cit available O Execute menu iter gt Display command assigned to menu tern
21. a Enter the coordinates of the desired region in the dialog box b Click OK Undo last zoom z1 HH Show full spectral width in F2 2r Show full spectral width in Fl fir fe al 4 Show full spectrum a11 fil Retain horizontal and vertical scaling when modifying dataset or changing to different dataset Effects all data windows keep Alternatively you can enter the corresponding commands as specified between square brackets 154 2D Display How to Shift a Spectral Region in the F2 direction left right r Click one of the following buttons Shift to the left half of the displayed region s1 Shift to the right half of the displayed region sr Or r Click hold the button and move the mouse Smoothly shift in any direction Alternatively you can enter the corresponding commands as specified between square brackets How to Shift a Spectral Region in the F1 direction up down r Click one of the following buttons Shift the spectrum up half of the displayed region su 4 Shift the spectrum down half of the displayed region sd or r Click hold the button and move the mouse Smoothly shift up down and left right Alternatively you can enter the corresponding commands as specified between square brackets 9 3 Show Display Properties Regions Files If you right click inside the data window the popup menu shown in Fig 9 4 will 2D Di
22. mand line just click the Close button to close the Relaxation Guide Extract Slice Prompts you for the FID or spectrum to be extracted for peak determination see Fig 14 4 Click FID to extract an FID or Spectrum to extract a spectrum Note that the latter only works if the pseudo 2D data have been processed If you click Analysis 255 FID the extracted FID is automatically processed We recommend to enter the EA Extract a row from d data 2 Fid or Spectrum must be extracted From the 2d relaxation data This rowe should correspond to an experiment vith the maximum or minimum delay time All further data preparation will be done in respect to this row Figure 14 4 FID or spectrum number which was measured with the longest delay It can be found in the vdlist file in the EXPNO data directory Then you can choose be tween e Manual Integration This will switch to Interactive integration mode The highest peak in each region will be used for relaxation analysis e Manual Peak Picking The selected peaks will be used for relaxation analysis Ey Define Peaks and or Intervals lf you choose manual integration module you can define integration regions Most intensive peaks within the intervals will be found automatically lf you choose manual peak picking module you can define peaks without intervals or peaks within integration r gions Manual Integration Manual Peak Picking Figure 14 5 Peaks Ranges Swi
23. r Click the indicated button in the upper toolbar 2d 3d 4 A MO SJ jar or enter basl1 on the command line The Tab bar of the active data window will be replaced by a toolbar see Fig 11 14 206 1D Interactive Manipulation examid_1H 2 1 Crbio guest O x Ae MBs ela Bc DeElolan iA m s fa gt Mouse Sensitivity 1 0 3 16 ppm 954 20 Hz Figure 11 14 Data window in baseline correction mode A The yellow button indicates that the data window is in baseline correc tion mode Some buttons will turn green when they are clicked As long as a button is green it is active How to Perform Polynomial Baseline Correction 1 Click the following button button turns green Fy Perform polynomial baseline correction In the data window a red horizontal line will appear as well as the equation that describes the polynomial function f x A B x C x D x E x 2 Click hold button A and move the mouse until the red line coincides with the first point of the spectrum 3 Repeat step 2 with the buttons B C D and E until the red line coincides with the entire baseline of the spectrum How to Perform Sine Baseline Correction 1 Click the following button button turns green 1D Interactive Manipulation 207 E Perform sine baseline correction A red horizontal line will appear as well as the equation describing the sine function f x A B sin C x D 2 Click hold button A and mo
24. 1 Switch to phase columns mode to display columns of selected peaks Eb The yellow button indicates that you are in phase correction mode Toggle the contour display on off Switch to phase row mode to display rows of selected peaks mi Save the phase values to the 3D data from which this 2D was extracted Return How to Perform a Typical 2D Interactive Phase Correction In this example we will perform F1 phase correction columns only Take the fol lowing steps 1 Select two or more peaks in different parts of the spectrum To do that a Zoom in on a peak by drawing a box around it To do that click hold the left mouse button and move the mouse see Fig 12 2 b Right click at the peak position and choose Add from the popup menu 2D Interactive Manipulation 217 examz2d_HC 1 1 Cbio guest WER ct a ERS ma Click the right mouse button to select the peaks for phase correction q LL m yr q Lid cs q 75 7 4 7 3 7 2 7 1 F2 ppm Figure 12 2 c Click the 4 button to display the full spectrum d Zoom in on the next peak and add in the same way as the first one e Zoom in on the next peak etc Fig 12 3 shows an example of three selected peaks 218 2D Interactive Manipulation exam d_HC 1 1 Cjbio guest loj x AJER tg a EE Click the right mouse button go F EB a rT to select the peaks for phase jcorrection A wy ap EA i mea j kl q
25. 239 in 1D peak picking mode 211 in 1D phase correction 184 in 2D calibration mode 236 in 2D multiple display mode 229 in 2D phase mode 216 223 in baseline correction mode 206 in calibration mode 197 in integration mode 187 in multiple display mode 199 in S N measurement mode 251 in spline baseline correction mode 209 objects 23 popup menu 140 154 printing 103 reopen 110 tab bar 1D 115 tab bar 2D 157 toolbar 22 dataset active 241 colors 205 dir 19 289 directory tree 19 68 expno 19 56 61 289 files 82 146 handling 27 53 last 2D 32 last 3D 32 last used 314 name 19 56 61 69 procno 19 56 61 289 procno directory 68 properties 143 selection in multiple display 200 specification 68 241 title 61 top level directory 56 user 19 56 61 289 variables 74 datastation configuration 283 dcon command 26 330 dconpeaks txt file 26 deconvolution 26 default color scheme 319 command line size 326 configuration 283 find criteria 79 menu font 323 pivot point in 1D phase correction 184 pivot point in 2D phase 219 plane in 3D display 171 printer 104 Tab bar 316 zero order phase correction 185 define cubic spline baseline points 208 integral regions 188 NMR ADMINISTRATOR password 281 NMR SUPERUSER 281 peak ranges 211 peaks 213 de iconify data window 245 delete AU program 287 data 75 integrals from display 193 noise region S N 252 peaks from a peak list 213 signal region S N 252 spline baseline points 209
26. Click hold the left mouse button at one peak position and drag the mouse to another peak position The distance in ppm will be displayed 3 Right click in the data window to quit distance mode button turns grey examed HC 1 1 Cobiol guest 5 F2 2 34 ppm 702 72 Hz Fl 18 96 ppm 1431 19 He Distance 19 10 ppm 1594 40 HE 12 10 g 6 4 2 F2 ppm Figure 12 17 Data window in distance measurement mode Chapter 13 Data Window Handling 13 1 Data Windows The TOPSPIN window has a data area that may contain multiple data windows The size of the data area depends on the overall size of the TOPSPIN window and on presence of the Browser and or Processing Guide Fig 13 1 shows the TOPSPIN window with the Browser and three data windows 240 Data Window Handling PY Bruker TOPSPIN 2 0 on NMR datastation as Jos van Bo Sei File Edit View Spectrometer Processing Analysis Options Window Help Dangal alt Aa T Bee 2722 8 2 TCN E Browser Last50 Groups Alas p BB sah 13C 1 1 Cibio on examid 130 J examid 1H a examed_CH E J exam2d_He ta xam2d_HH exam a Pa jh 4 Ciibiot El ES ga c ts13 Gl EJ c ts16 H ES g c ts2 0 Figure 13 1 Note that the three data windows show different data objects 1D processing parameters a 1D spectrum and a 2D spectrum How to Move a Data Window t Click hol
27. How to Toggle between Superimposed and Stacked Display r Click the following button itt Toggle between superimposed and stacked display How to Shift and Scale Individual Spectra To compare the intensity and chemical shift of corresponding peaks you can shift and scale individual spectra To do this 1D Interactive Manipulation 203 Display the spectra in multiple display mode as described above Expand the spectra to display the desired region or peak Select one of the spectra e g by clicking it in the lower part of the browser e Click hold the c button and move the mouse to align the intensities nan amp WwW N m Click hold the button and move the mouse to align the peak positions The alignment can be facilitated by showing the difference spectrum 4 button and minimize that Note that you can also scale the selected spectra up down with the buttons 2 and 4 The a button allows you to move the selected spectra vertically Clicking the p button resets individual scaling and shifting The performed scaling and shifting are displayed in the data window see Fig 11 12 and 11 13 ig R it d E E Ej ajs fe M da 3 1e9 2 sales TEEI C bio 123 3 123 2 123 1 123 0 ppm Figure 11 12 204 1D Interactive Manipulation examid_13C 1 1 Cbioi guest l _ O x Hele Row ltt es ts SME E na a 3 examld 130 Je 1 Oribia quest a Gone a ee fg o
28. Intensity Annotation 126 2981 32061 761 36 pk1 F44625 9059544 24 pk 59 4354 9562402 76 pk3 50 3070 8589950 29 pk4 Figure 9 8 This displays list of peaks if these have been calculated command pp The list 2D Display 159 is basically the same as for 1D spectra The only difference is that there are two columns for the two dimensions v F2 ppm the chemical shift in the F2 direction v F1 ppm the chemical shift in the F1 direction To specify or edit an annotation click inside the Annotation field and enter a character string The peak annotations are shown in the correlated spectrum see Fig 9 9 exam2d_HC 1 1 Cjbio guest 1 _ O x 30 F1 ppm ad a8 3 4 3 0 F2 ppm Figure 9 9 How to Display the Integral list t Click the Integrals tab 160 2D Display exam2d_HC 1 1 Crbio guest OJ ES Spectrum ProcPars AcquPars Tite PuisProg Peaks Integrals Sampie Strug a gt VOF2 ppm F1 ppm Intensity HHntegral 1 0 00 0 0000 EHntegral 2 0 00 0 0000 EHntegral 3 0 00 0 0000 EHntegral 4 19717450 50 1 0000 0 00 E a E 55751 126 2371 3446703 37 peak 7 56356 126 2227 4532891 75 EHrtegral 7 0 00 0 0000 1 Figure 9 10 This displays list of integrals if these have been calculated command int The list is basically the same as for 1D spectra The only difference is that when peaks are shown there are two columns f
29. Password n OK cancel Figure 18 4 The TOPSPIN browser will show the exported data directory trees of the remote sys tem You are now ready to acquire process or analyse remote data 18 2 3 Setup the firewall A remote system in a network can be protected by a firewall Any firewall between the local and remote TOPSPIN must be configured for TOPSPIN remote access If the remote PC is running under Windows XP with Service Pack 2 the Windows Firewall is by default installed and running Consider the following possibilities Remote Control 307 Firewall on PC with Windows XP SP2 Topspin installed If TOPSPIN 1s installed the firewall is probably configured for TOPSPIN re mote access If it is not or you are not sure you can configure it as follows 1 Click Start Programs Bruker TOPSPIN gt TOPSPIN 2 0 gt Bruker Utilities 2 Click Miscellaneous 3 Double click Command Prompt 4 In the Command Prompt window enter cd prog bin utilities Miscellaneous setfirewall cmd auto Firewall on PC with Windows XP SP2 no Topspin installed Configure the firewall as described in the Installation Guide for Windows XP On all other systems the firewall must be configured manually by the network administrator To do that view the file lt tshome gt prog server corba conf and open the ports specified here incremented by 50 For more information please refer to the installation guides for Windows or L
30. during the installation of TOPSPIN on a new computer a new disk or in a new TOPSPIN installation directory The default configuration name is Bruker_default_av500 and corresponds to a Avance 500 MHz spectrometer For manual or interactive data processing the automatic default configuration is sufficient If however you want to use AU programs you must execute expin stall once selecting Installation for Datastation Default How to Perform a Customized Configuration on a Datastation If you want to configure your datastation according to a spectrometer other than default you must first copy the configuration directory lt tshome gt conf instr lt instrum gt from that spectrometer to the datastation Here lt tshome gt is TOPSPIN home the directory where TOPSPIN is installed Note that this can be different on the spectrometer than on the datastation lt instrum gt is the configuration name After copying the configuration directory you have to perform expinstall1 as follows e Click Spectrometer gt Setup Experiment installation or enter expin stall on the command line Follow the instructions on the screen In successive dialog boxes check select the options below and click Next to continue e Installation for Datastation Customize e High Resolution Systems e The configuration name as it was copied from your spectrometer e The items you want to install e Select the desired printer and paper format for th
31. edmac on the TOPSPIN command line and insert the RASmol commands in the appearing editor Here is an example jmol load mystructures alphahelix pdb load a structure 138 1D Display jmol backbone 0 7 display its backbone with 0 7 Angstrom size jmol color backbone yellow change backbone color jmol background green change background color jmol zoom 200 zoom structure The available RASmol commands are described in the Jmol Help menu e Multiple molecules or multiple aspects of one molecule can be displayed simultaneously To do that just open multiple data sets or open the same dataset in multiple data windows and click on the Structure Tab in each window How to Display the FID t Click the Fid tab fid A examid 1H 1 1 C bio guest 1 E m x Ti a E z aT 1 2 3 4 5 5 displays the raw data If these do not exist the text No raw data available ap pears The following additional buttons appear at the right of the lower toolbar ji Show FID in shuffled mode Iw Show FID in unshuffled mode If you open a new dataset the Spectrum tab 1s activated no matter which tab was selected before If you enter any interactive mode for example phase correction mode the Tab bar is replaced by a toolbar for that mode 1D Display 139 8 5 1D Display Options How to Toggle between Hertz a
32. in 1D phase correction 184 185 in 2D calibration 236 in 2D phase correction 219 referencing 93 reg file 195 relaxation curve 253 remote connections 311 remove commands 329 data from multiple display 201 menus 329 toolbar buttons 328 reopen a dataset 110 reopen command 63 110 rep command 21 69 repw command 70 rescale I 12 2D projection 163 data in multiple windows 111 reset 1D baseline correction 208 1D phase values 185 3D cube size and orientation 175 F1 zoom factor in 2D 153 F2 and F1 zoom factor 153 intensity 1D 112 intensity in 2D 151 search mask 79 zoom factor 33 113 resize command line 327 data window 240 graphics 107 resolution of a screen dump 23 108 restore adjusted acquisition parameters GS 275 size and position of a data window 245 toolbar 328 uncorrected baseline 208 retrieve previously entered commands 35 rew command 21 69 Right Arrow key 35 40 58 rotate 3D cube 170 174 routing parameters 92 S S N value 252 Sample tab 135 sav command 32 38 save 1D baseline correction 207 208 1D integrals 196 1D phase correction 186 acquisition data 74 adjusted acquisition parameters GS 274 AU program 28 286 color scheme 318 cubic spline baseline points 210 current window layout 246 data 25 32 38 73 data in analog filtered format 74 data to a JCAMP DxX file 26 data to a ZIP file 25 data window to a graphics file 23 108 entire dataset 73 74 integral regions 195 macro 27 parame
33. see Fig 8 10 2 Click Table properties 3 In the appearing dialog box with 3 tabs 4 Columns Allows you to select the columns to be displayed set the column e width and the number of fraction digits Furthermore you can switch on off scientific notation of values for each individual column e Colours Allows you to set various colours of the table e Spacings Allows you to set various spacings of the table 134 1D Display Table properties Column Colours Object Integral abs S integral rel Feaks Fange F1 trom Fange F1 to WF 1 pem Intensity abs d Column properties Column width Fraction digits Scientific notation sph Figure 8 10 Shortcuts Enter key zoom into spectrum i e show region around selected inte gral s Delete key delete the selected integral s from the integral list Ctrl c copy selected integrals to the Clipboard 1D Display 135 Ctrl a select all peaks Home select the first peak End select the last peak Shift Home select current and first peak and all in between Shift End select current and last peak and all in between Double clicking an integral will show the peaks within the integral region if they exist It they do not exist 1t will zoom into spectrum showing the inte gral region Note that these keys only work when the cursor focus is in the data window How to view Sample Information
34. the integral number Integral abs the absolute integral value Integral rel the relative integral value 1D Display 129 Peaks the number of peaks within the integral range Range F1 from the left edge of the integral range Range F1 to the right edge of the integral range Please note the difference between the following items e selected integral the entry that has been clicked last Integral 3 in Fig 8 7 If you right click an entry it is selected and you can execute one of the commands from the popup menu see Fig 8 8 The keys Enter and Delete work on the selected entry e active integral the entry on which cursor resides Integral 1 in Fig 8 7 The active integral is also marked in the correlated spectrum by a black vertical line see lower part of Fig 8 7 and description below When you move the cursor over the integral list the vertical line in the correlated spectrum moves along with it and vice versa Note that the colours of the selected and active integral can be set in the table properties see above Display the spectral region around an integral To display the spectral region around a particular integral r Right click the desired integral 130 1D Display This will open the popup menu shown in Fig 8 8 Expand Expand all Show spectrum b Expand spectrum P In current window Delete In correlated window Define a reference Calibrate by reference Copy Export Print
35. 158 Integral A 20473361 47 1 5647 0 3 979 4 489 Integral 6 1068216295 19 61 6376 a2 0 304 3 977 Figure 7 2 How to Print the Peak list 1 Click the Peaks tab of the data window see Fig 7 3 2 Enter print or Ctrl1 p Printing Exporting Data 107 examid 1H 1 1 Cibio quest Spectrum ProcPars AcquPars Title Integrals 5 6147 0 10 ERNIE E A 2 6 oO SB6 0 11 0 0044 a 0 5561 o 01 OOo E 4 a541 O 00 0 0007 5 5 5279 O 00 0 0015 Ei 5 5059 O 00 0 0000 T 5 4974 01 0 0016 Figure 7 3 7 2 Exporting Data How to Copy data to Other Applications Under MS Windows you can easily copy the data window contents to other ap plications To do that r Click Edit Copy copy This will copy the data window contents to e the clipboard After that you can paste the clipboard contents to any Win dows application e the Windows Metafile file screenDump wmf in the user properties directory enter hist to locate this directory The Windows Metafile can be imported by other applications or send to a different computer Please note Some programs when importing spectra from the clipboard or metafile do not display the contained information correctly Particularly when you resize the im ported graphics sections of the text the spectrum or the axis sometimes have dis appeared Usually this is only a display problem When you print the respective page the representation is correct 108 Printing Exp
36. 180 zero order phase correction How to Reset the Phase to the Original Values Click the following button Reset zero and first order phase How to Change the Mouse Sensitivity Click one of the following buttons 1 Increase double the mouse sensitivity inc tx Decrease halve the mouse sensitivity dec IIl Reset the mouse sensitivity to 1 0 How to Show the Next Previous Row or Column To show the next row column click the following button Show next row column Note that only the selected row column is increased If all rows columns are se lected only the first one is increased To show the previous row column click the following button Show previous row column 222 2D Interactive Manipulation Note that only the selected row column is decreased If all rows columns are se lected only the first one is decreased How to Arrange Rows or Columns Click one of the following buttons Arrange rows columns horizontally Arrange rows columns vertically see Fig 12 6 Arrange rows columns vertically in a split window How to Return from Multi 1D Phase to 2D Phase Display Click the following button Hj to save execute and return This will perform the following tasks e Execute phase correction e Save the current phase correction values e Leave the multi 1D phase mode Click the following button to return to the 2D phase display without save How to Return from 2D P
37. 196 IP address of a remote system 305 IUPAC standard 26 J JCAMP DX format 26 71 72 74 Jeol spectrometer 71 Jmol molecule structure viewer 136 137 JNMR data 71 K KDE konqueror 82 keyboard commands 31 kill command 51 Konqueror 82 146 L Left Arrow key 35 40 58 Levenberg Marquardt algorithm 257 258 li command 128 186 Liouville equation 27 lipp command 128 lippf command 128 list 159 1D integrals 128 2D integrals 159 2D peaks 158 AU programs 284 baseline points 209 Bruker AU programs 286 color schemes 319 data files 81 144 EXPNOS PROCNOS 65 found data 79 integrals 106 195 macros 27 opened datasets 55 56 57 parameter sets 61 peaks 106 213 peaks 1D 119 plot layouts 104 solvents 61 user defined AU programs 286 local Topspin interface 301 lock parameters 92 signal 270 lock command 271 lock display colors 318 mode 270 window 246 264 267 270 lockdisp command 264 270 lock in procedure 270 Lorentzian deconvolution 26 lower toolbar 33 M macros in AU programs 97 335 in Topspin 27 44 94 334 339 342 magnitude calculation 94 matching the probehead 269 MAXI parameter 213 maximize all data windows 246 data window 245 maximum command line size 327 MC2 parameter 88 menu bar 31 commands 31 configuration table 329 331 entries 31 329 font 322 323 settings 311 MI parameter 213 minimize data window 244 minimum command line size 327 Minus key 40 mixtures 27 mole
38. 265 extend the Topspin functionality 333 external projection 22 extract a row column in 2D 234 F F1 dimension 154 161 215 F1 key 15 38 F1 F2 plane 172 175 F2 dimension 154 161 215 F2 key 38 57 F2 F3 plane 173 175 F3 key 44 F3 F1 plane 171 173 175 F5 key 44 F6 key 38 44 242 fid command 138 160 FID display 264 267 273 276 Fid tab 138 144 160 File Chooser 20 File menu 20 31 file size of raw data 265 files of a dataset 69 74 82 144 146 find command 38 78 find data 31 78 first order phase correction 1D 185 2D 219 220 fitting peaks 26 fmc command 94 focus 35 38 57 58 font of dialog windows 324 of the browser 324 of the command line 325 of the interface 321 of the menu 322 of the status line 325 of the tab bar 323 forward peak picking 213 Fourier transform 93 94 fp command 94 fromjdx command 26 fromzip command 26 ft command 24 93 ftf command 24 329 function keys 38 G Gaussian deconvolution 26 Gaussian window multiplication 94 genfid command 74 genser command 74 geometric sequence of levels 166 geometry of a Topspin window 246 247 getprosol command 91 117 gf command 94 gfp command 94 Gnome Mozilla 82 grab rows columns in 2D 232 gradient enhanced spectroscopy 27 graphic functions 335 graphics files 23 108 grid display 33 164 271 window arrangement 242 gs command 88 266 273 GS parameter adjustment window 273 H halt an acquisition 264 265 halt comman
39. 2D dataset nothing happens Sort This Column Sort the selected column in ascending order Dataset Handling 81 Sort Reverse Sort the selected column in descending order Save Selection Save the list of selected datasets in a text file First opens a file dialog where you can select or specify a filename The saved dataset list can for example be used for serial processing command serial see also Process Selected Da tasets below File properties Show main dataset parameters like Dimension Pulse program Acquisition Date Nuclei Spectrometer frequency and Solvent Files Show the files in the processed data directory of the selected dataset Process Selected Datasets Perform serial processing on the selected datasets Opens a dialog where you can change or edit the dataset list and specify the command macro or Python pro gram to be executed starts the command serial The Close button allows you to close the search result dialog 4 8 Handling Data Files How to List Open the Current Dataset Files A Bruker dataset 1s represented by a directory tree which contains files in the ex pno and procno subdirectories These files contain the actual data parameters lists etc 82 Dataset Handling c Right click inside the data window and choose Files from the popup menu Display Properties Save Display Region To Restore Display Region From Params Fife Set plot height for current position File Proper
40. 31 38 66 71 Options menu 31 overview spectrum 1D 139 2D 161 P paper format 283 paracon command 284 parameter adjustment window 88 273 change 87 91 92 display 21 editor 85 86 88 89 field 87 90 91 files 81 handling 85 name 85 89 search 116 117 value 87 90 parameter set 61 74 PARMODE parameter 117 paste command 32 69 72 peak alignment 23 202 display 21 fitting 26 group 26 labels 142 213 list 213 214 list 1D 119 213 list 2D 158 picking mode 210 position 250 position alignment 203 ranges 214 peak picking 1D automatic 210 1D interactive 210 mode 32 mode 1D 211 ranges in 1D 212 peak txt file 214 peakrng file 214 Peaks tab 106 119 158 phase correction 1D automatic 93 94 1D interactive 183 2D interactive 215 first order 1D 185 mode 32 mode 1D 184 mode 2D 216 pivot point in 1D 184 values 1D 186 zero order 1D 185 PHCO parameter 87 185 220 PHC1 parameter 185 221 pivot point in 1D phase correction 184 in 2D phase correction 219 pk command 186 plane display in 3D 172 plot data from the menu 103 data from the Plot Editor 105 data from the Processing Guide 105 layouts 23 plot command 104 105 Plot Editor 23 104 Plus key 40 polynomial baseline correction 206 position of a Topspin window 247 position of a Topspin window 246 position the baseline of a row column in 2D 235 positive 2D levels 170 pp command 127 142 143 PPARMOD parameter 88 92 116 ppl comm
41. A typical 1D processing AU program is proc_1d A simplified version of this AU program iS EF APK SREF ABS AUTOPLOT QUIT It executes the commands ef apk sref abs and autoplot Torun this AU 98 Data Processing program just enter proc 1d on the command line You can create your own AU programs with the command edau Note that an AU program must end with QUIT or QUITMSG your message and that all statements must be specified in capital letters For more information on AU programs please refer to the AU pro gramming manual t Click Help gt Manuals gt Programming Manuals AU Programming As an alternative to AU programs you can also write Python programs which allow you to use TOPSPIN commands User Interface functions and Graphic func tions For more information 0s Click Help gt Manuals Programming Manuals Python Program ming 6 4 Serial Processing using Python programs TOPSPIN allows you to process a series of datasets using serial scripts The dataset list and command s to be used can be easily setup from the TOPSPIN interface as follows Enter the command serial on the command line This will open the 1 Before you can use any Bruker AU program expinsta11 must have been executed once Data Processing 99 dialog window shown in Fig 6 3 x Options Process specified data set list with specified script Browse for a data set list Browse for a serial script Edit
42. A user may only select meanings that were assigned to him by the NMR administrator during user administration 296 Regulatory Compliance 17 2 3 17 2 4 17 2 5 SIGNATURE COMMENT Any text Displaying the electronic signature in the data window The electronic signature can be displayed in the data window by setting the corre sponding display component To do that 1 Right click in the data window and choose Display Properties dopt 2 Check Electronic Signature in the appearing dialog box and click OK The electronic signature will appear at the upper left corner below the title Plotting the electronic signature When plotting a dataset using TOPSPIN s plot editor commands plot and auto plot an electronic signature is automatically plotted unless this feature is disabled if the last entry of the audit trail of the data to be plotted is an electronic signature This ensures that after signing no more data manipulations have been performed Multiple signatures The command esign may be applied several times to a data set for instance if two persons say an operator and an administrator must sign in accordance with company regulations 17 2 6 Validity and security of signatures TOPSPIN electronic signatures of data sets must not be confused with digital signa tures as defined in applicable law Digital signature laws are usually country dependent They require the administration of passwords more gener
43. Browser To change the font of the browser 1 Click Options Preferences set User Preferences 325 Click Fonts Dialogs Icons in the left part of the dialog box Click the Change button to the right of the Dialog window font object Select the desired name style and or size in the appearing dialog box Click OK to store the new font 6 Click Apply nan Aa U N TOPSPIN must be restarted for this change to become effective Note that this change will affect all dialog boxes How to Change the Font of the Command Line Click Options Preferences set Click Fonts Dialogs Icons in the left part of the dialog box Click the Change button to the right of the Command line font object Select the desired name style and or size in the appearing dialog box Click OK to store the new font Click Apply Non amp WwW NK How to Change the Font of the Status Line Click Options Preferences set Click Fonts Dialogs Icons in the left part of the dialog box Click the Change button to the right of the Status line font object Select the desired name style and or size in the appearing dialog box Click OK to store the new font Click Apply Non amp WwW NH 19 1 6 Changing Acquisition settings How to Auto Archive existing expnos 1 Click Options Preferences set 2 Click Acquisition in the left part of the dialog box 3 Click the Change button to the right of the item
44. Configure Accounting amp Data Archiving after zg see Fig 19 10 4 In the appearing dialog see Fig 19 11 configure archiving as described in 326 User Preferences the dialog 5 Click OK Acquisition Overwrite existing FID without inquiry 2G safety off F Alto open acquisition window atter zg Configure accounting amp data archiving after zg Figure 19 10 PH Setup Auto Archiving amp Accounting When acquisition 2g is finished Topspin allows you to write accounting info to be evaluated by the command account to copy the acquired dataset to a desired archiving directory When zg is executed multiple times on the same dataset TopSpin will Increment the EXPNO while archiving s0 as to never override already archived data You may specity an additional EXPMO offset for this case The accounting into is stored in the folowing directory one file per day stopepin hoamedir progicurdiracghistory Auto archive after zg Archiving directory EXPHO offset Write accounting info after zg Figure 19 11 19 2 Command Line Preferences How to Resize the Command Line By default the TOPSPIN command line shows one command the command that is User Preferences 327 currently entered e g lapk However you can resize the command line to show the currently entered com mand plus the last and second last command e g em apk You can toggle bet
45. Delete key 35 depth cueing in 3D 175 deselect data in multiple display 200 201 integral regions 188 dialog box font 324 difference spectrum in baseline correction 207 in multiple display 201 dimensionality of a dataset 30 88 92 116 dir command 21 disable commands 329 menus 329 toolbar buttons 328 Display button 20 70 79 menu item 64 199 display 1D acquisition status parameters 117 1D data 109 1D FID 138 1D integral list 128 1D peak list 119 1D processed data 115 1D raw data 138 1D spectrum 115 1D spectrum overview 139 2D contours 165 2D data 149 2D FID 160 2D grid 164 2D integral list 159 2D peak list 158 2D projections 162 2D spectrum in contour mode 165 2D spectrum in oblique mode 168 2D spectrum in pseudo color mode 168 3D cube 174 3D data 171 columns in 2D phase correction 216 contours in 2D phase 216 data from the browser 20 55 data from the portfolio 55 data in multiple windows 110 dataset file list 144 dataset properties 143 expno procno list 65 found dataset 79 full spectrum in 2D phase correction 217 integrals 21 JCAMP data 26 manipulation 111 manipulations 33 mode of the lock window 270 molecule structure 137 options 32 options 1D 139 peaks 21 planes of 3D data 171 172 positive negative 2D levels 170 processing status parameters 1D 116 projections 22 rows in 2D phase correction 216 settings 31 special data formats 71 spectra 19 spectrum overview in 2D 161 sta
46. Figure 8 6 As soon as you click a peak it is selected and by default displayed in red see peak 1 in Fig 8 6 Note that this peak remains selected 1 e is used by Enter and Delete until a different peak is selected To extend the peak list with Regions Type and Index entries right click any part of the header bar To sort the peaks according to peak number ppm value or intensity click the header of the respective entry Note that when you delete peaks from the peak list they are automatically re moved from the corresponding file You cannot undo a delete action Peaks are only available if peak picking has been done command pp The peak list can be printed with print Ctr1 p List items can be selected with the 128 1D Display mouse copied with Ctr1 c and pasted to other applications e g a text editor How to Display the Integral list t Click the Integrals tab 1i lipp lippf O x examid_ 1H 1 1 Cobio guest 1 mintegral 1 21807940 16 Integral 2 20864697 25 1 5943 T rori r 4110 Integral 4 131427635 19 10 0425 0 6 155 4 491 integral 5 20492465 62 1 5658 0 4 459 3 979 integral 6 10685317028 12 01 6307 0 ESTE 0 304 5 x rocPars AcquPars Title PulsProg Peaks Integrals Sample aj 0 5 1 0 rel 8 0 7 5 7 0 65 ppm Figure 8 7 This displays the integral list upper part of Fig 8 7 By default this shows the following items Object
47. How to Copy a Data Window to Clipboard Under MS Windows you can easily copy the data window contents to other ap plications To do that type copy or click Edit gt Copy This will copy the data window contents to the clipboard After that you can paste the clipboard contents to any Windows application How to Store Export a Data Window as Graphics File The clipboard and metafile formats are resizable vector formats In addition to this TOPSPIN allows you to save the contents of a data window in a graphics file of selectable type e g png jpg jpeg bmp emf and wmf To do that click File gt Export The resolution of such a screen dump equals the resolution of your screen Note that when you import a graphics file into another program resize it you loose information Therefore we recommend to resample rather than resize graphics 24 Getting Started 1 12 How to Process Data Since this manual is not a general NMR text book we assume here that you are familiar with terms like window multiplication Fourier Transform phase correc tion etc Any Fid or a spectrum displayed in a TOPSPIN window can be processed by e typing a command on the command line e g ft e invoking a command from the Processing or Analysis menu e g Process ing Fourier Transform e entering an interactive mode by clicking a tool button e g J e entering a user defined command usually an AU or a Python program see Help
48. How to Perform Exponential Baseline Correction 207 How to Preview the Baseline Corrected Spectrum 207 How to Reset the Baseline Correction Line 4 208 How to Change the Mouse Sensitivity 0 0 00 eee eee 208 How to Save the Baseline Correction and or Return 208 How to Perform Cubic Spline Baseline correction 208 How to Delete Spline Baseline Points from the screen 209 How to Return from Cubic Spline Baseline mode with without Save 210 ID Interactive Peak Picking eurin dod8c Ace ered hawt ene es 210 How to Switch to Peak Picking Mode 0 0000 eee 211 10 How to Define New Peak Picking Ranges 04 211 How to Change Peak Picking Ranges aaaea 212 How to Pick Peaks in Peak Picking Ranges only 212 How to Delete all Peak Picking Ranges 0040 212 How to Define Peaks Manually 0 0 0 cece eee eee 213 How to Pick Peaks Semi Automatically 000 213 How to Delete Peaks from the Peak List 213 How to Return from Peak Picking Mode with without Save 214 Chapter 12 2D Interactive Manipulation cccccccccccees 215 12 1 2D Interactive Phase Comection 403 4ii008o wniediedd tess ete 215 How to Switch to 2D Interactive Phase Correction 215 How to Perform a Typical 2
49. Integral Regions 1 Click the following button button turns green Cut integral region 2 Move the red cursor line into an integral region to the position where it must be cut and click the left mouse button 3 Do step 2 for each integral region that must be cut 1D Interactive Manipulation 195 4 Click the green button to leave the cut integral mode button turns grey In case of overlapping integrals you must select the integral to be cut before you actually cut it How to Save Integral Regions 1 Click the following button Save integral regions The following popup menu will appear Save Regions To intrag Save Regions To reg Export Regions To Relaxation Module and ret save amp Show List Figure 11 7 2 Choose one of the following entries e Save regions to intrng Save the currently displayed integral regions including the slope and bias correction values e Save Regions to reg Save the integral regions to the file reg e Export Regions To Relaxation Module and sret Used on relaxation data only Exports the integral regions for T1 T2 relaxation analysis and exits from integration mode e Save amp show list Save the currently displayed integral regions including the slope and bias correction values and show the integrals on the screen How to Undo the Last Region Operation r Click the following button 1 Undo the last region operation 196 1D Interactive
50. Peaks Integrals sample Structure Fid ACHU F2 ppm Figure 9 13 Axis aligned grid display How to Display a 2D Spectrum in Contour Mode r Click the following button in the upper toolbar Switch to contour display mode co In contour mode a spectral region looks like this 50 48 46 F1 ppm 5 4 5 2 5 0 4 8 F2 ppm 166 2D Display How to Set the 2D Contour Levels r Click the following button in the lower toolbar Edit contour levels edlev 1v This will open the following dialog box shown in Fig 9 14 Contour levels can be entered manually or they can be calculated Manual setup This allows you to create an arbitrary sequence of levels 1 Enter the level values in the fields 1 2 at the top of the dialog box 2 Click Apply to update the display or OK to store the levels update the display and close the dialog box Calculation This allows you to easily create a geometric or equidistant sequence of levels 1 Click one of the following items Multiply with increment to create a geometric sequence of levels e Add increment to create a equidistant sequence of levels 2 Enter the desired Base level Level increment and Number of levels 3 Click Fill to display and activate the sequence 4 Click Apply to update the display or OK to store the levels update the display and close the dialog box The Contour level sign allows you to select positive levels negative levels or
51. TOGGLE_TIP Switch to 2D processing Top row button definition TOP BUTTONS EMS SFTS PKS S TOP C OLORSSYELLOWILIS YELLOWLS YELEOWL TOP_CMDS emsS ECS pk TOP_TIPS Exponential multiplication Fourier transforms Phase correction 1 To locate this enter hist and look for the entry User properties directory 338 User Extensions Panel button definitions LAYOUT format rows columns hgap vgap PAN _ LAYOUT 15 35 85 8 PAN _BUTTONS PrintS EXPORTS SSEND TOS PAN _COLORS BLUE1S BLUE1S BLUE1 PAN _CMDS prnt exportfileS smail PAN_TIPS Print the spectrum lt br gt as it appears on the screens Export the dataset lt br gt tO Phos JPar DAL ETON Send the dataset by email If you type bpan exam a panel with 75 buttons will appear 5 rows and 15 col umns The corresponding panel file is called cmdpanel_exam prop which resides in the directory lt tshome gt classes prop English In the same directory you can find the files cmdpanel_bnmr prop and cmdpanel_bnmrsel prop which are used to display the bnmr and bnmrsel panels described above The texts displayed on the buttons can be graphically adjusted in various ways because the text may optionally be specified in html format In the example above the PAN_BUTTONS property has no html tags therefore the texts are displayed in black using the default TOPSPIN Dialog window font as specified in the User Pref erences command set If you replace the
52. The ID of the user logged in at the time esign was executed This is either the user who was logged into the operating system Windows or Linux user and who started TOPSPIN or the TOPSPIN internal user Which of these two modes is applied depends on how the NMR administrator configured TOP SPIN If the option Enforce login for working with TOPSPIN is disabled see below command uadmin the first mode 1s active otherwise the second What is the difference between the modes In the first case the System User Windows or Linux user who started TOPSPIN signs the data set Prior to signing esign requests this user s password which is administrated by the operating system OS No internal TOPSPIN user management plays a role Advantage This mode is entirely OS compliant Disadvantages a TOPSPIN ter mination restart 1s required when a different user wants to sign data alternatively several licenses would admit simultaneous TOPSPIN ses sions b All TOPSPIN users must have an OS login In the second case any TOPSPIN internal user who is enabled by the NMR administrator with uadmin may sign Advantage Conven ient and easy usage Disadvantage TOPSPIN internal user manage ment is required internal users and their passwords USER NAME The complete name of the signer as specified by the NMR administrator dur ing user administration Command uadmin SIGNATURE MEANING The meaning of a signature e g Review or Approval
53. and Return sret This will e Save the peak list to the file peak xm1 and the peak ranges to the file peakrng e Leave the peak picking mode To return while discarding any changes r Click the following button 4a Return discarding any changes ret 12 1 12 1 1 Chapter 12 2D Interactive Manipulation The upper toolbar of the 2D menu offers various buttons for interactive manipula tion If you click such a button the active data window will switch to the corre sponding mode An interactive manipulation mode is data window specific 1 e it only applies to the active window 2D Interactive Phase Correction 2D spectra can be phase corrected interactively in both the F2 and F1 direction by selecting certain rows and or columns and phase correct them 2D Interactive Phase Correction Procedure How to Switch to 2D Interactive Phase Correction Click the corresponding button in the upper toolbar as indicated below Id 3d 4 4A Ta or enter ph on the command line The Tab bar of the active data window will be replaced by a toolbar Fig 12 1 216 2D Interactive Manipulation shows an example of an unphased 2D inverse spectrum exam2d HC 1 1 Cibio quest q oO x ABR I u p lt gt Click the right mouse button to select the peaks for phase correction np t amp on i LL im 12 10 g 6 4 2 F2 ppm Figure 12 1 Data window in phase correction mode Me a E
54. can be performed automatically with the commands pps or interac tively in the peak picking mode 1D Interactive Manipulation 211 How to Switch to Peak Picking Mode r Click the indicated button in the upper toolbar ad 3d 4 A MO J jar or enter pp on the command line The Tab bar of the active data window will be replaced by a toolbar see Fig 11 17 0 x ie xpd e a ae 0 97 ppm 483 04 Hz CY 420 00 rel MAXI 19 50 rel MI 0 00 rel 10 15 20 1e6 5 0 10 g 6 4 2 ppm Figure 11 17 Data window in peak picking mode The yellow button indicates that you are in peak picking mode a Some buttons will turn green when they are clicked As long as a button is green it 1s active Note that the E button is automatically activated i e you are in Define peak picking range mode How to Define New Peak Picking Ranges 1 Put the cursor at the upper left corner of a peak picking range 212 1D Interactive Manipulation 2 Left click hold and drag the mouse to the lower right corner of the range The peak picking range will be marked green The minimum and maximum intensity are set and the peaks in the range are picked and displayed 3 Repeat step 1 and 2 for each peak picking range to be defined 4 Click the green button to leave the Define peak picking range mode Note that the parameters MI and MAXI are set to the lowest minimum and the highest maximum intensity res
55. cee eee ees 64 How to Automatically Select the first expno procno of a dataset 65 Chapter 5 How to Open Data from the Topspin menu 005 66 How to Open Data from the Explorer Konqueror or Nautilus 68 How to Open Data from the Command Line 69 How to Open Special Format Data anaana 0 cee eee eee 71 How to Open a ZIP or JCAMP DX file from the Windows Explorer 72 Ad Savins Copying Dalarossie sran eae ecaan eek an eoees teases 73 Howto save or Copy Data reserse akakana na skit ane ch ib ew aba 73 How to Save an Entire Dataset 2 2 2 0 miriadi cae eee eee 74 Howto Save Processed Data ansible ceed sicura ETE oea 74 How to Save Acquisition Data 0 0 ccc cece eens 74 How to Save Processed Data as Pseudo Raw Data 74 Ay Delenie Dalios ena aiara ead e teed ode ees 75 How to Delete a Specific Dataset ate DEn 00 EEEE E 75 How to Delete Types of Datasets 0 0 0 cece eee 75 AO Rename Dai 5 38ehee beet ite ed dh eads RRE A 75 How to Rename a Specific Dataset 0 00 75 Ar S archine Pindine Data tes vedas bean anaE EEE A 78 Howto Pnad DAU o2 caer Mee ceak e aa e OS sae MER SRS 78 How to Display one of the Found Datasets 79 AS Handling Data Flessen set ase ti ches Peewee a E eae ees 81 How to List Open the Current Dataset Files 81 How to List Open the current Datas
56. contains a column for each of the two di mensions F2 and F1 see Fig 9 6 Note that not all parameters exist in both di mensions Pxam d HC 1 1 Chio quest spectrurri ProcPars ACGUP ars Title PuleeProg Peaks Integrals Sarnple Structure Fid Scou o Frequency axis FY Reference S 4096 4096 Size of real spe SF MHz 500 1 300000 125 7577090 Spectrometer ft OFFSET ppm 9 570 157 023 Lowy field lirit a SR Hz Spectrum refer HfpPT Hz Spectral resolu Y window function QSINE s SIME Window tunctic ill gt Figure 9 6 How to Set Acquisition Parameters r Click the AcquPars tab eda The 2D acquisition parameter editor contains a column for each of the two di mensions F2 and F1 see Fig 9 7 Note that not all parameters exist in both di 158 2D Display mensions DOK 2 AE L onsi e Y Experiment PULFPROG Atl rod FniiiDe TD NS DS TOO P Fi Fi Frequency axis Aimigcgpcgt LEJ Current pulse p Acquisition mac Acquisition moc Size of fid Number of scar Number of durri Loop count for wt gt Figure 9 7 How to Display the Peak list t amp Click the Peaks tab i examz2d_HC 1 1 Cibin guest F2 ppm r 2405 4 2892 5 7906 5 3677 spectrum ProcPars AcquPars Title PulsProg Peaks Integral OF 1 ppm
57. deon or click Analysis gt Deconvolution 1 16 How to Compute Fids by Simulating Experiments TOPSPIN includes a virtual spectrometer that computes fids of any dimension A real spectrometer excites a sample with high frequency pulses defined by a pulse Getting Started 27 1 17 program and measures the resulting fid The virtual spectrometer performs this task mathematically by solving the quantum mechanical Liouville equation The sample must be entered in form of a spin system description For the computa tion the same pulse program and acquisition parameters are taken as for the real experiment The result is a time domain signal which can be processed with TOP SPIN in the same way a measured fid is processed Techniques such a selective excitation gradient enhanced spectroscopy and the handling of mixtures are sup ported To start the virtual spectrometer tS Enter nmrsim on the command line or click Analysis gt Simulate Fid How to Add Your Own Functionalities The TOPSPIN functionality can be extended with various user defined commands programs etc How to Create Macros Writing a macro is the simplest way to create a user defined command Just enter the command edmac select a file and enter a sequence of regular TOPSPIN com mands and or Python commands Save the file under a name of your preference You have created a new TOPSPIN command Just enter its name on the command line to execute
58. experiments 1 1 SUE See eee 4 When the acquisition has finished r Enter efp to process the FID The processed spectrum will be displayed in the data window that was opened upon creating the dataset see Fig 15 15 Acquisition 279 protona 1 1 CABO guest Spectrum ProcPars AcquPars Title PulseProg Peaks Integrals Sample Structure Fid Acgu Ji u Lal O246 6 Figure 15 15 From here the processed data can be analysed printed and or archived 15 11 Shape tool The Shape tool interface allows you to create manipulate RF shapes and gradients To start the Shape Tool interface us Click Spectrometer Shape Tool or enter stdisp on the command line The Shape Tool window will appear see Fig 15 16 This consists of a toolbar a command line and a split pane with a data section at the right and a parameter sec tion at the left 280 Acquisition Shapelrool 1 Gauss Armolitude Parameters 1000 size of Shape Truncation Level 5 Figure 15 16 By default a 1000 point Gauss shape is displayed with Truncation level 1 0 The TOPSPIN menu is changed showing the additional Shapes and Manipulate menus and the adjusted File Analysis and Options menus File Edit View Shapes Analysis Manipulate Options Window Help Note that all functions of the interactive Shape Tool
59. following button it turns green and move the mouse b Integral bias correction until the integral bias is correct 3 Release the mouse button turns grey To perform interactive slope correction 1 Select the integral s that you want to correct right click in the region If no integral is selected slope correction will work on all integrals 2 Click hold the following button it turns green and move the mouse Integral slope correction until the integral slope is correct 3 Release the mouse button turns grey How to Set the Limit for Bias Determination r Click the following button Limit for bias determination How to Change the Mouse Sensitivity r Click one of the following buttons 1 Increase double the mouse sensitivity inc 192 1D Interactive Manipulation t Decrease halve the mouse sensitivity dec IIl Reset the mouse sensitivity How to Calibrate Normalize Integrals Calibrating integrals means setting the value of a reference integral and adjusting all other integrals accordingly To do that 1 Right click in the reference integral region 2 Choose Calibrate from the popup menu see Fig 11 6 3 Enter the desired value for the reference integral and click OK Normalizing integrals means setting the sum of all integrals and adjusting indi vidual integral values accordingly To do that 1 Right click in the reference integral region 2 Choose Normalize from
60. gt lt BRUKER LL User Manual Manual for TopSpin 2 1 Version 2 1 0 Copyright C 2007 by Bruker BioSpin GmbH All rights reserved No part of this publication may be reproduced stored in a retrieval sys tem or transmitted in any form or by any means without the prior consent of the publisher Part Number H9469SA2 Product names used are trademarks or registered trademarks of their respective holders Bruker software support is available via phone fax e mail or Internet Please con tact your local office or directly Address Bruker BioSpin GmbH Service amp Support Department Silberstreifen D 76287 Rheinstetten Germany Phone 49 721 5161 455 Fax 49 721 5161 943 E mail nmr software support bruker biospin de FTP ftp bruker de ftp bruker com WWW www bruker biospin de www bruker biospin com Contents Chapter 1 Chapter 2 Getinge Started csr i cena cea adanthar eee 15 It lt DocimentU Conventions eieiei e ete edhe viwteiinscs 15 PONUCONVENUONS aie hii E a E ek Pach eee aes as 15 File directory Conventions 000 cece cece nnan 15 User Action Conventions 3 ci353 5 cis oa i hs mec aw EETAS 15 EZ TOPSPIN OVI Wecare t ua ee bounds a nemaared eae bridge eat 16 FPancHhonalily sessirnar a be ae ee en eas 16 Available Documentation 000 cece ce cee 17 be TOPSPIN CENS soeia 4s ee Gee E a eure de a dem Bek wee EAT 17 LA Startup TOPSPIN cercare naer keane tase baie anbt aes ew aes
61. it The command xmac shows a list of all available macros and allows you to exe cute one How to Create AU automation Programs Writing an AU program is another way of creating a new TOPSPIN command AU programs are more complex and more powerful then macros They are C lan guage programs which may contain C statements regular TOPSPIN commands and various predefined AU macros and functions AU programs can perform var ious tasks such as dataset handling parameter handling acquisition processing analysis and printing Note that AU programs do not support graphics related tasks TOPSPIN is delivered with a large set of Bruker AU programs for data processing and acquisition Just enter edau to see them listed in a dialog box The easiest Getting Started way to create anew AU program is to select a Bruker AU program save it under a new name and modify it to your needs The chosen name is now available as a new TOPSPIN command Alternatively you can open a new file from the AU dia log box and write your AU program from scratch For details on Bruker AU programs and writing your own AU programs click Help Manuals Programming Manuals AU Programming How to Create Python Programs Writing a Python program is yet another way of creating a new TOPSPIN com mand Python is a new generation scripting and object oriented programming lan guage Python programs are even more powerful than AU programs They are easy to u
62. name 283 of a datastation 19 of a spectrometer 19 of the acquisition status bar 266 of the tab bar 316 of the Topspin menu 329 password 281 consistency check 291 contour display 216 of 2D spectra 165 of 3D planes 172 contour levels 150 166 control keys 38 convdta command 74 conventions in this document 15 convert data to JCAMP DX 74 data to text 74 data to ZIP 74 copy amp paste data 31 69 72 copy command 23 32 107 copy data 73 C program 97 create an AU program 27 98 286 334 an empty data window 64 data window color scheme 318 dataset 31 macro 27 334 new data window 20 new dataset 61 275 plot layouts 23 105 Python program 28 335 set of user preferences 311 user defined command 27 1 4 user notebook 333 C statements 27 Ctrl key 58 65 77 112 151 199 200 Ctrl c key 35 38 128 Ctrl d key 29 38 Ctrl f key 38 Ctrl F3 key 44 Ctrl F5 key 44 Ctrl F6 key 44 Ctrl n key 31 38 61 275 Ctrl o key 31 38 66 71 Ctrl p key 23 32 38 106 127 Ctrl s key 25 32 38 73 74 Ctrl v key 35 38 Ctrl w key 38 cube display 171 cubic spline baseline correction 208 cursor information 141 customized configuration 283 cut integrals 194 D data area 20 29 64 69 72 239 242 245 compression 26 dimensionality 30 88 92 116 117 directory 53 60 77 field 34 109 114 149 object colors 317 data window 20 29 31 64 69 72 2D 149 3D 171 color scheme 318 contents 23 107 creation 64 handling 31
63. new one belonging to the new raw data file By default the user is warned when the current dataset already contains raw data thus preventing accidental overwriting The option Override existing fid without inquiry is by default off see Options Preferences Acquisition The processed data audit trail Each procno sub directory contains a text file auditp txt the audit trail of the processed data It reflects the processing state of the processed data and contains a checksum for the file itself auditp txt and a checksum for the real proc essed data files 1r 2rr 3rrr The latter links the audit file with the proc essed data By means of the checksums any illegal manipulation of the audit file or the processed data file can be detected using the TOPSPIN commands audit or auditcheck Whenever a processing command is performed the current audit file is updated with this command and its associated parameters When processing starts from scratch from a raw data file the existing audit file is overwritten As such the processed data can always be regenerated from raw data by applying the commands and parameters listed in the audit trail If the laboratory management does not allow data files or audit trails to be deleted a respective saving procedure must be established For this purpose TOPSPIN pro vides data copying commands which may be called in a user defined macro or AU program before a new acquisition or pro
64. offering a large number of drawing tools 250 Analysis e DNMR Dynamic NMR Lineshape Analysis A program to simulate temperature dependent NMR spectra interactively set up and iteratively refine the model parameters to get the best fit of the measured and simulated 1D NMR spectra Structure analysis tools can be started from the Analysis menu They are all described in the following manuals 0s Click Help gt Manuals Analysis and Simulation Structure Analysis Tools except for Daisy which is described in the separate manual r Click Help gt Manuals Analysis and Simulation Daisy 14 2 1D Chemical Shift Distance Measurement How to Measure a Chemical Shift Distance 1 Click the following button button turns green q Chemical shift distance measurement 2 Left click hold at one peak position and drag the mouse to another peak position The distance in ppm will be displayed 3 Right click in the data window or move the cursor out of the data window to leave distance measurement mode button turns grey 14 3 1D Signal to Noise Calculation How to Perform Interactive S N Calculation 1 Click Analysis gt Signal Noise Calculation sino The current signal region parameters SIGF1 SIGF2 and noise region pa rameters NOISFI NOISEF2 are displayed Analysis 25l NOISEREG 1 94 ppm 581 90 Hz SIGREG 7 70 ppm 2311 67 Hz 10 0 5 0 0 0 Figure 14 1 Data window in S N measurem
65. opening datasets that are stored in the following di rectory structures lt mydata gt lt name gt lt expno gt pdata lt procno gt You can do that with the TOPSPIN command reb or from the Operating System File Browser with Copy amp Paste or Drag amp Drop Actually the data are copied to the data directory lt tshome gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt where lt tshome gt is the TOPSPIN installation directory and lt user gt is the current internal TOPSPIN user How to Open Data in Other Ways TOPSPIN provides various other ways of displaying data You can for example use command line commands like re rew rep and dir Details on these fea tures can be found in chapter 4 3 and in the Processing Reference Manual 1 7 How to Expand a Spectral Region To expand a certain spectral region r Click hold the left mouse button on one side of the region drag the cursor to the other side and release the mouse If you want to cancel the expansion while dragging the mouse just move the mouse out of the data area and release it An alternative way of expanding a region is clicking the button repeatedly and then shifting the spectrum to the proper position 1 8 How to Display Peaks Integrals together with the Spectrum When a spectrum is displayed you can superimpose its title parameters integrals and peaks as follows 1 Move the cursor into the data window that contain
66. specified data set list Edi specified serial script Create new data set list Create new serial script Required parameters Data set list Tull path c jdata_list Serial script name ser_em script location Cott shlexpistaninime vists mac Show data sets during script execution YES v script type Python JRK Cancel Help Figure 6 3 Here you can set up and start data processing of a series of datasets using scripts which can be TOPSPIN macros or Python programs The dialog offers you the following options Process specified data set list with specified script Process the data in the specified dataset list using the specified serial script The flag Show data sets during script execution allows you to either display the currently processed dataset or remain on the current dataset Browse for a dataset list Browse for an existing dataset list starting in the users home directory Browse for a serial script 100 Data Processing Browse for existing serial script Depending on the parameter Script type the browser opens the exp stan nmr py for Script type Python or exp stan nmr lists mac Script type macro TOPSPIN by default searches for for files named ser_ Edit specified data set list View or edit the list specified in the field Data Set List Edit specified serial script View or edit the script specified in the field Serial script name Create new data set list Opens a di
67. the following format lt tshome gt prog bin sendgui lt topspincommand gt where lt tshome gt is the TOPSPIN installation directory Examples C ts2 1 prog bin sendgui ft executes a 1D Fourier transform C ts2 1 prog bin sendgui re examld_1H 11 C bio joe reads the dataset C bio joe nmr exam1d_13C 1 pdata 1 Under Linux 1 Open a Linux Shell 2 Enter a TOPSPIN command in the following format lt tshome gt prog bin scripts sendgui lt topspincommand gt where lt tshome gt is the TOPSPIN installation directory or sendgui lt topspincommand gt 38 The TOPSPIN Interface if the TOPSPIN home directory is in the users search path Examples C ts2 1 prog bin scripts sendgui ft executes a 1D Fourier transform sendgui re examld_1H 1 1 C bio joe reads the dataset C bio joe nmr exam1d_13C 1 pdata 1 Note that commands are executed on the currently active TOPSPINdata window 2 5 Function Keys and Control Keys For several TOPSPIN commands or tasks you can use a control key or function key short cut Focus anywhere in TOPSPIN Esc Put the focus in the command line Display menu bar and toolbars if hidden F2 Put the focus in the browser F1 Search for string in command help or NMR Guide help Ctrl c Copy a text that you selected highlighted in an error box dialog box pulse program title etc to the clipboard Paste text from the clipboard into any editable field The TOPSPIN Interface 39 Fo
68. the popup menu see Fig 11 6 3 Enter the desired sum of all integrals and click OK Select Deselect Calibrate Normalize Lastscal Delete Figure 11 6 Calibrating and normalizing only effects the current dataset To scale integrals with respect to a reference dataset choose lastscal from the right click popup menu see below How to Scale Integrals with respect to Different Spectra Integrals can be scaled with respect to the last spectrum that was integrated inter actively To do that 1 Right click in the reference integral region 2 Choose Lastscal from the popup menu see Fig 11 6 As such you can compare integrals of different spectra Note that this only make 1D Interactive Manipulation 193 sense for spectra which have been acquired under the same experimental condi tions The scaling factor is stored in the file lt tshome gt prog curdir lt user gt intscale How to Delete Integral Regions from the Display To delete the selected integral regions from the display r Click the following button Delete selected integral regions from the display To delete a single integral region from the display 1 Right click in the integral region 2 Choose Delete from the popup menu see Fig 11 6 To delete all integral regions from the display r Click the following buttons Select all integral regions Delete selected integral regions from the display Note that regions are only deleted fr
69. the upper toolbar or enter zg on the command line The data window toolbar will automatically switch to the Acqu tab and the FID display window will appear Acquisition 211 FID protona 1 1 Cabin guest Title PulseProg Peaks Integrals Sample Structure Fid Argu 7 Se a fA Cyelasoern Figure 15 14 The buttons in the toolbar have the following functions Iw Show FID in shuffled mode 4 Show FID in unshuffled mode horizontally arranged i Show FID in unshuffled mode vertically arranged Iw Show FID in unshuffled mode interleaved ki Switch between FID and spectrum Gi Stop the acquisition stop m Halt the acquisition halt Clicking the button to switch to real time FT turns the button green and opens two extra buttons 278 Acquisition ki Switch between FID and spectrum Real time FT settings i Toggle calculation of peak with at 50 5 5 and 1 1 height Shown as status parameters Clicking the lt button opens the following dialog window PA Configure realtime ft l x Set options for realtime ft Phase correction mode me Baseline correction mode quad OK Cancel The acquisition information will appear in the acquisition status bar at the bottom of the TOPSPIN window for example Window function Acquisition information Fid Flash sample Time spooler scan Ji 16 10 49 running O residual time 1m2 fs Herm 1 gueuegd 0
70. to display the highlighted dataset in the current window r Double click a dataset to display it in the current window Dataset Handling Remove Selected Items From List Remove the selected dataset from the list Open Saved Last List Open a dialog to select a Last50 list Save Lastad List As Open a dialog for saving the current Last50 list Figure 4 4 Each line displays one dataset showing its name expno procno top level directory and user The Groups tab Clicking the Groups tab displays the list of user defined dataset groups Here you can create modify and display groups of datasets Defining a group is useful is you work on projects where each project involves multiple datasets It allows you to easily organizes your projects and access all data belonging to a certain project Display Display selected dataset s in active window Display In New Window Display selected dataset s in new window Display Group Display all datasets in group in new windows Add Selected Data Window Add selected data window to selected group Add All Open Data Windows Add all open data windows to selected group Update Window Bounds amp Display Limits Update window bounds and dislay regions Remove Selected Datasets From Group Remove selected datasets from group Collapse All Groups gt Collapse all groups Toggle DinvPulproc Title Show hide dimension pulse program title Add new Dataset G
71. two further options Print with layout start Plot Editor plot If you select this option and click OK the Plot Editor will be started This option is equivalent to entering plot on the TOPSPIN command line Print with layout plot directly autoplot Selecting this option activates the Plot Editor layout list box Select the desired layout and click OK to print Standard layouts are delivered with TOPSPIN They use the Windows default printer User defined layouts use the Printing Exporting Data 105 printer defined in the Plot Editor On a 1D dataset only 1D layouts are listed on a 2D dataset only 2D layouts are listed etc For the last two options the following Required Parameters are available Use plot limits e from screen CY The plot limits and maximum intensity are used as they are on the screen processing parameter F1P F2P and CY respectively from Plot Editor Reset Actions The plot limits and maximum intensity are set according to the Plot Edi tor Reset Actions right click inside the Plot Editor data field and choose Automation to set the Reset Actions e as saved in Plot Editor The plot limits and maximum intensity are set in the specified layout Fill dataset list from your default portfolio The portfolio contains the current TOPSPIN dataset plus the data from the default Plot Editor portfolio e from port folio saved in dataset The portfolio contains the current TOPSPIN dataset plus the data f
72. txt peaks portt portfolio por proc procs title cen Figure 8 17 The contents of any file in the list can be displayed as follows 1 Select a filename it will be highlighted 2 Click Open Note that this only makes sense for ascii files e g acqu proc or files with the extension t xt Dataset files can also be displayed opened with the command exp1 This opens the Windows Explorer or under Linux the Konqueror or Mozilla showing the contents of the procno directory 1D Display 147 8 7 Saving Display Region The currently displayed spectral region can be stored as follows n Right click in the data window and choose Save Display Region To This will open the dialog box shown in Fig 8 18 EY Save display region to Options O Parameters F172 e g used by restore display 1 dpl Pi Parameters ABSFU2 e g used by abst apkt O Parameters STSRASTSI used by strip ft CO Parameters SIGF1 2 signal region used by sino O Parameters MOISF1 2 noise region used by sino O 4 text file for use with other programs Figure 8 18 Here the following options are available e Parameters F1 2 dp1 to save the displayed region for restoring the display later The region is stored in the parameters F1P and F2P To restore the saved region right click in the data window and choose Restore Display Region from Params F1 2 e Parameters ABSF1 2 to save the displayed region for baselin
73. 0310 To 27 4876 OK Cancel b Click OK Undo last zoom z1 HH Reset horizontal scaling to show the full spectrum hr 4 Display the entire spectrum baseline position and intensity scaling are adjusted if necessary a11 li Toggle interactive zoom mode When switched off interactive zoom ing only selects a horizontal region baseline position and intensity scaling remain the same When switched on interactive zooming draws a box selecting the corresponding area fil Retain horizontal and vertical scaling when modifying dataset or changing to different dataset keep Effects all data windows Alternatively you can enter the corresponding commands as specified between 114 1D Display square brackets How to Shift a Spectral Region to the Left or to the Right r Click hold the following button and move the mouse Smoothly shift to left or right or r Click one of the following buttons Shift to the left half of the displayed region s1 Shift to the right half of the displayed region sr W Shift to the extreme left edge of the spectrum s10 Shift to the extreme right edge of the spectrum sro Alternatively you can enter the corresponding commands as specified between square brackets How to Shift the Spectrum Up or Down To shift the FID or spectrum display up or down r Click hold the button and move the mouse t Smoothly shift the spectrum baselin
74. 18 Ney HCOMMOUTANOM is 05 6 58 oe 4 8 eh Sr ee Suet iat s ae hoes Beek as 19 LO Howto Display Specia sinc kcoe tangs bhai ieee a a om 19 How to Open Data from the Menu 00 cece eee 20 How to Open Data from the Browser 000 cece eens 20 How to Define Alias Names for Data 0 0 0 0 20 How to Open Data in Archive Data Directories 21 How to Open Data in Other Ways 00 cece eee ees 2i 1 7 Howto Expand a Spectral Region 0 0 000 21 1 8 How to Display Peaks Integrals together with the Spectrum 21 1 9 How to Display Projections 1D Spectra with 2D Spectra 22 1 10 How to Superimpose Spectra in Multiple Display 22 1 11 How to Print or Export the Contents of a Data Window 23 Howto PANEDA eion ack ete eae er enn eee ees eed 23 How to Copy a Data Window to Clipboard 004 23 How to Store Export a Data Window as Graphics File 23 kiz Howto Process Dad 24 3 43 4 weer eetaeaw ate eee abbas oe ares 24 DAS HOw Archive Dataa ek ack ed ane he Sind ie 25 1 14 How to Import NMR Data Stored in Special Formats 26 1 15 How to Fit Peaks and Deconvolve Overlapping Peaks 26 1 16 How to Compute Fids by Simulating Experiments 26 1 17 How to Add Your Own Functionalities n onanan aanne 2 Howto Create Macros eeraa oghs4 eee Weed od awed oh E 27 How t
75. 5 dec command 186 192 208 221 dopt command 142 143 151 296 dx files 72 emf files 23 fir command 153 f2r command 153 gif files 340 342 gr command 164 hr command 33 113 hz command 139 161 im command 168 inc command 186 191 208 221 nt command 187 223 Jpeg files 23 340 342 Jpg files 23 340 342 keep command 34 113 153 ls command 168 lt command 170 lv command 166 md command 22 198 ov command 139 161 ph command 42 183 215 ph180 command 185 ph90 command 185 phr command 185 png files 23 108 340 342 pp command 211 pr command 22 162 prop files 246 ret command 186 196 204 208 210 214 retsab command 210 s2d command 186 sd command 35 114 154 sino command 250 sl command 34 114 154 sl0 command 34 114 sr command 34 114 154 srO command 34 114 sret command 186 196 208 214 st command 168 su command 34 114 154 tif files 108 txt files 146 vr command 33 112 151 wmf files 23 108 y command 139 Z1 command 34 113 153 zl command 34 113 153 zo command 34 113 153 Zx command 34 113 153 2 command 33 40 112 151 8 command 33 112 151 command help 43 Numerics 180 degree phase correction 1D 185 2D 221 3D molecule viewer 249 90 degree phase correction 1D 185 2D 221 90 degree phase correction 1D 185 2D 221 2 A abs command 93 97 186 187 190 205 absd command 205 absorption mode 184 185 21
76. 5 8 0 7 5 7 0 ppm Figure 8 9 Note that the integral entries can be collapsed hiding the peaks or expanded showing the peaks As soon as one or more integrals entries are expanded two extra columns appear showing v F1 ppm the chemical shift of the peak Intensity the peak intensity Depending on whether or not integrals are expanded the right click popup menu contains the following extra items e Expand Expand the current integral showing all peaks within it 1D Display 133 e Expand all Expand all integrals showing all peaks within them e Collapse all Collapse all integrals hiding all peaks within them In addition to the integral entry an individual peak within an integral can be activated by placing the cursor on it or selected by clicking it In Fig 8 9 peak 7 is selected and the correlated spectrum is displayed Peak 5 is active which is also shown by the vertical line in the correlated spectrum Delete an Integral from the Integral List To delete one integral r Right click the integral and choose Delete from the popup menu To delete multiple integrals 1 Select the integrals while pressing the Ctrl or Shift key 2 Right click one of the integrals and choose Delete from the popup menu Note that these keys only work when the cursor focus is in the data window Table properties Various properties of the integral table can be configured To do that 1 Right click an entry to open the popup menu
77. 66 lock parameters 92 phase pivot point 184 processing parameters 85 processing parameters 1D 116 routing parameters 92 user preferences 312 set command 115 311 SFO1 parameter 265 Shell 18 shift 1D data down 114 1D data smoothly 114 1D data to the extreme left 114 1D data to the extreme right 114 1D data to the left 114 1D data to the right 114 1D data up 114 1D 2D data 34 40 2D data down 154 2D data smoothly 154 2D data to the left 154 2D data to the right 154 2D data up 154 data in multiple windows 111 individual spectra in multiple display 22 198 202 row column in 2D phase 220 Shift key 58 65 77 199 200 Shift Tab key 87 91 short description of an AU program 287 shortcuts for processing 94 show command 51 SIGF1 parameter 250 SIGF2 parameter 250 signal region 250 251 signal to noise calculation 250 Simplex algorithm 258 simulating experiments 26 sine baseline correction 206 single commands 93 slider sensitivity 273 slope correction 190 191 smail command 26 32 smooth 1D phase correction 220 1D scaling 33 1D shifting 114 1D zooming 34 113 1D 2D shifting 34 2D shifting 154 scaling of 1D integrals 193 scanning of planes in 3D 173 shifting of 1D integrals 194 solvent 61 spec command 115 special format data 26 spectrometer frequency 265 1 14 spectrometer hardware 19 Spectrometer menu 31 263 spectrum display 1D 115 objects 311 312 overview 1D 139 overview 2D 161 Spectrum tab 115 138 145
78. 9 220 221 acqu command 264 acquisition commands 264 267 mode 283 parameters 88 89 276 status bar 266 278 toolbar 263 265 Acquisition Reference Manual 19 92 271 272 284 AcquPars tab 88 117 157 276 activate a data window 241 the next data window 246 add comment to audit file 292 directory to the browser 20 functionalities to Topspin 27 peak in 2D phase correction 216 peak to peak list 213 add increment in 2D levels 166 align intensities in multiple display 203 peak positions in multiple display 203 Alt F11 key 112 150 Alt F4 key 38 44 Alt F6 key 44 Analysis menu 24 31 apk command 93 97 183 apks command 183 arrange data windows 242 data windows horizontally 244 data windows vertically 243 rows columns in 2D phase correction 222 ascii files 82 146 ased command 91 117 Aspect 3000 data 71 ATM probehead 269 270 atma command 270 AU macros 27 334 335 AU program reference manual 98 AU programs 19 27 97 284 334 339 342 audit trail check 291 automate data acquisition 28 automatic 1D baseline correction 93 1D calibration 93 196 1D integration 186 1D peak picking 210 1D phase correction 93 183 2D calibration 235 compilation of an AU program 287 configuration of a datastation 283 selection of the first expno procno 65 tuning and matching 270 automatic mode of the Acquisition Guide 262 of the Processing Guide 24 95 automation 27 28 284 autoplot command 97 104 autostart mac file 314 Avance spec
79. AcquPars Title PulseProg f g Spectrum ProcPars Peaks Integrals Sample structure Fir anis E Eg ve o Installed probe not defined Fa F2 F1 Experiment uir width Receiver F Experiment PULPROG hechdigpsd LL Mucleus Durations AG_mod Baer FnMODE States TFPI Program TD 128 Probe Ne Lists DS 256 Wootle too Lock l Automation N Figure 10 6 acquisition parameter display of a 3D dataset 10 4 nD Fid Display nD raw data can be displayed as a series of 1D FIDs To do that r click the FID tab of the data window Or cS enter fid on the command line 178 nD Display 10 5 nD Peak and Integral Display TOPSPIN 2 1 and newer support peak and integral display of up to 8D data To show the nD peak list i enter peaks on the command line m click the Peaks tab of the data window Fig 10 7 shows the peak list of a 3D dataset Pxamsd 1 1 Cobio guest Spectrum 367 11 156 426 591 e yfF 3 ppm 4 7636 4 5952 4 5927 4 5927 4 5194 4 4995 4 4995 4 4995 4 4995 Ty F 2 1 pprm Lili ProcPars AcguPars Title PuleeProg 50 5341 46 5005 3 4667 a 4667 51 7706 19 4212 34 3554 21 9103 29 9996 Figure 10 7 wF 1 ppm 4 Pare 4 5617 2 044 2 352 4 5035 1 0025 1 9022 1 0025 1 1590 Intensity abs 1173060 00 1165831 00 g39474 50 996713 50 1739391 50 92131275 1163631 25 2510150 75 1037 060 25 Th
80. Annotate by reference shitt peaks Show detailed information Copy Export Import Print Print preview Table properties Figure 8 4 Here you can choose from the following options t Show spectrum In correlated window to open a new data window showing the full correlated spectrum tS Expand spectrum In current window to change the current data window to spectrum display showing the region around the selected peak w Expand spectrum In correlated window to open a new data window showing the region around the selected peak us Edit Annotation Edit the annotation of the current integral t Define as reference Complete table Define the entire peak table as a reference for annotation w Define as reference Selection Define the selected peaks as a reference for annotation 122 1D Display w Annotate by reference Create annotations according to the peaklist of the reference dataset You will be prompted for the allowed variation in chemical shift 0s Shift peaks Shift all peaks You will be prompted for the number of ppm to be shifted r Show detailed information Show peak information dataset information and peak picking parameters Export entries of the peak list Entries of the peak list can easily be exported to Excel or any other program as follows 1 For multiple peaks Select the desired entries while pressing the Ctrl or Shift key 2 Right click a p
81. As 20 Projection scroll to active dataset Fully Expand Selection Show PULPROG Title show Date Sort by Date Copy File Properties Delete Rename Files Add Mew Data Dir Remove Selected Data Dirs The Last50 tab Display in current data window Display in new data window Display 1D data as projection of active 2D data Scroll to PROCNO of active data window Fully expand selected node Switch pulsprogram title display on off Show acq date expno or last mod date name Sort data by last modified date Copy dataset entry to clipboard Show dataset properties Delete selected entry name expno or procno Rename dataset name expno or procno Show files in selected entry expno or procno Add new top level data directory Remove selected top level data directory Figure 4 2 Clicking the Last50 tab displays the list of the last 50 displayed datasets Each dataset that you open is automatically added to the current list Fig 4 3 shows a Last50 list with four datasets As in the browser different colors are used to indi cate the data dimensionality Browser Lasti Groups Alias examid 130 1 1 CBio guest zgpgs0 13C71H AY 300 Automation Cholesterylacetate eg examad 1 1 CoBio quest hechdigesd exam2d HCO 1 1 CoBio guest Amgcgpat Hat Cyclosporin examid 1H 1 1 C Bio quest zg 1H Cyclosporin Figure 4 3 0s Hit the Enter key
82. Bo EA upper File Edit View Spectrometer Processing Analysis Options Window Help close toolbar T Ae a button lower LP aa e G Bl id al AL TES BS toolbar 23 8 a F A Ei FAIA a Qe Browser PFolio Alias exam2d_HC 1 1 Czibio g m SE F 2 Chia Spectrum ProcPars AcquPars Title 7 4 guest exam d_13 EA browser E examtd 1H H examzd_ CH G HE varmad HE a E exem2d HH G Eg examsd a a Cbiot p fa C tts13 oe fa ee command line status bar 1D data window 2D data window Figure 2 1 Note that the menus and toolbars depend on the data dimensionality The descrip tions below hold for 1D data For 2D and 3D data the menus and toolbars are sim ilar and will be discussed in the chapters 9 10 and 12 respectively How to Use Multiple Data Windows TOPSPIN allows you to use multiple data windows Data windows can be opened from the browser or from the Window menu They can contain the same of dif ferent datasets Data windows can be arranged from the Window menu One of them is the active current data window The active data window e is the only data window receiving commands from the command line The TOPSPIN Interface 31 e can be selected by clicking inside the window or hitting F6 repeatedly e has a highlighted title bar e has the mouse focus A cursor line 1D or crosshair 2D is displayed in all data windows at the same position Moving the mouse affects the cursor
83. D Interactive Phase Correction 216 How to Scale or Shift Individual Rows Columns 219 How to Perform Smooth Phase Correction 000 220 How to Perform 90 90 or 180 Zero Order Phase Correction 221 How to Reset the Phase to the Original Values 221 How to Change the Mouse Sensitivity 0 0 0 0 221 How to Show the Next Previous Row or Column 221 How to Arrange Rows or Columns 0 000 e ee eens 222 How to Return from Multi 1D Phase to 2D Phase Display 222 How to Return from 2D Phase Mode 0 000 ee eee 222 22 2D Interactive lite cation n4 h3 08 68208 aeaa BASS a e 222 How to Move an Integral region 0 0 cece eee ees 227 How to Copy an Integral region 0 ccc eee ees 221 How to Delete all Integral Regions 0 000000 227 How to Read Import Integral Regions 0000000 221 How to Save Export Integral Regions 0000s 22 How to Return from 2D Integration mode 000 228 12 3 2D Multiple Display and Row Column Handling 228 How Switch to Multiple Display mode and Read Multiple Spectra 228 How to Align Multiple 2D Spectra 0 000 230 How to Display the Next Previous Name Expno 231 How to Scan Rows Columns 0 0 ee eens 231 How to Grab a Row Column
84. Date Sort by Date Copy File Properties Delete Rename Files Add Mew Data Dir Remove Selected Data Dirs Figure 4 8 How to Show Dataset Dates in the Browser c Right click the data name folder button and choose Show Date The last modified date is shown to the right of the dataset NAME whereas the acquisition date is shown to the right of the dataset EXPNO see Fig 4 9 60 Dataset Handling Browser Last50 Groups Alias EQ CAbio 6 4 ie E examid_13C 2007 04 12 12 06 59 Be examid_1H 2006 05 16 15 13 27 cd ene 7 2004 03 30 15 00 44 pee 1 H Cyclosporin i 99999 1H Cyclosporin H E examzd_ CH Figure 4 9 How to change the default Top Level Data Directory By default the browser shows the TOPSPIN installation directory with the Bruker example datasets To suppress this feature click Options Preferences set click Administration and uncheck Show TOPSPIN data examples directory in data browser How to Add Remove or Interpret Alias Names To add an alias name 1 Click the Alias tab in the browser 2 Right click in the Alias table to open the popup menu see Fig 4 7 Click Define alias names for data in selected window 3 Enter an alias name in the appearing dialog box and click OK Note that alias names must begin with a letter To remove an alias name 1 Right click the alias name 2 Click Remove selected aliases from the popup menu see Fig 4 7 Furthermore the po
85. Forts Dialogs flcons z a Window settings Auto spooling LI Miscellaneous Spectrum Directory path names Tabbed pane layout Acquisition status bat Change spectral window color scheme Acquisition BEZEME display Save spectral window colors as a new color scheme E Lock display Background color Color of 1st 10 spectrum P Change Figure 19 1 Click the cathegory of which you want to view change certain objects It will become highlighted and the corresponding objects will be displayed at the right part of the dialog box For example if you click Spectrum the spectrum objects will appear at the top of the dialog box The rest of this paragraph will describe some examples of setting various user preferences 19 1 1 Define User Preferences Location for all Users User Preferences are by default stored in the current users home directory lt userhome gt topspin lt hostname gt During the first TOPSPIN session files with default settings are created there They can then be modified with the set command and used in later sessions You can however also store user preferences at one central location which are then used by all users This location can even be a remote drive allowing you to use the same preferences on all computers in the network User Preferences 313 To do that 1 Make a backup copy of the file lt t shome gt javaenv cmd 2 Open the file lt t shome gt javaenv cmd using a text editor 3 Locate the line set SY
86. Interactive Manipulation is green it is active Furthermore the browser is split in two parts as shown in Fig 11 10 exami d 130 Cobiol guest examid 137 2 1 Cobiol quest examid 130 Cobiol quest Figure 11 10 The additional lower part shows e which datasets are displayed in the active data window e which datasets are selected these are highlighted How to Select Deselect Datasets To select a dataset r Click in the corresponding area in the data window or Click the small square at the upper right of the spectrum or Click the corresponding entry in the lower part of the browser In the lower part of the browser you can r Click one dataset to select it or Hold down the Ctr1 key and click multiple datasets to select them or Hold down the Shift key and click two datasets to select these two and all datasets in between When you select a dataset the corresponding small square is filled see Fig 11 9 and its entry in the lower part of the browser is highlighted see Fig 11 10 1D Interactive Manipulation 201 Note that e no spectrum selected all spectra selected e scale shift buttons of the data window toolbar only work on selected Spectra To deselect a dataset r Select a different dataset To deselect all datasets r Click the following button 4 Deselect all datasets How to Remove a Dataset from Multiple Display 1 Select the dataset s you want to remove 2 Click the following
87. LL o o q o T ym 12 10 8 6 4 2 F2 ppm Figure 12 3 2 Click the button CT to phase correct the columns F1 A new data window called Phase 2D will appear showing the columns of the selected peaks see Fig 12 4 Wi Phase 2D examed HC 1 1 Cobia guest Figure 12 4 2D Interactive Manipulation 219 Note that the toolbar and the right click popup menu offer the full 1D phase correction functions By default all columns are selected as indicated by the filled blue squares J The red vertical line indicates the default pivot point in the upper column 3 A typical way to perform phase correction is e Click hold the Q button for zero order correction and move the mouse until the reference peak of the first column is exactly in absorption mode e Click hold the 1 button for first order correction and move the mouse until the reference peak in other column is exactly in absorption mode e Click the Hj button to execute save and return see Fig 12 5 O x Aljo 1 R 9 mi a s nj ju l a EELS pivot 1265 44 ppu Fhase increment 0 20 ph 63 356 phl 150 80 olumn 899 9748 ppm Figure 12 5 12 1 2 2D Interactive Phase Correction Details How to Scale or Shift Individual Rows Columns To select one row or column r Click in the corresponding part of the data window The selected row column will be marked with a filled blue square J whereas un selected rows columns will be m
88. Manipulation How to Return from the Integration Mode with without Save To return and save the integrals to the current dataset r Click the following button j Save integrals and return sret As such you will e save the integral regions and corresponding slope and bias corrections to the file intrng e save the integral regions slope and bias corrections and integral val ues to the file integrals txt This file is displayed when you click the Integrals Tab e leave the integration mode To return without save r Click the following button 4a Return discarding any changes ret 11 4 1D Interactive Calibration A 1D spectrum can be calibrated referenced automatically with the command sref or interactively as described below How to Switch to Calibration Mode r Click the indicated button in the upper toolbar 2d 3d A A A L SD oa or enter cal on the command line The Tab bar of the active data window will be replaced by a toolbar 1D Interactive Manipulation 197 exam id_13C 1 1 Cjbio guest l I O x A al 0 005 ppm 0 3736 He 75 40469965 MHz DEFINE REFERENCE FREQUENCY Define Lett click inside data window Figure 11 8 Data window in calibration mode A The yellow button indicates that the data window is in calibration mode How to Calibrate a Spectrum Interactively In calibration mode 1 Position the red cursor line at the reference peak 2 Left click at that positio
89. O E mail Archive S Baseline Corr Figure 6 2 2 In the Processing Guide window a Check Automatic mode b Click Open data set and click OK to open a dataset manually e g from the browser or click Browse to open the File Chooser Data Processing 97 c Click Window function Fourier Transform ete Each processing step will be executed without user interaction How to Use the Processing Guide in Interactive mode The Processing Guide in interactive mode guides you through the entire process ing sequence of data selection processing printing and archiving requiring some user interaction 1 Click Processing Processing Guide The Processing Guide window will appear as an integral part of the current data window 2 In the Processing Guide window a Uncheck Automatic mode b Click Open data set and click OK to open a dataset manually e g from the browser or click Browse to open the File Chooser c Click Window function Fourier Transform ete For each step a dialog box will appear where you can enter options parameters etc For details on these items please refer to the corresponding commands in the Processing Reference Guide 6 3 Processing Data with AU programs Data processing can be performed by using AU programs An AU program is actu ally a C program which contains TOPSPIN commands macros and or C language statements Various standard AU programs are delivered with TOPSPIN
90. Pars Title PulseProg Peaks Integrals Sample structure Fid Acgu m 120 80 F1 pp q F2 ppm Facure 9 1 9 2 Changing the Display of a 2D spectrum TOPSPIN offers various buttons to scale or shift a 2D spectrum both vertically and horizontally How to Change the Intensity Scaling contour levels r Click the button Change the intensity scaling contour levels edlev or r Hit one of the keys e Alt PageUp Increase the intensity by a factor of 2 e Alt PageDown Decrease the intensity by a factor of 2 e Alt Enter Reset the intensity Or 2D Display 151 m Click one of the following buttons gt Increase the intensity decrease the levels by 2 2 f Increase the intensity decrease the levels by 8 8 2 Decrease the intensity increase the levels by 2 7 2 8 Decrease the intensity increase the levels by 8 78 Reset the intensity to the last saved intensity contour levels vr Alternatively you can enter the corresponding commands as specified between square brackets To manipulate all data windows press the Ctrl key while clicking one of the above buttons How to Smoothly Change the Vertical Scaling contour levels To change levels multiplying all levels with the same factor t Click hold the button and move the mouse or c Turn the mouse wheel while the cursor is in the data window To change the
91. STEM _PROPS DX WINNMRHOME XWIN NMRHOME DCOMPUTERNAME COMPUTE near the beginning of the file 4 Append a white space character and then DPROPDIR lt dir gt to the end of this line where lt dir gt is the definition of the storage directory consisting of one or more parts see below 5 Close the editor The definition of the storage directory for User Preferences can take three forms DPROPDIR lt mydir gt Stores the user properties in lt mydir gt prop Example DPROPDIR x y z DPROPDIR lt mydir gt USER Stores the user properties in lt mydir gt lt login id gt prop where lt login id gt is the id under which the user is logged into the operating system Example DPROPDIR x y z USER DPROPDIR CURDIR Stores the user properties in lt tshome gt prog curdir lt login 1d gt prop where lt login id gt is the id under which the user logged into the operating system Please note that the specified directory must writable for all TOPSPIN users 19 1 2 TOPSPIN Startup Actions How to Open the Last Used Dataset on Startup 1 Click Options Preferences set 1 The double quotes are only required if the directory contains white spaces 2 Specify exactly 1 space between the pathname and the string USER 314 User Preferences 2 Check under Administration items the option Auto open last used data set How to Define the Startup Actions TOPSPIN allows you to define any comma
92. Save other file 3 Select File type Ir li as fid genfid or 2rr 2ii as ser genser 4 Click OK 5 Enter a destination expno Dataset Handling 75 optionally you can specify further data path specifications 6 Click OK 4 5 Deleting Data How to Delete a Specific Dataset r Right click the data name expno or procno in the browser then click Delete A confirmation dialog will appear Just click OK if you are sure you want to de lete Note that TOPSPIN does not allow you to delete the last available dataset e g the last procno under an expno the last expno under a name or the last name under a user How to Delete Types of Datasets To delete certain types of data like 1D raw data 2D processed data etc c Click File Delete Or rs Enter delete on the command line The dialog window shown in Fig 4 20 will appear Here you can select the data type and selection criteria 4 6 Renaming Data How to Rename a Specific Dataset 1 Right click the data name expno or procno in the browser then click Rename 2 In the appearing dialog Enter the new name expno or procno 3 Click OK Dataset Handling Browse Options OQ An entire data set with all EXPMOs PROCNOs E Acquisition data CO Processed data O Data acquired at certain dates 1D raw data fid OQ 1D processed data 11i O 2D9D raw data ser CO 2D processed data 2rri2ii O Imaginary processed data 11 OQ Macr
93. Spectrum Overview display r Click the following toggle button in the upper toolbar UL Switch the spectrum overview display on off ov 162 2D Display With the spectrum overview on the data window will for example look like this Bk exam zd HC 1 1 Cobio guest E i Spectrum ProcPars AcguPars Title PulseProg Peaks Integrals Sample Structure Fig Acqu 5 0 F2 ppm How to Switch on off the Projection display r Click the following toggle button in the upper toolbar 4f j Switch the projection display on off pr With the projections displayed a 2D dataset looks like this exam d HC 1 1 Cibio quest SPE Spectrum PracPars AcguFars Title FPulseProg Peaks Integrals Sample Structure Fid ACU F2 ppm 2D Display 163 In this example the F1 projection is selected as indicated by the filled blue square whereas the F2 projection is not selected A selected projection can be rescaled using the toolbar rescale buttons of function keys If you right click inside the pro jection area of the data window the following popup menu appears External Projection Internal Projection Baseline At Center Baseline At Bottom Clicking External Projection opens the a dialog box where you can specify or search for a 1D dataset and display this as a projection of the current 2D dataset Clicking Internal Projection calculates and displays the positive projection and display
94. TOPSPIN instance for other users This solves the problem of users leaving TOPSPIN open and blocking a floating license although they do not currently use it How to Define Auto Locking after Idle Time TOPSPIN can be configured to lock the interface after a user specified idle time To do that 1 Click Options Preferences set 2 Click the Change button to the right of the object Automatic locking of TOPSPIN when idle time has exceeded enter the NMR Administration password as requested and enter the number of minutes of allowed idle time 3 Click OK to close the dialog click OK to close the Preferences dialog If the user does not any commands from the command line menu or tool but tons the TOPSPIN interface will be locked see Fig 19 2 TopSpin locked by user carol at Wed Jul 13 16 53 52 BST 2005 Please press a button to unlock carol to unlock MMF administrator to unlock Figure 19 2 316 User Preferences How to Change the Preferred Editor You can choose your preferred editor as it is used by commands like edau ed pul edcpd etc To do that 1 Click Options Preferences set 2 Click Miscellaneous in the left part of the dialog box 3 Click the Change button to the right of the object Preferred text editor enter the desired Editor and its path For example for Wordpad under Windows 2000 XP this would look like EN Editor definition Please specify an ID name and the editor s path
95. Undo the Last Region Operation 000 195 How to Return from the Integration Mode with without Save 196 ID Interactive Calibration saseta i ee A EEA Ga eee 196 How to Switch to Calibration Mode 0 2 0 0 e eee 196 How to Calibrate a Spectrum Interactively 040 197 ID Viti ple Dis play iis gna 2c5 5S wie nS dole a ee OER PO ook Feel 198 How Switch to Multiple Display Mode and Read Multiple Spectra 198 Howto Select Deselect Datasets at 2d2i seg srie eni dire ies 200 How to Remove a Dataset from Multiple Display 201 How to Display the Sum or Difference Spectra 201 How to Save the Sum or Difference Spectra 201 How to Display the Next Previous Name Expno 201 How to Toggle between Superimposed and Stacked Display 202 How to Shift and Scale Individual Spectra 202 How to move the selected spectrum one place up down 204 How to Switch on off the Display of Datapaths and Scaling Factors 204 How to Return from Multiple Display mode 204 How to Set the Colors of the 1 24 Dataset 000 00 ee 205 1D Interactive Baseline Correction 0 000 eens 205 How to Switch to Baseline Correction Mode 00 205 How to Perform Polynomial Baseline Correction 206 How to Perform Sine Baseline Correction 0005 206
96. Up Increase the intensity by a factor of 2 e Alt PageDown Decrease the intensity by a factor of 2 e Alt Enter Reset the intensity or r Click one of the following buttons gt Increase the intensity by a factor of 2 2 f Increase the intensity by a factor of 8 8 2 Decrease the intensity by a factor of 2 7 2 8 Decrease the intensity by a factor of 8 8 Reset the intensity vr Alternatively you can enter the corresponding commands as specified between square brackets To manipulate all data windows press the Ctrl key while clicking one of the above buttons How to Smoothly Change the Vertical Scaling of the FID Spectrum 0s Click hold the button and move the mouse or c Turn the mouse wheel while the cursor is in the data window How to Change the Horizontal Scaling of the FID or Spectrum r Click hold the button and move the mouse 1D Display 113 amp Zoom in out smoothly or r Click one of the following buttons 1 Zoom in to the center spectrum or left edge FID of the displayed re gion increasing the horizontal scaling zi Zoom out from the center spectrum or left edge FID of the displayed region decreasing horizontal scaling zo El Perform an exact zoom via a dialog box zx a Enter the coordinates of the desired region in the dialog box EJexactzoom ued Please enter the exact coordinates of the desired expansion F1 ppr Fror b11
97. adjustment window enter gs Parameter Handling 89 How to Set an Acquisition Parameter from the Command Line Enter the parameter name on the command line For example to set the time do main size 1 Enter td for 1D data the following dialog box will appear CT x Size of fid TD e5536 JRK Cancel for 2D data the following dialog box will appear TT x Size of fid F2 F1 TD fi O24 256 JRK Cancel 2 Specify the desired value s e g 65536 or 64k 3 Click OK How to Set Acquisition Parameters from the Parameter Editor To open the acquisition parameter editor r Click the AcquPars tab in the Tab bar of the data window or r Enter eda on the command line Fig 5 2 shows an example of the acquisition parameter editor with the Experi ment parameters displayed 90 Parameter Handling exami d_13C 1 1 CiBio guest SpectrUrN FrocPars 4cquPars Title PulseProg Peaks Integrale Sample structure Fid Scqu w IL se muaa Experiment Wictthi Recelver Mucus Durations Power Program Probe Lists Wobble Lock Automation F Experiment PULPROG zqgpg su Le Current pulse pr Arts mod Acquisition mace To Size of fid MS Number of Scar DS Number of durrirr TODO Loop count for t B idth g YF Receiver RG 32 f Be Receiver gain Figure 5 2 The processin
98. age formats retain the audit trails When unpacking such files with fromjdx or fromzip respectively the original data set in standard Bruker format is restored The command auditch eck may be used to check whether the data are still consistent If for example JCAMP DX or ZIP file have been manipulated the data might not be consistent 17 2 Electronic Signatures 17 2 1 Signing a data set The command esign adds an electronic signature to the raw data or to the proc essed data of a data set It opens a dialog where you can select the data component to be signed the signature meaning and optionally add a comment esign requires that the NMR administrator has set up a list of users who are allowed to sign a data set along with definitions of signature meanings e g review approval See below for details command uadmin EA esipn Add Electronic signature To Data Set esam to 13aC 1 1 Cbio quest Data component to be signed Raw amp Processed Data Select Signature Meaning Comment Figure 17 4 Regulatory Compliance 295 17 2 2 Structure of a signature In TOPSPIN an electronic signature is realized as a special entry appended to the audit trail of the raw or processed data It is therefore linked with the data and pro tected against manipulations just like any other audit trail entry Signatures can be viewed with the command audit An electronic signature consists of the follow ing items USER ID
99. al electronic keys which authenticate the owner of the document to be performed by authorized trust centers In contrast TOPSPIN uses OS encrypted passwords or internal user passwords encrypted by TOPSPIN itself For this reason a Standard Operating Procedure SOP of the company or institu tion that wishes to apply TOPSPIN signatures must exist defining the role of TOP SPIN signatures For this reason companies and institutions that want to apply TOPSPIN signatures Regulatory Compliance 297 must have a Standard Operating Procedure SOP which defines the role of these signatures Note that digital signatures complying with respective laws requires special soft ware and the involvement of trust centers Bruker refers to the respective commer cial software for this purpose 17 3 Password Controlled Login Identification 17 3 1 Definition of an internal user In TOPSPIN the NMR administrator may set up a list of internal TOPSPIN users An internal user need not have a user account for the operating system and is only known to TOPSPIN Such a user is characterized by the following items USER ID A short unique string of characters identifying a user e g guest USER NAME A long string of characters usually the full name of a user e g Franz J Maier SIGNATURE MEANINGS A list of items separated by comma e g Approval Review an empty string or the special string NONE In the latter two cases this us
100. alog box for finding datasets Proceed as follows 1 Specify all search criteria and click OK 2 In the appearing Search result box a Select the desired datasets b Click Save selection 3 In the appearing browser a Navigate to the desired list directory b Enter or select the list filename c Click OK Alternatively you can create a dataset list manually The format of a list entry 1S lt name gt lt expno gt lt procno gt lt dir gt lt user gt An example of a dataset list is examld_13C 1 1 C bio guest examld_13Cc 2 1 C bio guest examld_13C 3 1 C bio guest Alternatively you can create a dataset list by specifying the absolute pathnames of a dataset e g C bio data guest nmr examld_13C 1 pdata 1 Create new Serial script Data Processing 101 Opens the appropriate editor to create a new script For Script type Python edpy is executed for Script type macro edmac is executed The name of a se rial script macro of Python must start with ser_ Python scripts must have the extension py A standard example is the python script ser_efp py An example of a simple processing sequence is exponential window multiplica tion Fourier transform and automatic phase correction of a 1D dataset A TOPSPIN macro performing this task would be ef apk A Python programs performing the same task would be RF APK Note that Python programs are much more versatile than macros Details on Python programmin
101. an be opened e in an existing data window replacing the current dataset e inadata window which is in multiple display mode being superimposed on the current spectra e in anew data window which becomes the active window Note that if a dataset is already displayed in one window and it 1s opened in a sec Dataset Handling 63 ond existing window it still replaces the dataset in the latter one As a result the same dataset will be displayed in two windows see also command reopen How to Open Data Windows Cascaded By default a new data window appears maximized filling the entire data field and covering possibly existing window You can however configure TOPSPIN to open new windows cascaded This is convenient if you want to open several data win dows and then select one To open new windows cascaded 1 Click Options Preferences set 2 Click Window Setting in the left part of the dialog box The right part of the dialog box shows the window settings see Fig 4 11 nwe new internal windows cascaded rather than maximized Configure cascaded window TE Figure 4 11 3 Check Open new internal windows cascaded rather than max 4 Optionally you can configure the cascaded windows by clicking the respec tive Change button This will open the dialog box shown in Fig 4 12 64 Dataset Handling 0 x Define the properties of cascaded windows All numbers must be in the range 0 1 They are
102. and 212 ppm axis units 139 161 pps command 210 preferences 31 311 pre scan delay 283 preview the baseline corrected spectrum 207 previous commands 35 dataset in browser 39 parameter field 87 91 plane in 3D 173 row column in 2D phase correction 221 233 print 1D peak list 127 active window 23 104 colors 318 data from the menu 103 data from the Processing Guide 105 integral list 106 metafiles 107 peak list 106 the current dataset 38 print command 32 38 103 106 127 printer colors 318 prnt command 104 probehead solvent dependent parameters 91 proc_ld AU program 97 process data 24 31 from the command line 93 from the Processing Guide 94 with AU programs 97 with composite commands 94 processing parameters 85 86 parameters 1D 116 parameters 2D 157 Processing Guide 24 95 Processing menu 24 31 Processing Reference Manual 21 procno 65 69 70 74 82 145 ProcPars tab 24 85 86 116 157 projections of a 2D spectrum 22 162 properties of a dataset 143 of a printer 104 prosol parameters 276 pseudo raw data 74 pulse program 19 26 58 119 display 119 parameters 91 117 276 PulsProg tab 119 Python programs 28 335 339 342 Q QUIT AU macro 98 QUITMSG AU macro 98 R re command 21 69 198 read color scheme 319 data formats 71 integrals from disk 190 the prosol parameters 276 window layout 246 reb command 20 70 re enable disabled commands 331 reference peak in 1D calibration 197
103. and first order phase values phr How to Change the Mouse Sensitivity r Click one of the following buttons 186 1D Interactive Manipulation 1 Increase double the mouse sensitivity inc t Decrease halve the mouse sensitivity dec Il Reset the mouse sensitivity How to Return from Phase Correction Mode with without Save To return while saving the phase correction to the current dataset r Click the following button J Save execute and return sret This will perform the following tasks e Execute phase correction command pk e Save the current phase correction values e Leave the phase correction mode To return without save r Click the following button Return discarding any changes ret To return while saving the phase correction to the source 2D dataset r Click the following button ElL Save to 2D s2d This is only applicable on rows or columns extracted from 2D data The phase values will be saved to the 2D dataset from which the current 1D data set was extracted 11 3 1D Interactive Integration Integration of 1D data can be done automatically with the commands abs and 1i or interactively as described in this paragraph 1D Interactive Manipulation 187 How to Switch to Integration Mode r Click the indicated button in the upper toolbar 2d 3d 4 A MO J jar or enter int on the command line The Tab bar of the active data window will be replaced by a to
104. andling 5 1 Processing Parameters Processing parameters can be set changed in three different ways e from the parameter editor click the ProcPars tab or enter edp e from the command line e g enter si e from acommand dialog box e g wm How to Set a Processing Parameter from the Command Line Enter the parameter name on the command line For example to set the size 1 Enter si for 1D data the following dialog box will appear CT x Size of real spectrum 51 2768 OK Cancel 86 Parameter Handling for 2D data the following dialog box will appear x Size of real spectrum ol joz OK cancel 2 Specify the desired value s e g 32768 or 32k 3 Click OK How to Set Processing Parameters from the Parameter Editor To open the processing parameter editor r Click the ProcPars tab in the Tab bar of the data window Or rs Enter edp on the command line examid 1H 1 1 Cibio quest Spectrum ProcPars AcquPars Title PulseProg Peaks Integrals Sample Structure Fid Acque los Va Fef E NE F Reference Window Phase sl Size of real Spec Baseline SF MHz spectrometer tre Fourier OFFSET ppm Low field limit of Integration SR Hz ooo ooo spectrum referel Peak HZpPT Hz Spectral resolutic Automation l l b Vindoy function Miscellaneous til User Y Phase correction PHO degree 111 456 Cth order correct s Figure 5 1 Para
105. arked with an unfilled blue square _ Selecting 220 2D Interactive Manipulation a single row column allows you to shift and scale it separately from the other rows columns as shown in Fig 12 6 Bi Phase 2D exam2d_HC 1 1 Csbio guest l ojx Alel o 1 R wila s n l a EELS pivot 1265 44 ppm Fhase increment 0 20 ph 63 356 phl 150 80 _ SIL 644 i JE a BIT Column 899 j 9748 ppm Figure 12 6 To select all rows or columns m Click the following button ie Select all rows or columns How to Perform Smooth Phase Correction To perform zero order phase correction 1 Click hold the following button it turns green and move the mouse 0 Zero order phase correction until the reference peak of the first row column is exactly in absorption mode 2 Release the mouse button turns grey The parameter PHCO will be set accordingly To perform first order phase correction 1 Click hold the following button it turns green and move the mouse 1 First order phase correction 2D Interactive Manipulation 221 until the reference peak of the second and further rows columns is exactly in absorption mode 2 Release the mouse button turns grey The parameter PHC1 will be set accordingly How to Perform 90 90 or 180 Zero Order Phase Correction Click one of the following buttons 4 90 zero order phase correction 4 90 zero order phase correction 180
106. art of the active data window and acts on that Bruker delivers a few standard button pan els like bnmr and bnmrsel To create your own button panels you can modify one of these or write them from scratch In this description we will create a very simple button panel with some 1D processing commands and print export buttons see Fig 20 2 1D Processing Panel Close To 20 Tips Figure 20 2 To write this button panel take the following steps 1 Open the Windows Explorer and navigate to the subdirectory userdefined User Extensions 337 2 5 of the users properties directory z Create a text file with the name cmdpanel_ lt name gt prop where lt name gt is the name of the button panel Enter the button definitions including Panel title Colors Toggle buttons Top buttons Panel layout Panel buttons and Tooltips Save the file under a name cmdpanel_ lt xxx gt prop where lt xxx gt is the actual name of your command panel Make sure the extension of the file is prop and not txt prop txtor anything else Enter bpan lt xxx gt on the command line to open the button panel Here is an example for a small button panel for 1D processing Color definitions used in this file RGB BLUE1 51S 2045 255 YELLOWI 2555 2555 0 GREEN1 845 196S 20 Title geting on TITLE 1D Processing Panel TITER COLOR 08 05 255 Toggle button definition TOGGLE _BUTTON To 2D TOGGLE _CMD bpan bproc2d
107. as described above and hold at the desired posi tion 2 Right click in the data window 3 Choose Grab Row Column from the popup menu see Fig 12 13 Note that a grabbed row column appears in the lower apart of the browser It can be selected there and individually scaled or shifted Toggle Rows Columns Extract RowlColumn Grab RowsCoalumn Baseline At Center Baseline At Bottom Figure 12 13 2D Interactive Manipulation 233 exam d HC 3 1 Chio guest BE e Row lt e E Ei Ss ts de tjat MT a Row 57 746 ppm 619 of 1024 5 4 F2 ppm Figure 12 14 Fig 12 14 shows row 619 with the 1D baseline at the center of the data window How to Show the Next Previous Row or Column To show the next row column click the following button Show next row column To show the previous row column click the following button Show previous row column Alternatively you can turn the mouse wheel while pressing the Shift key to show the next previous rows columns How to Move the Selected Dataset Up Down in the Dataset List To move the selected dataset up click the following button Move the selected dataset up To move the selected dataset down click the following button 4 Move the selected dataset down 234 2D Interactive Manipulation How to Extract a Row Column 1 Scan rows or columns as described above and hold at the desired position 2 Right click in the data w
108. ase Pivot Point By default the phase pivot point is set to the biggest magnitude intensity of the displayed region of the spectrum To change the pivot point 1 Right click on the desired pivot point position 2 Choose Set pivot point from the popup menu see Fig 11 2 1D Interactive Manipulation 185 How to Perform Default Zero Order Phase Correction 1 Right click in the data window 2 Choose Calculate phO in the popup menu see Fig 11 2 The spectrum will automatically be corrected according to the calculated value How to Perform Interactive Zero Order Phase Correction 1 Click hold the following button button turns green 0 Zero order phase correction parameter PHCO 2 Move the mouse until the reference peak is exactly in absorption mode 3 Release the mouse button turns grey How to Perform Interactive First Order Phase Correction 1 Click hold the following button button turns green 1 First order phase correction parameter PHC1 2 Move the mouse until the entire spectrum is exactly in absorption mode 3 Release the mouse button turns grey How to Perform 90 90 or 180 Zero Order Phase Correction r Click one of the following buttons gl Perform 90 zero order phase correction ph90 Perform 90 zero order phase correction phm90 180 Perform 180 zero order phase correction ph180 How to Reset the Phase to the Original Values r Click the following button Reset zero
109. asets or different aspects of the same The TOPSPIN Interface 45 dataset e g raw processed regions scalings etc When the dataset is re processed in one interface its display is automatically updated in all TOPSPIN interfaces The command exit closes the current Topspin interface Interfaces that were opened from this interface remain open Entering exit in the last open TOPSPIN interface finishes the entire TOPSPIN session The position and geometry of each TOPSPIN interface is saved and restored after restart Chapter 3 Trouble Shooting 3 1 General Tips and Tricks On a spectrometer make sure the commands cf and expinstal1l1 have been executed once after installing TOPSPIN c f must be executed again if your hard ware configuration has changed Sometimes executing cf is useful in case of acquisition problems On a datastation a default configuration 1s automatically done during the installa tion No configuration commands are required Only if you want to use AU pro grams you must run expinstall once 3 2 History Log Files Spooler Reports Stack Trace If you have a problem with TOPSPIN and want to contact Bruker it is useful to have as much information as possible available If TOPSPIN is still running you can view log files with the commands hist and ptrace If TOPSPIN hangs you can create a stack trace by hitting Ctr1 Linux or Ctr1 Break Windows in the TOP SPIN startup window 48 Trouble Shooting
110. aste d Switch to the last 2D dataset 2d 3d Switch to the last 3D dataset 3d For more information on dataset handling please refer to chapter 4 3 Buttons for interactive functions A AM I ak Ss The functions of the individual buttons are A Enter phase correction mode Enter calibration mode I Enter baseline correction mode ii Enter peak picking mode T Enter integration mode it Enter multiple display mode 4 Enter distance measurement mode For more information on interactive functions refer to chapter 11 and 12 Buttons for display options hp EL ok EE The TOPSPIN Interface 33 The functions of the individual buttons are ha Toggle between Hz and ppm axis units Ei Switch the y axis display between abs rel off ul Switch the overview spectrum on off HH Toggle grid between fixed axis off How to Use the Lower Toolbar 1D data The lower toolbar contains buttons for display functions Buttons for vertical scaling intensity f2 4 fh gt Increase the intensity by a factor of 2 2 2 Decrease the intensity by a factor of 2 7 2 amp Increase the intensity by a factor of 8 8 8 Decrease the intensity by a factor of 8 7 8 Change the intensity smoothly Reset the intensity baseline positions remains unchanged vr Note that vertical scaling can also be changed with the mouse wheel Buttons for horizontal scaling zooming AARAA o ah 4H Reset zooming horizon
111. at each step open a dialog box offering you the available options and Acquisition 263 required parameters Note that the last button To processing will open the process ing equivalent of the Acquisition Guide the Processing Guide 15 2 Acquisition Toolbar Acquisition can be prepared started and controlled from Spectrometer menu Clicking this menu opens the pulldown menu shown in Fig 15 2 a E Processing Analysis Opt Interactive Acquistion Guide topgquide Data Acquisition Flowchart Basichselective Experiments ICOR AMR Adjustments Acquisition setup sample Shim contral Tr Y F F F F F F Accessories Shape Tool stdisp Excitation Profile exprot Acquisition Status Bar omot Figure 15 2 Here you find several cathegories of acquisition related commands Each entry give access to a submenu with various commands Fig 15 3 for example shows the Setup submenu 264 Acquisition Hardware Configuration cf Ethernet addresses of hardware ha Experiment Installation expinstall Parameter set conversion paracon Probe table setup edhead Solvent dependent parameter setup edprosall Lock parameter setup edlock Nuclei table setup ednuc Solventtable setup edsoly Amplifier linearization setup carta Convert gradient fleld maps convieldmaps Figure 15 3 For most entries the command line command for example expinstal1l1 is specified in square brackets Furthermore Topsp
112. ata e Saving a dataset in JCAMP DX format This format is a IUPAC standard and is available for 1D and 2D datasets Data and parameters are stored in readable text ASCII format To store data in JCAMP type tojdx click File gt Save or type Ctr1 s To convert and display a JCAMP DxX file type fromj dx e E mailing data to a desired destination Type smail or click File Send To The mailing format is either zip or JCAMP DX both of which allow for data compression in order to keep the transferred data size as small as possible 1 14 How to Import NMR Data Stored in Special Formats TOPSPIN allows you to convert various data formats to standard Bruker format for display and processing Click File gt Open and select Open NMR data stored in special formats Then follow the instruction on the screen 1 15 How to Fit Peaks and Deconvolve Overlapping Peaks Peaks of a 1D and 2D NMR spectrum can be approximated by a Lorentzian Gaus sian or a mixture of these line shapes Overlapping peaks may be deconvolved into a sum of such line shapes TOPSPIN shows the deconvolution result 1 e peak positions line widths and inte grals on the screen and stores it in the file dconpeaks txt Furthermore it switches to multiple display mode to show the original spectrum and the sum of the computed line shapes superimposed To start deconvolution expand the spectrum on the display to show the peak or peak group of interest Then type
113. ata points for T2 calculation of 1D raw data View the Fitting Results When the fitting procedure has finished the fitting curve is displayed in the data section and a Brief Report appears in the parameter section see Fig 14 6 The latter consists of e the calculated relaxation value e the fitted parameters e the standard deviation SD For further examination of the result click one of the following buttons Show the fitting result of the previous peak area Show the fitting result of the next peak area Switch x axis to linear scaling a Switch x axis to logarithmic scaling E Switch x axis to square root scaling E Switch y axis to logarithmic scaling Note that this only works for curves with positive intensities areas only E Import integrals from dataset TEMP Export integrals to dataset TEMP Toggle button to hide show information in the curve field including al gorithm peak number and relaxation value H E T Show an extended report including the fitted intensity or area distribu tion This consists of the same information as the brief report plus a ta ble with the intensity or area distribution Example Dataset C bio data guest nmr titest 1 pdata 1 INTENSITY 430 TEETSTLO jae exp o 771 260 Analysis t2 points tor Peak 1 Cursor Point 7 221 pom Results Comp L D a I ZL OSEAO00 P 2 521 LeFO00 T1 19 449s SD 3 685e 003 tau ppm integral intens
114. atically recalculated and displayed How to Change the Width of the Signal Region or Noise Region 1 Right click in the data window 2 Choose Change region width from the popup menu see Fig 14 2 Analysis 253 3 Enter new width values in the appearing dialog box El sino Define sino parameters width SIGRE G MOMSEREG 4 Click OK Note that as you change the width the right limit is modified correspondingly The left limit is kept The S N value is automatically recalculated and displayed 14 4 Relaxation Analysis Typically relaxation data consist of a series of 1D FIDs measured with varying delays and stored as pseudo 2D data To analyze these data Topspin offers an easy to use T1 T2 Relaxation Guide Relaxation curves of various experiment types with up to six components can be fitted To start the Relaxation Guide w Click Analysis gt T1 T2 Relaxation t1lguide This will open the dialog box as shown in Fig 14 3 254 Analysis MMF Relaxation Guide i Fitting Furcti Vane ing 7 ior Extract Slice gt 4 h Start Calculation ae Define Ranges a Relaxation window PrintvExport Figure 14 3 Just click the successive icons and follow the instructions on the screen Note that holding the cursor over an icon shows the command line command that is executed when the icon is clicked If you prefer to execute these commands from the com
115. bels of the existing points are displayed on the screen If you choose Overwrite no labels are displayed Nevertheless the existing points are only overwritten when you define and save new points To define new baseline points 1 Move the cursor line to a baseline point and left click at that position 2 Do this for at least five baseline points Fig 11 15 shows a spectrum with five defined baseline points Note that here the points have been chosen at the right part of the spectrum for display reasons on ly How to Delete Spline Baseline Points from the screen To delete one baseline point 1 Right click the baseline point position in the data window 2 Choose Delete Current from the popup menu see Fig 11 16 210 1D Interactive Manipulation Quit save amp UIt List baslonts Delete All Delete Current Enter zoom Figure 11 16 To delete all baseline points 1 Right click any position in the data window 2 Choose Delete All from the popup menu see Fig 11 16 How to Return from Cubic Spline Baseline mode with without Save To return while saving the baseline points r Click the following button Hj Save baseline points and Return retsab To return while discarding any changes r Click the following button Return Discarding any changes ret Alternatively you can right click in the data window and choose Save amp Quit or Quit respectively 11 7 1D Interactive Peak Picking Peak picking
116. better fitting curve 2 Click the button to open the parameter dialog box Select a Func tion Type and set the required parameters see below 3 Click OK 4 Perform fitting and calculate the relaxation time B Fit the relaxation curve for the current peak gt Fit the relaxation curve for all peaks ast Fit data according to the ASCII file tlascii View and interpret the results as described below Function Types and Parameters The TOPSPIN relaxation routine offers functions for various relaxation experi ments with up to 6 components uxnmrtl for one component T1 experiments Set the parameter List file name to the list type used during the acquisition Set Pick data points to PD or PDO see below The T1 fitting function is defined by the function I t 1 0 Px exp where is Intensity or Area according to the Fitting Type The best fit is cal culated by varying I 0 P and T1 in an iterative process according to the Lev enberg Marquardt algorithm Clicking and executes the commands ct1 current peak and dat1 all peaks respectively 258 Analysis uxnmrt2 for one component T2 experiments Set the parameter List file name to the list type used during the acquisition Set Pick data points to PD or PDO see below A T2 fitting function is defined by the function I t Px exp 5 where is Intensity or Area according to the Fitting Type The best fit is cal culated by varying P and T2
117. both 2D Display 167 PY exam d HC 1 1 C bio guest z 0 o E A e i a Required parameters Calculation method O biultiply with increment Add increment Contour level sign G Positive amp Negative O Positive O Negative Postive Negative Base level 56691 27 1 S6691 27 1 Level increment 71 800 1 200 Number of levels Figure 9 14 How to Store interactively set Contour Levels To store contour levels that were set interactively for example by clicking 9 or 168 2D Display pressing Alt PageUp r Click the following button in the lower toolbar Ef Store contour levels 1s The levels are stored in the file lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt clevels How to Display a 2D spectrum in Pseudo Color Mode r Click the following button in the upper toolbar Switch to image color display mode im In pseudo color mode a spectral region looks like this 50 48 46 F1 ppm 5 4 5 2 5 0 4 8 F2 ppm Note that in pseudo color mode the contours are superimposed in black when you Zoom in on a small region of the spectrum How to Display a 2D Spectrum in Oblique Mode r Click the following button in the upper toolbar x Switch to oblique display mode st In oblique mode a spectral region looks like in Fig 9 15 2D Display 169 5 4 5 2 5 0 F2 ppm Figure 9 15 In this mode you can manipulate the display in va
118. button iti Remove selected data from the screen Note that the data on disk are not affected Furthermore the first spectrum cannot be removed from the screen How to Display the Sum or Difference Spectra r Click one of the following button button turns green A Show the difference between the first and the sum of the other datasets Show the sum of all datasets in the multiple display window How to Save the Sum or Difference Spectra 1 Click the following button Save the displayed sum or difference spectrum 2 In the appearing dialog box specify the destination procno How to Display the Next Previous Name Expno To compare a series of spectra you can interactively increment or decrement the dataset name or expno A dataset name is incremented according to the ICON 202 1D Interactive Manipulation NMR naming convention of increasing extensions e g name 001 name 002 etc r Click one of the following button button turns green E Show the previous name expno procno of the last dataset E Show the previous name expno procno of the last dataset Ei Set the increment options Clicking this button will open the following dialog Data set increment options clncrement E Procna O Expno E Mame Expno increment Preserve individual scaling Figure 11 11 Here you can choose to increment the procno expno or name set the expno increment and switch individual scaling on off
119. c signature entered with esign will appear below the title How to Display the Main Dataset Properties r Right click inside the data window and choose File Properties An information box as displayed in Fig 8 15 will appear 144 1D Display EA Properties examid 1H 1 1 amp Bio guest Dimension Proci amp cquy 10710 Pulse programm zg Acquisition date Mar 2004 15 00 44 Nuclei TA 1a AXNUC 41H SFO MHz 50043250065 Solvent CDCIS Acquired data available es Processed data available Tes TITLE H Cyclosporin Figure 8 15 Note that this is status information which cannot be changed How to Display a List of Files of a Dataset ms Right click inside the data window choose Files Fig 8 16 shows the file list when the Fid tab is active i e when the raw data are displayed It is the contents of the expno directory 1D Display 145 Directory CBI Wataiguestininrexan d_ 1A audita txt cyclosporina pdb fid format temp brosoal History pulseprograr sample infto prop Scorn Uxnitrir par cen Figure 8 16 Fig 8 17 shows the file list that appears when the Spectrum tab 1s active 1 e when the processed data are displayed It is the contents of the procno directory 146 1D Display PY File list Directory CBI Wataiguestinimr lexan d_ 1TH ypdatai qi a auditp txt curdat urn wp email xarniid 1H_1_1 pdt intryg last plot wp layout swp outd parm txt peak
120. can also be performed non interactively with the TOPSPIN command st This command must entered with the appropriate arguments on the command line while the associated dataset 1s dis played and selected A full description of the interactive and non interactive Shapetool can be found under w Click Help gt Manuals Acquisition Application Manuals Shapetool Chapter 16 Configuration Automation 16 1 NMR Superuser and NMR Administration password During TOPSPIN installation you are prompted to define the username for the so called NMR Superuser Under Windows this must be the name of an existing user Under Linux it can also be a non existing user which is then automatically created by the installation program After the installation the NMR Superuser is the owner of all TOPSPIN program files Logging in as this user allows you to remove these files change file permissions etc The name of the NURSUPERUSER will be stored in the file lt tshome gt conf nmrsuperuser the NMR Administration password to be used for TOPSPIN configuration commands This password can be freely chosen and is not connected to any user It is asked for by TOPSPIN commands like cf expinstal11 etc The encrypted NMR Administration password is stored in the file lt tshome gt conf nmradminpassword Note that the NMR Superuser login password and the NMR Administration password have different purposes and are totally independent Changing one of th
121. cates the start of the second icon column e NM2 the text to appear underneath of the icon The sign is mandatory e CMD the command to be executed when the icon is clicked This can be a regular TOPSPIN command a macro or an AU or Python program e TIP the tooltip to be displayed when the cursor is held over the icon Note that the sign is mandatory Before you can start a user defined guide you must edit the file cmdtab_user prop and define the corresponding command in the file for example mytlguide EM J MC N CL tutor TutStarter ME startTuto rial AR MyT1T2Toolbar My T1 T2 Tutorial Here e MyT1IT2Toolbar is the toolbar identifier as it is used in the file toolbar_user prop e My T1 T2 Tutorial is the title as it appears at the top of the guide If your guide is a Bruker modified guide you can also redefine the origi nal Bruker command 1 e specify t 1 guide instead of myt 1guide Note that the original Bruker guide is then no longer accessible If you want to access a user defined guide from the TOPSPIN toolbar you have to 346 User Extensions create a new toolbar button To do that right click in an empty area of the toolbar and define a button in the appearing dialog Index Symbols 2 command 33 40 112 151 8 command 33 112 151 2d command 32 3d command 32 all command 33 113 153 basl command 205 bmp files 23 bzip files 25 72 cal command 196 235 co command 16
122. ces 331 How to Re enable a disabled Command Menu 1 Open the Menu Configuration table as described above 2 Set the Status of a disabled or removed invisible entry to enabled 3 Click OK to close the Configuration table How to Re enable All Commands Menus 1 Open the Menu Configuration table as described above Click the Reset button to enable all menus and commands 2 3 Click OK to confirm the appearing message 4 Click the OK button to close the Configuration table 19 4 Resizing Shifting Toolbar Icons How to Change the Toolbar Icon Size 1 Right click of the toolbar 2 In the appearing popup menu see Fig 19 13 click t Change Icon Size Reactivate All Invisibleinactive Buttons Add User Defined Button Change Icon Size Change Toolbar Offset Hide Toolbars wpe SHIFT ESC to reset Figure 19 13 3 Enter the icon size in the appearing dialog and click OK How to Shift Toolbar Icons to the Right 1 Right click at an empty area of the toolbar 2 In the appearing popup menu see Fig 19 13 click t Change Toolbar Offset 332 User Preferences 3 Enter the toolbar offset in the appearing dialog and click OK 4 19 5 Defining Source Directory for Programs Lists etc TOPSPIN 2 1 and newer allow you to defined the source directories for pulse pro grams AU programs integral ranges various lists etc In TOPSPIN 2 0 and older the source directory for these items was fix
123. cessing starts Viewing audit trails Since audit trails are regular ASCII text files they can be viewed or printed with any text editor outside of TOPSPIN Within TOPSPIN you can use the command audit for this purpose This opens the dialog box show in Fig 17 1 Regulatory Compliance 291 PN Audit trail audit check Options O Views audit trail of processed data OQ Views audit trail of acquisition data O Add a comment to audit trail of processed data O Add a comment to audit trail of acquistian data Figure 17 1 The first two entries allow you to view the audit trail files The third entry per forms an audit trail check 1 e a data consistency check If both raw and processed data are consistent you will get the message shown in Fig 17 2 Ea auditcheck audit file for acquisition OK processing OK raw data checksum OK proc data checksum OK Figure 17 2 If the data have been manipulated outside of TOPSPIN e g with third party soft ware the checksum will be inconsistent Fig 17 3 shows the message for incon 292 Regulatory Compliance sistent processed data Ea auditcheck audit file tor acquisition OK processing OK raw data checksum OF proc data Invalid data checksum Figure 17 3 The fourth and fifth entry in Fig 17 1 allow you to add a comment to the raw or processed audit trail files respectively 17 1 4 Audit trail contents The contents of an audit file is group
124. ch for specified parameter Changed parameters are automatically saved Note that the and E button to the right of the PULPROG parameter allow you to show the pulse program list or edit the current pulse program respectively 118 1D Display How to Edit the Title Click the Title tab edti _ 1 eR uest ox Spectrum ProcPars AcquPars Title PulseProg Peaks Integrals Sample Structure Fid Acqu Pxamid 13C 1 1 CiBio guest asc AY 300 Automation Cholesterylacetate This allows you to edit the title that appears in the data window and on the plot F Save the title file under its current name H Save the title file under a new name 1 Reload the title file Undo modifications since the last save E Open the title file with the external editor defined in User Preferences 1D Display 119 How to Edit the Pulse Program t Click the PulsProg tab edcpul1 examid TC 1 1 CiBio guest Sle Spectrurn ProcPars AcguPars Title PulseProg Peaks Integrals sample Structure Fid Acqu l ze dll pllz fz 30m do fz l u pll3 fz agli camels TE DELTA du do fzZ This allows you to edit the current pulse program The following extra buttons are available here F Save the pulse program under its current name E Save the pulse program under a new name 7 Reload the pulse program Undo modifications since the last save amp Switch t
125. ck Options Preferences set 4 Click Miscellaneous in the left part of the dialog box Remote Control 305 5 Click the Change button at the entry Setup remote systems In the appearing dialog see Fig 18 2 Server ID lega Host name or address ledalsottware bruker de TEPAF port number SoU Figure 18 2 enter the following information e Server ID an arbitrary name for the remote system e Hostname or address the hostname or IP address of the remote host e TCP IP port number of the remote TOPSPIN as identified in chapter 18 2 1 6 Click Add to add the remote host 7 Click OK to save the changes and close the dialog Note that you can define multiple remote systems for example different spec trometers in your laboratory Connect to the remote system 1 Click Options Remote connection 2 Select the desired Remote system from the appearing dialog box and click OK 306 Remote Control Ey Connect Please select the system you want to connect to This requires a properly configured TOPSPIM be running on that system Remote systems can be set Up in the Preferences panel see Options menu under the Miscellaneous terri Remote system e Figure 18 3 Now you are prompted for a user and password both case sensitive on the remote computer xl Please enter the name and password forthe TOPSPIN session on the remote computer This connection is secure User guest
126. ck the VTU field to open the following popup menu start Edte Options Clicking Options will open the following dialog box Cn x Temperature monitor options Scale kelvin Update rate s 30 OK Cancel Figure 15 6 15 5 Command Queuing and Scheduling TOPSPIN 2 0 and newer support command queuing spooling and scheduling Acquisition commands like zg go rga and atma are automatically queued if this feature is on default off This allows you for example to enter multiple zg commands on different datasets Automatic queuing can be switched on as fol lows 1 Click Options gt Preferences 2 In the User Preferences dialog r Enable Auto Spooling under Administration Items Processing commands can be queued with the command qu For example the command sequence zg quxfbona 2D dataset will start an acquisition and when this has finished process the data Acquisition and processing commands can be scheduled with the command at Enter help qu or help at fo more details on the respective commands Queued commands can be viewed in the Spooling field of the acquisition status bar Note that the spooling field must be activated in the User Preferences window command set Acquisition 269 15 6 Tuning and Matching the Probehead Tuning and matching of conventional probeheads non ATM is performed with the wobble procedure To start this 1 Enter wobb on the command line The
127. cule structure viewer 136 mouse sensitivity in 1D baseline correction 208 in 1D integration 191 in 1D phase correction 185 in 2D phase correction 221 move data window 240 Mozilla 82 146 multiple display 1D 32 198 228 1D 2D 22 65 70 2D 22 228 in deconvolution 26 multiple display mode 65 198 multiple window display 110 multiplet 188 multiply with increment in 2D levels 166 N nbook command 333 negative 2D levels 170 new command 31 38 61 275 newtop command 44 next channel for wobbling 269 command 39 dataset in Browser 39 parameter field 87 91 plane in 3D 173 row column in 2D phase correction 221 233 window in data area 38 242 246 NMR ADMINISTRATION password 281 NMR SUPERUSER 281 nmradminpassword file 281 nmrsim command 27 119 nmrsuperuser file 281 noise region 250 251 NOISF1 parameter 250 NOISF2 parameter 250 notebook 333 NS parameter 264 O O1 parameter 265 O2 parameter 265 O3 parameter 265 objects of a dataset 23 110 240 311 316 317 318 oblique display of 2D spectra 168 170 of 3D planes 172 online help 42 online manual plot editor 105 Topspin 41 open browser portfolio 57 data 31 38 53 64 66 I 10 data from the browser 20 data from the command line 69 72 data from the Explorer 68 data from the menu 20 IconNmr interfaces 28 Linux Shell 18 new data window 242 new procno 69 70 online help documents 42 special format data 71 Topspin command index 43 open command
128. cus in the Command Line Ctrl Backspace Kill current input Ctrl Delete Kill current input Select previous command if available Select next command if available Focus in the Browser Select previous dataset Select next dataset Enter dir user name expno selected expand node or col lapse node depending on the current state procno selected display this dataset name expno selected display this dataset Enter multiple procnos selected show in multiple display Delete one or more name expno procno nodes selected delete these datasets 40 The TOPSPIN Interface Focus anywhere in TOPSPIN Scaling Data Alt PageUp scale up the data by a factor o Alt PageDown CerI alt PageUp CerI alt PageDown Alt Enter Perform a vertical reset Ctrl Alt Enter Perform a vertical reset in all data windows Ale Plus Zoomin 2i SSS Ale Minus Zoomout zo OOo CerI ATt Plus Zoom in in all data windows CerI Alt Minus Zoom out in all data windows hift spectrum down sd hift spectrum to the right sr hift spectrum down in all data windows hift spectrum to the left in all data windows hift spectrum to the right in all data windows Focus in a Table e g peaks integrals nuclei solvents en Sect the ast entry O oo Select the current and last entry and all in between i Nn Select previous entry The TOPSPIN Interface 4 Focus in a Plot Editor F1 Open the Plot Editor Manual F 5 Refres
129. d commands Therefore it is only suitable for the advanced user New or intermedi ate users are recommended to use the Processing Guide for semi automatic processing see chapter 6 2 How to Process Data with Single Commands Data can be processed by entering single commands on the command line A typ ical 1D processing sequence would be em exponential window multiplication ft Fourier transform apk automatic phase correction sref automatic calibration referencing abs automatic baseline correction This allows you full control over each individual processing step 94 Data Processing How to Process data with Composite Commands Data can also be processed with so called composite commands These are com binations of single processing commands The following composite commands are available e ef Exponential multiplication Fourier transform e efp Exponential multiplication Fourier transform phase correction e fmc Fourier transform magnitude calculation e fp Fourier transform phase correction e gf Gaussian multiplication Fourier transform e gfp Gaussian multiplication Fourier transform phase correction They can be entered on the command line or clicked from the menu For the latter option us Click Processing gt More transforms Shortcuts Just like single commands composite commands can be used in Macros AU pro grams and Python programs 6 2 Semi automatic Processing
130. d 130 Zqgigs0 2004 03 30 13 55 54 Figure 4 23 Note that on exiting TOPSPIN the search criteria will be rest to default How to Display one of the Found Datasets In the search result window see Fig 4 23 1 Click one or more datasets to select them 2 Click Display 80 Dataset Handling to display the selected dataset s in the current data window If multiple datasets are selected they are displayed in the new data window in multiple display mode The search result window offers a right click context menu with various options see Fig 4 24 Display Display in Mew window Display As 2D Projection sort This Column sort Reverse t Show Details save selection File Properties Files Process selected Datasets Figure 4 24 Display Display the selected dataset s in the current data window If multiple datasets are selected they are displayed in the same data window in multiple display mode Equivalent to clicking the Display button or pressing Enter Display In New Window Display the selected dataset s in anew window If multiple datasets are selected they are displayed in the one new data window in multiple display mode Display As 2D Projection Display the selected dataset as a projection of the current 2D dataset A dialog will appear allowing you to choose F1 projection F2 projection or both If mul tiple datasets are selected only the first one 1s considered If the current dataset is not a
131. d 264 266 277 helium level 271 Help button 43 menu 31 42 help in Topspin 41 on commands 42 help command 43 Hertz axis units 139 161 hist command 44 48 107 337 342 344 history file 342 hostname of a remote system 305 HTML page 43 I iconify all data windows 246 data window 244 iconnmr command 28 image display of 2D data 168 of 3D planes 172 import data 26 inconsistent dataset 88 initial guess 258 install AU programs 19 284 pulse programs 19 Topspin 281 installation directory 60 282 283 installnmr script 282 int command 142 Integral list 2D 159 integral bias 191 display 21 label 189 list 1D 128 regions 187 188 190 194 scaling factor 194 slope 191 I 8 trails 142 194 values 187 Integrals tab 128 159 196 integrals txt file 196 integration 1D automatic 186 190 1D interactive 186 190 mode 32 187 196 intensity alignment in multiple display 202 decrease 1D 112 150 increase 1D 112 150 manipulation 33 reset 1D 33 112 150 scaling 2D 151 interactive 1D baseline correction 205 1D calibration 196 1D data manipulation 181 1D integration 186 1D peak picking 210 1D phase correction 181 183 1D signal to noise calculation 250 2D calibration 235 2D data manipulation 215 2D phase correction 215 data manipulation 24 32 316 modes 31 parameter adjustment 88 273 processing 93 Processing Guide mode 97 interface fonts 321 internal projection 22 Internet Browser 69 intrng file 190 191 193
132. d for remote access and furthermore individual data directories must be exported 302 Remote Control Enable the system for network access 1 Start TOPSPIN mn amp WwW N Log in on the remote system Click Options gt Preferences set Click Miscellaneous in the left part of the dialog box Click the Change button to the right of the object Configure remote access 6 Enter the Administration password as requested 7 In the appearing dialog box see Fig 18 1 a Click Remote Access Enable b Click Add and enter the data directories that you want to export for remote access e g C bio and click OK c Click OK to close the dialog Remote Control 303 Ey Configure remote access Enable or disable remote access to TopSpin Select Remote access enabled to allow remote access to this Topspin installation select Remote access disabled to prevent remote access default Warning ou must restart TopSpin to activate the modification Any previous modifications in the file omniork cont will be lost Directories must be exported in order to enable remote access to these directories Use INSTDIR for the data directory in the Topspin home directory Remote access Remote access disabled Exported directories AMS TOR Figure 18 1 8 Click OK to save and close the preferences dialog 9 Restart TOPSPIN A list of exported directories is stored the file lt tshome gt prog se
133. d the title bar and move the mouse How to Resize a Data Window 1 Move the cursor to the window edge until it becomes a double headed arrow 2 Left click hold that position and move the mouse Depending on the position of the double headed arrow you can change the win dow height width or both see Fig 13 2 Data Window Handling 241 felcjexamid_13C 1 1 Cbio guest PaCyTA DRA S00 Chalac 106 7 ppm 8049 1 Hz Index 46 850 Value 4 24947 520E 1 5 1e10 0 5 a a A 50 0 0 0 50 0 ppm Figure 13 2 How to Select activate a Data Window The active data window is the window of which the title bar is highlighted The TOPSPIN menu tool bars and command line commands correspond to and act on that window Only one data window is active at a time To activate a different data window t amp Click in the desired data window or click its title bar Or r Click one of the colored radio buttons above the data area The pressed ra dio button the green one in the example below corresponds to the current dataset M2 examid TH 2 1 Clbio quest If you hold the cursor over one of the buttons without clicking it and wait a few seconds the corresponding dataset specification will be shown Or t Click Window x dataname expno procno dir user 242 Data Window Handling where x is the number of the desired window and dataname expno proc no dir and user refer to the dataset dis
134. data window toolbar switches to the Acqu tab and the wobble window is opened see Fig 15 7 WOBEB protona 1 1 C guest oj x Figure 15 7 The buttons of the wobble toolbar have the following functions Change the number of wobble steps wbs t Change the wobble sweep width wbsw B Change the wobble frequency Tt Switch to the next channel nucleus if available 2 Stop the wobble procedure 270 Acquisition 2 Turn the tuning and matching knobs on the probehead until the wobble curve 1s exactly in the middle and its minimum reaches the zero line Automatic tuning and matching of ATM probeheads can be performed with the command atma 15 7 Locking The lock display can be opened by clicking the Es button in the toolbar or enter ing Lockdisp on the command line The lock display window will appear see Fig 15 8 x L WERP u Figure 15 8 Here you can view the lock signal either during the lock in procedure or as shown above after lock in has been successful At the top of the lock window the following buttons are available Open the user preferences window set Toggle lock monitor mode lg Lock the magnetic field lock Toggle lock display mode between single and dual color Colors can be Acquisition 271 set in the User preferences command set HH Switch grid mode between both vertical horizontal and off T Make the lock display external
135. datatquestnimriexarn d 130A Jodatan SARPO _T Z H T Documents and Settings Administrator topspin nmr datastation prop iprotacol txt Cott S61 Siprogicurdir Administratorthistory Cott Sb SiproagicurdirAdministratarinistory traffic tt Sb SiprogicurdirAdministratar stdout dataserver 1504 Figure 3 1 Here TOPSPIN log messages from various log files are displayed time sorted 50 Trouble Shooting Messages from different log files are shown in different colours The color assign ment and location of the files is shown in the lower part of the dialog window ptrace supports the following functions Search keywords To search the displayed log files for a certain keyword just enter it in the text bar at the top of the window and hit Enter Anchor specific entries To anchor an entry double click in the first column of the entry The entry is marked with an X Now you can use the lt gt buttons at the upper right of the window to go to the previous or next entry respectively Add log files By default the procol txt history and dataserver log files are shown To include additional log files to the ptrace list click File gt Add specify the file and click Open Note that most log files are stored in the directory lt tshome gt prog curdir lt user gt Save the log messages To save log messages in a text file click File gt Save and specify the output text file 3 2 4 Create a Stack Trace If TOPSPIN hang
136. directory 283 startup 17 18 tailoring 311 window 29 I 15 topspin command 18 Topspin icon 18 totxt command 74 tozip command 25 74 tshome directory 18 42 283 tuning the probehead 269 U undo last parameter change 87 91 last region operation 195 unzip utility 26 Up Arrow key 35 39 upper toolbar 1D 31 181 2D 215 user defined AU programs 284 buttons 339 342 344 commands 24 27 functions keys 44 plot layouts 104 User Interface functions 335 user preferences 311 user properties directory 44 107 y Varian spectrometer 71 vertical scaling 112 151 View menu 31 141 virtual spectrometer 26 VNMR data 71 W walk up 28 wbst command 269 wbsw command 269 wildcards 76 window layout 246 Window menu 31 247 WINNMR data 71 wm command 24 85 wmisc command 74 wobb command 266 269 wobble display 267 frequency 269 procedure 269 steps 269 sweep width 269 window 269 wpar command 74 wra command 74 wrp command 74 wrpa command 25 74 X xau command 287 x axis rotation in 3D 170 174 xmac command 27 Y y axis display 33 139 y axis rotation in 3D 170 174 Z z axis rotation in 3D 174 zero order phase correction ID 185 2D 219 220 zg command 264 265 276 ZIP data format 25 71 zoom 1D data 33 113 2D data 153 in 2D phase correction 216 zoom 1D 2D data 40
137. dow n Click the x button in the data windows title bar or t Click the title bar and then click File gt Close Crt1 w To close all data windows t Click File Closeall closea11 246 Data Window Handling How to Iconify all Data Windows t Click Window Iconify all How to Maximize all Data Windows c Click Window Maximize all The active window will be displayed on top all other windows are hidden How to Activate the Next Data Window t Click Window Next window F6 The windows title bar will become highlighted 13 2 Window Layouts A data window layout defines the position geometry and window type of one or more TOPSPIN windows The following windows types are available e data windows e lock display window e acquisition display window e BSMS display window e temperature unit window How to Save the Current Window Layout 1 Click Window Save layout 2 In the appearing dialog box Specify the layout File name extension prop and click Save Layout How to Read a Window Layout 1 Click Window Read layout 2 In the appearing dialog box Specify or click the layout File name and click Read Layout Windows are arranged according to the following rules Data Window Handling 247 e Each currently displayed window type gets the position and geometry to the corresponding definition in the layout e Ifa window type is displayed but not defined in the layout it keeps its cur
138. e Manipulation 221 Integrate and use ref dataset for calibration The integral value defined on the reference dataset is used for calibration How to Move an Integral region Aa U N m Click the button m it turns green Move the mouse into the region to be moved Left click hold and move the mouse to move the region Release the mouse at the desired position How to Copy an Integral region mW N m Click the button E it turns green Move the mouse into the region to be moved Left click hold and move the mouse to the desired position Release the mouse to copy the region How to Delete all Integral Regions 1 2 Click the button hi Click OK to confirm deletion How to Read Import Integral Regions 1 2 Click the button a Click Read intrng to read the last stored integral ranges or Click Import Integration Regions to import an exported integral region file see below How to Save Export Integral Regions 1 2 Click the button Click Save Regions to intrng to save the regions to the current dataset PROCNO file int 2drng or Click Export Integration Regions to export the integration region file for general usage 1 e usage with other datasets 228 2D Interactive Manipulation How to Return from 2D Integration mode Click the following button J to save the current integral regions and return Click the following button to return to the 2D integration mode w
139. e Spectrum Overview display How to Switch Y axis Display 00 ccc cee eens Show Display Properties Regions Files 0000 ee eee How to Superimpose the Cursor Information How to Superimpose the Title on the Spectrum How to Superimpose the main Status Parameters on the Spectrum How to Superimpose the Integral Trails Labels on the Spectrum How to Superimpose Peak Labels on the Spectrum How to Show Peak Annotations on the Spectrum How to Show Individual Data Points of the Spectrum How to Superimpose the Electronic Signature on the Spectrum How to Display the Main Dataset Properties 0 4 How to Display a List of Files of a Dataset Saving Display REGION a4 40 sews ave eae ae ewe Dew ee wa sired Synchronize Visible Region of all Data Windows 2D Display e266 cate the oot ewes aaa thew tea eee 9 1 92 9 3 9 4 9 5 The 2D Data Window 2 2 524 s3 baaeavaeed R E a a a r Changing the Display of a 2D spectrum 000 0 eee How to Change the Intensity Scaling contour levels How to Smoothly Change the Vertical Scaling contour levels How to Display a Contour Levels Bar in the Data Window How to Switch on off Square 2D layout 0 000005 How to Zoom a 2D spectrum in out 00 eee How to Shift a Sp
140. e Zero Order Phase Correction 185 How to Perform Interactive First Order Phase Correction 185 How to Perform 90 90 or 180 Zero Order Phase Correction 185 How to Reset the Phase to the Original Values 185 How to Change the Mouse Sensitivity 0 0 0 eee 185 How to Return from Phase Correction Mode with without Save 186 11 3 1D Interactive dite oration ears iiien aane nese dys ese Raates 186 How to Switch to Integration Mode 0 0 00 cee eee ee 187 How to Define Integral Regions 0 0 0 0 cece cee eee 188 How to Select Deselect Integral Regions 040 188 How to Read Integral Regions from Disk 00000 190 How to Perform Interactive Bias and Slope Correction 191 11 4 11 5 11 6 11 7 How to Set the Limit for Bias Determination 191 How to Change the Mouse Sensitivity 0 0 0 0 191 How to Calibrate Normalize Integrals 2 2 0 0 0000 eee 192 How to Scale Integrals with respect to Different Spectra 192 How to Delete Integral Regions from the Display 193 How to Scale Selected Intesrals 2 40s 2002tnenecenen keane beac 193 How to Move the Integral Trails Up Down 0 194 How to Cut Integral Regions 2s 4 040 68 ioe Soa EOS Ed eh 194 Howto Save Inte oral R6cions 4 cwus tae as biren Shed eked eee 5 195 How to
141. e ane eae 3 3 Lt Jexamld 130 4 1 C bio guest La Seale e a 1 g5 Shift 4 i o 0028 ppi ua woa We aa a oe me em Difference l i 123 3 123 2 123 1 123 0 ppm Figure 11 13 How to move the selected spectrum one place up down r Click the following button t Move the selected spectrum one place up in the list r Click the following button Move the selected spectrum one place down in the list Note that the first spectrum and calculated spectra sum of difference cannot be moved up down How to Switch on off the Display of Datapaths and Scaling Factors r Click the following button 4 Switch on off display of datapaths and scaling factors How to Return from Multiple Display mode r Click the following button a Return from multiple display mode ret 1D Interactive Manipulation 205 How to Set the Colors of the 15 2 Dataset The colors of the different datasets in the multiple display mode can be set in the User preferences dialog box To set for example the color of the second spec trum us Click Options Preferences and click the Change button for the item Color of 2nd ID spectrum TOPSPIN 2 0 and newer allows you to set 8 different colors for different spectra in multiple display 11 6 1D Interactive Baseline Correction Baseline correction can be performed with commands like abs or absd or inter actively as described below How to Switch to Baseline Correction Mode
142. e chemical shift in each of the three dimensions is shown in a separate column nD Display 179 To show the nD integral list r click the Integrals tab of the data window Or rm enter ints on the command line Fig 10 7 shows the integral list of a 3D dataset examsd 1 1 Cobio guest i Integrals sample wF 2 ppm VIF 1 ppm Intensity abs 195 4 7636 50 5341 45r 11 73060 00 159 4 5952 46 5005 4 5817 1165831 00 ze 4 5927 af 4667 2 04 93947450 oe 4 5927 af 4667 2 5521 9967135 50 367 4 5194 51 7 r06 4 5035 1739387 50 11 4 4996 19 4212 1 0025 a a 156 4 4996 343554 1 S022 1163531 25 476 4 4996 21 9103 1 0025 2310150 75 591 4 4996 29 9996 1 1590 1037 7060 25 t i gt Figure 10 8 The chemical shift in each of the three dimensions is shown in a separate column Peaks and integrals only appear if they have been calculated commands pp and int respectively 180 nD Display Chapter 11 1D Interactive Manipulation The upper toolbar of the 1D menu offers various buttons for interactive manipula tion If you click such a button the active data window will switch to the corre sponding mode An interactive manipulation mode is data window specific 1 e it only applies to the active window 11 1 1D Interactive Window multiplication TOPSPIN 2 0 and newer supports 1D interactive window multiplication 11 1 1 1D Interactive Window Multiplication Procedure How to Switch to Window Multiplicat
143. e correction command abs f or phase correction command apkf The region is stored in the processing pa rameters ABSF1 and ABSF2 e Parameters STSR STSI to save the displayed region for Strip FT commands like ft and trf The 148 1D Display region is stored in the processing parameters STSR and STSI e Parameters NOISF1 2 to save the displayed region as the signal region for Signal to Noise calcula tion command sino The region is stored in the processing parameters SIGF1 and SIGF2 e Parameters SIGF1 2 to save the displayed region as the noise region for Signal to Noise calcula tion command sino The region is stored in the processing parameters NOISFI1 and NOISF2 e A text file for use with other programs to save the displayed region in a text file This file can be viewed with any editor or used by external programs 8 8 Synchronize Visible Region of all Data Windows The visible region of all data windows can be synchronizes as follows r Zoom in or out one dataset while holding the Ctrl key Or r Zoom in or out one dataset and then enter the sync command Chapter 9 2D Display 9 1 The 2D Data Window The 2D data window consists of a data field a title bar a Tab bar and buttons Fig 9 1 shows a data window with a 2D spectrum 150 2D Display data title bar minimize maximize close field Tab bar button button button exani2d_Hec 1 1 Cabio guest MER Spectrum ProcPars Acqu
144. e data win dow Or r Right click the dataset in the browser and choose Display from the popup menu Or r Enter re and specify the additional dataset in the appearing dialog box Another way to superimpose data in multiple display is to read multiple datasets simultaneously 1 In the browser 1D Interactive Manipulation 199 r Hold down the Ctr1 key and click multiple datasets to select them Or r Hold down the Shift key and click two datasets to select these two and all datasets in between 2 Right click any of the selected data us Choose Display from the popup menu This will show the data in the active data window if that is in multiple dis play mode or otherwise show the data in a new window Or r Choose Display in new window from the popup menu This will show the data in a new window In multiple display mode the Tab bar of the active data window is replaced by a toolbar Fig 11 9 shows three comparable 1D spectra and the sum of all three examid_13C 1 1 Ctbio1 guest l oj x Ee R t E L E E Eil 4 s fts la pmol SLI examld 130 3 1 Cit biol gest is examld 130 2 1 Citbiol gyest examld 13C 1 l Cis bigl gyest 1e9 10 200 150 100 50 ppm Figure 11 9 Data window in multiple display mode ab The yellow button indicates that the data window is in multiple display mode BA Some buttons will turn green when they are clicked As long as a button 200 1D
145. e parameter sets e The spectrometer frequency acquisition mode and pre scan delay In the last dialog box click Finish The installation of the selected items will start 284 Configuration Automation now Wait until this process has finished For more details on expinsta11 please refer to the description of this com mand in the Acquisition Reference manual 16 3 Parameter set conversion The command paracon changes the basic frequency in parameter sets This allows you to use parameter sets which were created on a spectrometer with a dif ferent frequency It opens dialog box shown in Fig 16 1 Here you can setup a list of available parameter sets You can select Bruker and or User defined parameter sets and use a match string The matching parameter sets appear in the right part of the dialog box To start the conversion select one or more parameter sets and click OK 16 4 Automation How to Install AU Programs To install AU programs you have to run the command expinsta11 see chap ter 16 2 How to Open the AU Program Dialog Box To get a list of all AU programs enter edau or 1 Click File gt Run 2 Click Execute an AU program in the appearing dialog box 3 Click OK A dialog box showing either the Bruker defined or User defined AU programs Fig 16 2 shows a dialog box with two User defined AU programs Configuration Automation 285 Ea Parameter set conversion Parameter set Conversion Select
146. e type Figure 4 18 How to Open a ZIP or JCAMP DxX file from the Windows Explorer Data stored in ZIP or JCAMP DX format can also be opened directly from the Windows Explorer You can do that in one of the tree following ways Drag amp drop r Click hold a file with the extension dx or zip and drag it into the TOP SPIN data area or data window Copy amp paste 1 Right click a file with the extension dx or zip and choose copy from the popup menu 2 In TOPSPIN click Edit Paste paste Associate JCAMP DX files with a script 1 Create a file with the extension cmd e g jcamp cmd with a text edi tor 2 Enter the following line lt tshome gt prog bin sendgui cmd fromjdx 1 and store the file 3 Open the Explorer and find the JCAMP DxX file 4 Right click the filename and choose Open with Choose program Dataset Handling 73 Browse 5 Find and select the script and click OK Now every file with the extension dx will automatically be opened in TOPSPIN when double clicked 4 4 Saving Copying Data How to Save or Copy Data You can save the current dataset as follows 1 Click File gt Save Ctri1 s This will open a dialog box see Fig 4 19 amp wrpa Options O Copy data set to a new destination O Save data set in a ZIP file OQ Save data set in a JCAMP Dx file save data of currently displayed region in a text file Save parameters as a new experiment
147. e up down or r Click one of the following buttons Shift the spectrum baseline to the middle of the data field su 4 Shift the spectrum baseline to the bottom of the data field sd Alternatively you can enter the corresponding commands as specified between square brackets 1D Display 115 8 4 Using the Tab bar Tabs of the data window can be activated by clicking them or by entering the cor responding commands as specified between square brackets on the command line Note that command line commands always work on the currently selected active data window The Tab bar can be configured from the User Preference box command set How to Display the Spectrum us Click the Spectrum tab spec examid_1H 1 1 Cxbio guest 7 O x Spectrum ProcPars AcquPars Title PulsProg Peaks Integrals Sample Structure Fid ee ee 15 10 5 0 ppm This displays the processed data If these do not exist the text No processed data available appears 116 1D Display How to Set Processing Parameters r Click the ProcPars tab edp examid 1H 1 1 Cobio guest pectrurn ProcPars AcquPars Title FulseFrog ll Peaks Integrals li sample Structure Fig ACHU 7 Y OMS TA o SF MHz 500 1300000 Spectrometer fre A OFFSET pgr 17 008 Lows field limit of SR Hz ooo Spectruri reterel HzpPT Hz 0 133399 Spectral resaluti F window function
148. eak entry to open the popup menu see Fig 8 4 3 Click Export to export the selected peaks 4 This opens a dialog box where you can specify the filename and file type For the latter you can choose from e Auremol peaklist ml e Comma Separated Values cvs e Mixed Shape deconvolution peak list peaklist e TOPSPIN peak list xml e XEASY peak list peaks e XWIN NMR peak list txt Important Check the box in the lower left corner to export the selected peaks only or uncheck it to export the entire list Then click Export Delete remove peaks from the peak list To delete one peak r Right click the peak and choose Delete from the popup menu To delete multiple peaks 1 Select the peaks while pressing the Ctrl or Shift key 2 Right click one of the peaks and choose Delete from the popup menu 1D Display 123 To remove possible duplicate peaks us Right click any entry and choose Remove gt Duplicate peaks To remove possible peaks outside of the spectrum c Right click any entry and choose Remove Peaks positioned outside of the spectrum To remove solvent peaks x Right click any entry and choose Remove Solvent Peaks Copy the peak List Instead of exporting entries of the peak list they can also be copied to the Clip board and pasted to another application like Excel To do that 1 For multiple peaks Select the desired entries while pressing the Ctrl or Shift key 2 Right click a peak e
149. ectral Region in the F2 direction left right How to Shift a Spectral Region in the F1 direction up down Show Display Properties Regions Files 0000 ee eee Usine the Tab Dar esar tesien na ae as E hes How to Set Processing Parameters 0 00 cece eee eens How to Set Acquisition Parameters 0 0 cece eee eee How to Display the Peak list 0 0 0 0 0 cee ees How to Display the Integral list 0 0 0 0 0000 Howto Display the FID a6 2 a58 echoed oe eke coh eee 21 Display OPON aca ceaks Ga tekderss eh aeatea cars ee eve ees How to Switch between Hertz and ppm Axis Units in F2 and F1 How to Switch on off the Spectrum Overview display How to Switch on off the Projection display 00 How to Switch on off the Grid display 0 0 0 How to Display a 2D Spectrum in Contour Mode How to Set the 2D Contour Levels 0 000 e eee 166 How to Store interactively set Contour Levels 167 How to Display a 2D spectrum in Pseudo Color Mode 168 How to Display a 2D Spectrum in Oblique Mode 168 How to Rotate a 2D Spectrum in Oblique Mode 170 How to Switch between Displaying Positive and Negative levels 170 Chapter 10 nD Display v0004 Goce cia sasw de ees dete stewed aaa 171 TO Display Planes of SD Daas ced s dade d Feo uaaa toed hu a ses
150. ed lt tshome gt exp stan nmr Now you can define a individual source directories for each item To do that 1 Open the dialog of any of the items e g with the command edau edlist or edmisc 2 Click Options Manage Source Directories A dialog will appear showing a list of items with the current source directo Colts explistaninimrAllists ppuser Colts expistaninmrlists pp Pulse Programs Colts expistaninmrlistsicadius er Colts expistaninmrllistsicpd CPD Programs Figure 19 14 ries By default two source directories are present one for user defined items and one for Bruker items This list can be modified or extended with your preferred source directories e g C my pulse programs C ts2 1 exp stan nmr lists pp user C ts2 1 exp stan nmr lists pp You can do this for each item separately Items will be searched for in the or der of the directories specified Chapter 20 User Extensions TOPSPIN offers various ways to extend the standard commands buttons programs etc 20 1 User Notebook You can create your own user specific notebook with the command rs View Notebook nbook Ea Notebook File Edit Search Figure 20 1 This can be used to store and retrieve any personal notes information etc 334 User Extensions 20 3 20 2 Macros A macro contains a sequence of TOPSPIN commands It can be created with the command edmac A simple macro for processing and plotting the cu
151. ed in the following way NUMBER WHEN WHO WHERE PROCESS VERSION WHAT These entries have the following meaning NUMBER Running number of an entry starting with 1 WHEN Date of the entry e g lt 2004 03 30 10 55 36 171 0200 gt where the last val ue represents the offset in hours to Universal Time UTC WHO The user logged in at the time the entry was generated It has one of the two forms lt userl gt or lt userl user2 gt lt user1 gt is always the user who is logged into the operating system Windows or Linux user and who started TOPSPIN lt user2 gt only appears if the NMR administrator has setup an internal TOP SPIN user administration and the option Enforce login for working with Regulatory Compliance 293 17 1 5 17 1 6 TOPSPIN in the User Administration dialog is enabled see below command uadmin In this case lt user2 gt is the current internal TOPSPIN user WHERE The network name of the current computer e g lt EOS2 gt PROCESS The TOPSPIN process module which performed the acquisition or process ing WHAT The type of acquisition or data manipulation performed Note that if only the entries NUMBER WHEN WHO WHERE WHAT be present then the audit trail was created by TOPSPIN 1 3 or older Adding a comment to an audit trail Audit trail entries are normally generated automatically by a respective acquisition or processing command However a user can also add a comment manua
152. em does not affect the other 282 Configuration Automation How to Change the NMR Administration Password The NMR Administration password can be changed as follows Under Windows 1 Login as NMR Superuser or Administrator 2 Open a Command Prompt 3 Enter lt x gt perl bin perl lt x gt prog bin installnmr lt x gt lt NMRSUPERUSER gt where lt x gt in the TOPSPIN installation directory 4 Enter the old password and new password as requested Under Linux 1 Login as NMR Superuser or root 2 Open a Shell 3 Enter lt x gt prog bin installamr lt x gt lt NMRSUPERUSER gt where lt x gt in the TOPSPIN installation directory 4 Enter the old password and new password as requested If you don t know the old NMR Administration password you can still define a new one In that case you have to delete the file lt x gt conf nmradminpassword before you run the installnmr script 16 2 Configuration The main configuration steps are performed by the commands cf and expin stall They can be started from the e Command line e Options Spectrometer tools menu e Spectrometer Setup menu However the Spectrometer menu is only available after c f has been performed Configuration Automation 283 once choosing Installation for spectrometer How to Perform a Default Configuration on a Datastation A default configuration can be used on a datastation It is automatically performed no cf required
153. ent mode 2 Move the mouse into the data window 3 Left click hold and drag the mouse from one edge of the signal region to the other edge A horizontal double headed arrow will indicate the signal region 4 Left click hold and drag the mouse from one edge of the noise region to the other edge A horizontal double headed arrow will indicate the noise region 5 Right click any position in the data window The popup menu as shown in Fig 14 2 will appear Quit Clear NOISEREG Clear SIGREG Edit Regions Change Region Widths Stat oh Calculation Enter zoom Figure 14 2 252 Analysis Choose Start S N calculation The other entries allow you to redefine or clear the regions After the noise calculation has finished the result will appear on the screen How to Delete the Signal Region or Noise Region To delete the current signal region 1 Right click in the data window 2 Choose Clear SIGREG from the popup menu see Fig 14 2 To delete the current noise region 1 Right click in the data window 2 Choose Clear NOISEREG from the popup menu see Fig 14 2 How to Edit the Limits of the Signal Region or Noise Region 1 Right click in the data window 2 Choose Edit regions from the popup menu see Fig 14 2 3 Enter new limit values in the appearing dialog box Define sino parameters From pern To pern SIGREG 8 6355 04351 NOISEREG 10 7777 9 2045 4 Click OK The S N value is autom
154. er lt tshome gt classes prop available for any user any directory the full pathname must be specified in the icon label field The formats gif jpg jpeg and png are supported Standard TOPSPIN toolbar icons have a size of 16 16 pixels If your own icons have a different size they are automatically rescaled and displayed at the standard size User Extensions 341 Ey Add tool button Options Add a button with a text label O Add a button with an icon Required parameters Assign this command to button Button tool tip 41D Fourier Thansfortn Button label text Font of button label text Button label text color Button background color Append separator to button Show button only for data of this dimension Figure 20 3 In the example above a button FT is created with a separator which only appears for 1D datasets and executes the command fe How do I Remove a User Defined Toolbar Button Right click the toolbar button and click Remove this user defined button in the appearing popup menu see Fig 20 4 How do I Shift a User Defined Toolbar Button to the left right Right click the toolbar button and click Shift left Or Shift right 342 User Extensions 20 7 in the appearing popup menu see Fig 20 4 Edit button properties Add User Detined Button Remove This User Defined Button Shift lett Shift right Make Button Invisible Make Button Inac
155. er cannot elec tronically sign data In all other cases the user is allowed to sign The esign dialog allows the user to select one of the items to specify the meaning of the signature PASSWORD A password for this user required for using TOPSPIN and for applying an elec tronic signature 17 3 2 How to set up internal users In order to define or modify the list of internal users rm enter the command uadmin or 298 Regulatory Compliance t Click Options Preferences Administration items Click the Change button to the right of the object Setup users for TopSpin internal loginNogoff and esign You will be prompted for the NMR administrator password A dialog will ap pear EA User Administration uadmin F Enforce login for working with Topspin User ID User Hame Allowed Signature Meanings Carol Smith Diane Lopez all James Evans review Larry Hill approval Add User Change Meanings Passywd Length Figure 17 5 where you can add remove and or modify users 17 3 3 How to change the internal user password To change the password of the internal user r enter chpwd on the command line Or us Click Options Administration Change internal user password and enter the new password twice as requested Regulatory Compliance 299 17 3 4 17 3 5 Login Logoff The uadmin command allows the administrator to make a TOPSPIN internal user mandatory To do that enable Enforce login for worki
156. et Files in the Windows Explorer 82 Parameter Handling 6 5 4 00 0 4 9 4 4 2biera le tee at G84 eas oe aes 85 Sal Processine Parameters ernn e Gaus ie tadan ddan erate wea wa ends 85 How to Set a Processing Parameter from the Command Line 85 How to Set Processing Parameters from the Parameter Editor 86 How to Undo the Last Processing Parameter Change 87 How to Display Processing Status Parameters 87 How to Switch to Maxent parameters 0 0 0 0 cece eee eee 88 How to Change Processed Data Dimensionality 88 52 Acguisiton Parameters 23h peso whoo Rae eae wed Dee 88 How to Set Acquisition Parameters 0 00 eee eee 88 How to Set an Acquisition Parameter from the Command Line 89 How to Set Acquisition Parameters from the Parameter Editor 89 How to Undo the Last Acquisition Parameter Change 91 How to Set Pulse Program Parameters 0 0 000 cee eee 91 How to Display Acquisition Status Parameters 91 How to Get Probehead Solvent dependent Parameters 91 How to Change Acquisition Data Dimensionality 92 How to Set Lock Parameters s 43 4424 2044edeco2daewndnd estas he 92 How to Set Routing Parameters i3 54546 64 42 646384440 Dee bee E bs 92 Chapter 6 Chapter 7 Chapter 8 Data Processino 6 455 5 oscSacessia st ina C AOS wees ae wee 93 Gil Nterac
157. eter frequency to the center of the current region Update the parameters SW and SFO1 respectively fi Setup a frequency list interactively 15 3 Data window Toolbar TOPSPIN 2 0 and newer support dataset specific acquisition the display It is acti vated by clicking the Acqu tab of the data window toolbar protona 1 1 Cabo guest Sl EJ Title PulseProg Peaks Integrals Sample Structure Fid ACqu EILA OO Yel om SD start acquisition on protona 1 1 C bio guest Figure 15 4 From here you can start various acquisition commands like hm Start acquisition zg 266 Acquisition m Halt the acquisition halt Gi Stop the acquisition stop 42 Probe matching and tuning wobb bp Interactive Parameter Adjustment gs Data specific acquisition display allows you to open multiple acquisition display windows one for each dataset Note that the Acqu tab is automatically activated when the acquisition is started from the TOPSPIN menu toolbar or command line 15 4 Acquisition Status Bar The acquisition can be followed and controlled from the acquisition status bar Before you use the acquisition status bar it must be configured from the User Pref erences window To do that 1 Click Options Preferences set 2 Click Acquisition status bar in the left part of the User preferences box This will show the status bar items see Fig 15 5 Acquisition status bar Auto open acquis
158. f a Data Window 245 How to Close a Data Window ccc eee ees 245 How to Iconify all Data Windows 0 cece eee eens 246 How to Maximize all Data Windows 0 0 0 0 eee eee 246 How to Activate the Next Data Window 0000000 246 13 2 gt Window Wayouts 21 6 4a4 Gan eee kn dne as aussiard d Aree a oe 246 How to Save the Current Window Layout 4 246 How to Read a Window Layout 00 0 eee 246 How to Swap Data Windows 0c cc cece eee teens 247 Chapter I4 gt Analysis lt i5inie idan Sid Adee ie eee eed i wedded 249 lAl AMCOGUCHON 422 400 sana ek oe ee aw woe hae Shes eae a be we 249 14 2 1D Chemical Shift Distance Measurement 250 How to Measure a Chemical Shift Distance 250 14 3 1D Signal to Noise Calculation 0 0 0 0 00 ees 250 How to Perform Interactive S N Calculation 250 How to Delete the Signal Region or Noise Region 252 How to Edit the Limits of the Signal Region or Noise Region 292 How to Change the Width of the Signal Region or Noise Region 252 14 4 Relaxation Analysis 0 0 ccc ccc cece ee eee eens 253 Chapter tS ACOuisiGion 2 656 so5s hs be Seka oo Ode Re ae Doe aes GS 261 51 Acquisition Guide iess su cinste he ex hay oR Do eb ah eae at oe 261 152 Acquisition Toolbar 24 42 se 8a0icehdn toy dee dt ceeket
159. g can be found under m Click Help gt Manuals gt Programming Manuals Python Program ming Note that serial processing can also be started as follows e Click Processing Serial Processing or e Click File Run select Execute Serial script on Data set list and click OK Chapter 7 Printing Exporting Data 7 1 Printing plotting Data How to Print Plot from the Menu The current data window can be printed as follows 1 From the TOPSPIN menu t Click the button amp in the upper toolbar or Click File gt Print or Enter print or Ctrl p All these actions are equivalent they open the Print dialog box see Fig 7 1 104 Printing Exporting Data Y Print Ctrl P plot Options O Print active window print Print wih layout start Plot Editor plot Print with layout plot directly autoplot Required parameters LAYOUT D_A wp Ww Use plot limits Fill data set list O from screen i CY irom Plot Editor Reset Actions C as saved in Plot Editor from portfolio saved in data set O from your default portfolio CURPLOT Dell Photo AlO Printer 922 Figure 7 1 In the Print dialog box a Select Print active window prnt b Click OK Before printing starts the operating system print dialog box will appear Here you can for example select the printer name and the printer properties The Print dialog box see Fig 7 1 contains
160. g parameter editor supports the following functions r Collapse expand a parameter section by clicking the button Note that the section Width in Fig 5 2 is collapsed r Collapse expand all parameter sections by clicking the large button of the data window toolbar c Enter part of a parameter name in the search field and click r Click a parameter section e g Experiment at the left of the dialog box The section becomes highlighted and the corresponding parameters will appear in the right part of the dialog box r Click in a parameter field e g TD to set the parameter value r Click the button to the right of parameters like PULPROG to open a list of the corresponding programs lists Parameter Handling 91 r Right click the E button to the right of parameters like PULPROG to open the current program list with an editor r Hit the Tab key to jump to the next parameter field c Hit Shift Tab to jump to the previous parameter field t Use the scroll bar at the right of the dialog box to move to parameters fur ther up or down in the dialog box How to Undo the Last Acquisition Parameter Change r Click the following button 1 Undo last acquisition parameter change How to Set Pulse Program Parameters r Click the following button JL Show pulse program parameters ased The button will change to a To make this the default setting Click Options Preferences click Miscellaneous check
161. g such processes may kill TOPSPIN Trouble Shooting 3 4 What to do if TOPSPIN hangs If for some reason TOPSPIN hangs please do the following Under Linux 1 Open a Shell 2 Enter lt tshome gt prog bin script killtopspin where lt tshome gt is the TOPSPIN installation directory Under Windows 1 Click Start Programs Bruker TOPSPIN TOPSPIN 2 1 Bruker Utilities 2 1 2 In the appearing window Click killtopspin Normally this kill all TOPSPIN processes including cpr cprserver dataserver and Java 3 5 How to Restart User Interface during Acquisition If Topspin hangs up during a data acquisition you can restart the user interface without disturbing the acquisition To do that 1 Open the file lt tshome gt prog curdir lt user gt history where lt tshome gt is the TOPSPIN home directory and lt user gt is the user who started TOPSPIN Look for the term Java Virtual Machine and check its PID Open the Task Manager Windows or System Monitor Linux Stop the Java w exe process with the PID found in the history file Open a Windows Command Prompt or Linux Shell Go to the TOPSPIN Installation directory Aun BW WN Enter topspin client Chapter 4 Dataset Handling 4 1 The Topspin Browser TOPSPIN offers a data browser from which you can browse select and open data The browser dialog offers the following tabs see Fig 4 1 e Browser data browser showing the data d
162. h Ctr1 F6 Display next layout Ctr1 i Open TOPSPIN Interface eC ee e a Lower the selected object Ctrl n Open a new layout Ctrl o Open an existing layout Ctrl1 p Print the current layout eer dep Print the current Tayout ooo CerT r Raise the selected object Cer x Cut the selected object and place it on the Clipboard Note that the function of function keys can be changed as described in chapter 2 7 2 6 Help in Topspin TOPSPIN offers help in various ways like online manuals command help and toolt ips How to get a Panorama Tour For a quick overview over TOPSPIN Interface Acquisition Processing Analysis and Documentation r Click Help Panorama Tour The TOPSPIN Interface How to Open Online Help documents The online help manuals can be opened from the Help gt Manuals submenu For example to open the manual that you are reading now r Click Help gt Manuals General User Manual To open the Avance Beginners Guide t Click Help gt Manuals Beginners Guides lt language gt To open the Processing Reference guide 0s Click Help gt Manuals Acquisition amp Processing References Proc Commands and Parameters Note that most manuals are stored in the directory lt tshome gt prog docu english xwinproc pdf The most recent versions can be downloaded from www bruker biospin de How to Get Tooltips If you hold the cursor over a button of the toolbar a tooltip will
163. hase Mode Click the following button a Return 12 2 2D Interactive Integration TOPSPIN 2 0 and newer supports interactive 2D integration 2D Interactive Manipulation 223 12 2 1 How to Switch to 2D Interactive Integration Click the corresponding button in the upper toolbar as indicated below Id 3d 4 4 Tj or enter int on the command line The Tab bar of the active data window will be replaced by a toolbar Fig 12 7 shows an example of a 2D inverse spectrum Pxamed HC 1 1 Cobio guest Siz Ed col 0 21 ppm 105 67 He Index row 140 4 ppm L es 5 He Index F2 ppm Figure 12 7 Data window in interactive integration mode E The yellow button indicates that you are in integration mode Define integral region mode active when green Move integral region green when active Copy a region x H Delete all integral regions 224 2D Interactive Manipulation Read import integral regions Save Export integral regions Save integral regions and return O E I Integrate current regions define reference J Return without save 12 2 2 2D Interactive Integration Procedure When you switch to 2D integration mode the Define integral region mode is active by default This means you can immediately start defining the integral regions To do that 1 Click and hold the left mouse button at any corner of a reg
164. he A button is active clicking the reset button will restore the original spectrum How to Change the Mouse Sensitivity r Click one of the following buttons 1 Increase double the Mouse Sensitivity inc t Decrease halve the Mouse Sensitivity dec Reset the Mouse Sensitivity How to Save the Baseline Correction and or Return To return while saving the baseline correction r Click the following button Hj Save baseline correction and Return sret This will perform the following tasks e Execute the baseline correction bem e Save the baseline correction values A B C D and E e Leave the baseline correction mode To return while discarding any changes Click the following button Return Discarding any changes ret How to Perform Cubic Spline Baseline correction r Click the following button ft Define points for cubic spline baseline correction The toolbar of the data window will change as shown in Fig 11 15 1D Interactive Manipulation 209 8 examid_1H 2 1 Cobo guest 0 41 ppm 124 28 Hg DEFINE LIST OF FOINTS Left click inside data window p 1 426 ppm Define Delete Right click on defined peak save Click right mouse button Figure 11 15 Data window in spline baseline correction mode The cursor line in the data window turns red If a list of baseline points already exists you are prompted to overwrite or append to these points If you choose Ap pend the la
165. he popup menu see Fig 12 13 This works both in the scan submode or on a grabbed row column 12 4 2D Interactive Calibration A 2D spectrum can be calibrated automatically with the command sref or inter actively as described below How to Switch to 2D Calibration mode r Click the corresponding button in the upper toolbar Id 3d 4 4 i I jiam or enter cal on the command line The Tab bar of the active data window will be replaced by a toolbar see Fig 12 16 236 2D Interactive Manipulation Wi exam2d_HC 1 1 Cbio guest F2 ppm Figure 12 16 Data window in calibration mode oo The yellow button indicates that the data window is in calibration mode How to Perform 2D Calibration In calibration mode 1 Left click in the data window at the reference peak The following dialog box will appear Fal calibrate x Spectrum calibration frequency F2 ppr F1 per Ti 24417 CK Cancel Note that the units for F2 and F1 Hz or ppm correspond to the axis units of the display 2 Enter the F2 and F1 frequency you want to assign to the reference peak 3 Click OK 2D Interactive Manipulation 257 The spectrum will be calibrated and re displayed The calibration button will turn grey again 12 5 2D Chemical Shift Distance Measurement How to Measure a 2D Chemical Shift Distance 1 Click the following button button turns green q Chemical shift distance measurement 2
166. heck Dis play dataset browser in a separate window You must restart TOPSPIN for the change to take effect How to Put the Focus in the Browser rs Hit the F2 key Or t amp Click inside the browser How to Select Folders in the Browser To select a particular folder 58 Dataset Handling r Left click the folder button or c Hit the arrow up down keys while the focus is in the browser To select multiple folders 0S Hold the Ctr1 key and left click multiple folders to select them or 0S Hold the Shift key and left click two folders to select these two and all in between How to Expand Collapse a Folder in the Browser To expand a collapsed folder r Click the button to the left of the folder button or Double click the folder button or Hit the Right Arrow key while the folder is highlighted To fully expand a collapsed folder t Right click the DIR NAME or EXPNO node and choose Fully Expand Selection To collapse an expanded folder r Click the button to the left of the folder button or Double click the folder button or Hit the Left Arrowkey while the folder is highlighted How to Show Hide Pulse program and Title in the browser 0S Right click the data name folder button and choose Dataset Handling 59 Show PULPROG Title from the popup menu see Fig 4 8 Display Display in Mew window Display As 2D Projection Scroll to active dataset Fully Expand Selection Show PLIILPROG Title Show
167. hoose Display from the popup menu A new window will be opened showing the selected datasets in multiple display mode However if the current window was al ready in multiple display mode the selected spectra will be superimposed on the currently displayed spectra How to Automatically Select the first expno procno of a dataset If you open a dataset from the Browser by clicking a data name there might be more that one expno and or procno available By default TOPSPIN then opens a dialog box from which you can select the desired expno procno combination see Fig 4 13 Clicking Open will open the selected dataset whereas clicking Print will print the displayed dataset list You can however configure TOPSPIN to automatically open the first available ex pno procno combination To do that 1 Click Options Preferences set 2 Click Miscellaneous in the left part of the dialog box 3 Uncheck the item Display EXPNO PROCNO list when opening data 4 Click OK to close the dialog box 66 Dataset Handling EN examid 13C This data set contains several EXPNO J PROCNO pairs corresponding to several ravv pracessed data files Open Display the selected data set Print Print the data set list Type set and navigate ta Printer gt Printer Font in order to change the font EXPMO SPROCNO dim pulsprog title zgpgs0 ACH AY a00 Automation Cholesterylacetate jmod 13C APT AY 300 Automation Cholesterylacetate depti
168. i swat chose 2a9 een payee sees 44 2 8 How to Open Multiple TOPSPIN Interfaces 005 44 Trouble Shootin csrssis neria raad ea a A 47 3 General Tips and Wicks iiiaae ee a e E 47 322 History Log Files Spooler Reports Stack Trace 47 3 3 How to Show or Kill TOPSPIN processes 000 0c eee eee 51 3 4 What to do if TOPSPIN hangs 0 eee eens 52 3 5 How to Restart User Interface during Acquisition 52 Dataset Handin 546 3 coins bh 5 Be SS 2 a Sow SASS 53 And he TOps pin Brow Seis 2 ba nde Ge aed ween a ee SR AA 53 How to Open the Browser in a separate window 04 57 How to Put the Focus in the Browser 000 0c eee eee 57 How to Select Folders in the Browser 20 000 57 How to Expand Collapse a Folder in the Browser 58 How to Show Hide Pulse program and Title in the browser 58 How to Show Dataset Dates in the Browser 00005 59 How to change the default Top Level Data Directory 60 How to Add Remove or Interpret Alias Names 60 AD Creaune Data ica isc te ier eh eee Ae WRK PDA eee esha 61 How to Create a New Dataset ss6 vies cohen ba bed Pol eulivtes a Hekate 61 Ad Opening Dates i 02 4 64e coaReea Raker Aa aebtAors daw de awe as 62 How to Open Data Windows Cascaded 000 cee eee 63 How to Open Data from the Browser 0 00
169. ick OK Note that the dataset specification consists of the five variable parts of the data directory tree in this case C bio data guest nmr exam1d_1H 1 pdata 1 The text boxes are initialized with the dataset in the current data window How to Open Data from the Explorer Konqueror or Nautilus You can open a dataset from the Windows Explorer as follows 1 Open the Windows Explorer You can do that in two different ways r from the Windows Start button Navigate to the data name expno or procno or r by entering the command exp1 in TOPSPIN The Explorer shows the con tents of the current dataset procno directory Navigate to the desired data Dataset Handling 69 name expno or procno exp1 can also be used with the argument top to open the TOPSPIN installation directory home to open user home di rectory or with an absolute pathname to open that directory 2 Now you can open a dataset with c drag amp drop click hold a dataset name or any of its sub folders or files and drag it into the TOPSPIN data area or data window Or t5 copy amp paste right click a dataset and choose copy from the popup menu In TOPSPIN click Edit Paste paste see Fig 4 17 Edit View Spectromete Copy Find data Ctrl F Figure 4 17 Likewise a dataset can be opened from the Windows window or Internet Browser How to Open Data from the Command Line To open a dataset from the command line 1 Enter re 2 Spec
170. ify a dataset in the appearing dialog box see Fig 4 16 3 Click OK To open a new procno of the current dataset 1 Enter rep 2 Specify a procno in the appearing dialog box 3 Click OK To open a dataset in a new window 1 Enter rew 2 Specify a dataset in the appearing dialog box 70 Dataset Handling 3 Click OK To open a new procno of the current dataset in a new window 1 Enter repw 2 Specify a procno in the appearing dialog box 3 Click OK To open a data browser and read a dataset from there 1 Enter reb 2 Select a dataset from the appearing dialog box 3 Click Display Note that re rep and reb e Replace the data in the currently selected data window e Open the data in a new window when they are used after typing Alt w n e Add the data in the currently selected window if this is in multiple display mode whereas rew and repw e Always open the dataset in a new window Topspin 2 0 and newer allows opening datasets stored in the following directories Structures lt mydata gt lt dataname gt lt expno gt pdata lt procno gt To do that c Enter reb on the command line browse to the desired dataset and click the Display button Or r Open the Operating System File Browser browse to the desired dataset and open it in Topspin with Copy amp Paste or Drag amp Drop Note that this will create a copy of the dataset in the standard Topspin datapath lt tshome gt data lt user gt nmr lt datana
171. ile does not exist it must be created Here is an example of a user modified T1 T2 guide MyT1T2Toolbar NM tlfid_40 gif NM2 SExtract Tid TIP SDo rser CMD _t1_fid END NM tlspec_40 gif NM2 STransform TIP SDo eftapk CMD _tl_spec END NM tlranges_40 gif NM2 SRanges TIP SEnter integ mode CMD _tl_ranges END NM tlscreen_40 gif NM2 SRelax Window TIP SEnter Relax mode CMD _tl_relax ENDe NM END NM myicon gif NM2 SFit Methods TIP Select fit funcs CMD tl func END NM c myicons myiconl gif NM2 S Start TIP S ctl1l ct2 sim fit CMD tl start END NM c myicons myicon2 gif NM2 SShow Report TIP Sreport CMD _tl_ report END User Extensions 345 NM tlorint 40 917 NM2 SPrint ity TEP Sprint CMD _tl_export END Notes to this guide definition e The original Bruker guides are defined in the file toolbar prop in the directory lt tshome gt classes prop The corresponding commands are defined in cmdtab_main prop in the same directory e The bold lines in the example above are user modified lines e NM t1fid_40 gif a Bruker defined icon with a size of 40x40 pixels e NM myicon gif a user defined icon which must be located in the user properties directory Caution not in its subdirectory userdefined e NM C myicons myiconl gif a user defined icon located C myicons Using the absolute pathname allows you to store icons in an arbitrary direc tory e NM indi
172. in all data windows How to Use the Menu bar The menu bar contains the following menus e File performing data file handling tasks e Edit copy amp paste data and finding data e View display properties browser on off notebook command history e Spectrometer data acquisition and acquisition related tasks e Processing data processing e Analysis data analysis e Options setting various options preferences and configurations e Window data window handling arrangement e Help access various information indices manuals etc Experienced users will usually work with keyboard commands rather than menu commands Note that the main keyboard commands are displayed in square brackets behind the corresponding menu entries Furthermore right clicking any menu entry will show the corresponding command How to Use the Upper Toolbar 1D data The upper toolbar contains buttons for data handling switching to interactive modes display settings and starting acquisition Buttons for data handling 1S e Bee 3 The functions of the individual buttons are Create a new dataset Ctr1 n new Open a dataset Ctr1 o open 32 The TOPSPIN Interface Save the current dataset Ctrl1 s sav Email the current dataset smai1 Print the current dataset Ctr1 p print Copy the data path of the active data window to the clipboard copy E Paste the data path on the clipboard to the active data window p
173. in an iterative process according to the Leven berg Marquardt algorithm Clicking and executes the commands ct2 current peak and dat2 all peaks respectively invrec satrec cptlrho expdec gaussdec lorgauss linear varbigdel var litdel vargrad vardamp these functions can be used for various experi ments with up to 6 components except for cptiIrho and lorgauss which allow only 4 and 3 components respectively They all use the simplex algo rithm and require some parameters to be set Enter the Number of components Click the Setup button to set the Iteration Control parameters For each component the initial guess G and step rate S can be set The initial guess for I O must be selected such that the sum of all compo nents does not exceed 1 If there is only one component I O is usu ally set to 1 The step rate is usually set to about one tenth of the initial guess If the step rate of a variable is set to zero then this variable is not changed during the iterations Note that the initial guesses can also be set with the 22 toolbar button Clicking gt and gt gt exce cutes the commands simfit current peak and simfit all all peaks respectively The Fitting Function to pick data points can be e pd pick data points for relaxation analysis Drift value inter preted e pdo pick data points for relaxation analysis at constant peak positions drift value ignored Analysis 259 e pft2 pick d
174. in can be configured such that right clicking any menu entry will display the corresponding command line com mand To do that right click in an empty part of the menubar and choose Define Right click Action For convenience common acquisition commands can also be started from the TOP SPIN toolbar The right part of the upper toolbar shows the following buttons F 8 b m D r TE S a Start the acquisition Acquires NS scans in the current dataset overwriting possibly existing data Equivalent to the command zg Halt the acquisition This stops the acquisition after the current scan has fin ished All data acquired so far are saved Equivalent to the command halt Stop the acquisition This stops the acquisition immediately Data acquired after the last disk write if any are lost Equivalent to the command stop Open the online FID display window Shows the currently acquired FID Only works during acquisition Equivalent to the command acqu Open the Lock display window Shows the lock signal Equivalent to the command lockdisp Acquisition 265 Calculate the experiment time Shows the total experiment time and file size of the raw data Equivalent to the command expt 4 Set SFO1 O1 O2 and O3 interactively Puts a red cursor line in the data win dow A left click at the desired frequency opens a dialog box where you can set O1 O2 and or O3 Set the sweep width to the current region and the spectrom
175. ind the corresponding menu entries e g us Processing Fourier transform ft f Menu entries which are not used very often appear without the corresponding command indicated e g ts Options Preferences However if you want you can look up the corresponding command in this case 330 User Preferences set in the configuration table and use it As an example we will describe how you can disable remove the menu entry Re mote connection in the Options menu 1 Open the configuration table as described above 2 Scroll to the Description Remote connection 3 Set the Status to disabled 4 Click Apply Clicking the TOPSPIN Options menu will now show the following popup menu Options Window Help Preferences Remote Connection Spectrometer Tools P Administration Tools F The entry Remote connection is greyed and can no longer be used Go back to the Configuration table change the Status of Remote connection to invisible and click Apply Clicking the TOPSPIN Options menu will now show following popup menu Options Window Help Preferences Spectrometer Tools P Administration Tools The entry Remote connection has disappeared Note that if you disable or remove a menu entry the corresponding command is automatically disabled For example if you disable t Analysis gt Deconvolution dcon entering dcon on the command line will lead to an error message User Preferen
176. indow and choose Extract Row Column from the popup menu see Fig 12 13 3 Specify the row column number and output procno in the dialog box Note that the ROW COLUMN field is initialized with the grabbed row column or if no grabbing was done with the current row column 4 Click OK The extracted row or column is stored as a 1D dataset under the specified PROC NO and displayed in a new data window In the upper left part is this the row number and source 2D dataset is specified see Fig 12 15 examed HC 1 999 Crbio guest Spectrum ProcPars AcquPars Title PulzeProg Peaks Integrals sample Structure Fid ACHU row 673 Crom examed HC 1 1 C bio quest a Shee kml Lid i i Lid q _ _ 0 5 Figure 12 15 How to Copy Contour Levels from First to Other Spectra Click the following button Copy contour levels from the first to the other spectra 2D Interactive Manipulation 235 Note that the contour levels are only changed on screen not on disk How to Switch on off 2D contour display Click the following button imi Switch on off 2D contour display How to Position the Baseline of the Row Column To put the baseline at the center of the data window 1 Right click in the data window 2 Choose in Baseline At Center from the popup menu see Fig 12 13 To put the baseline at the bottom of the data window 1 Right click in the data window 2 Choose in Baseline At Bottom from t
177. ine font Dialog plains Plain 16 Change Status line font Dialog plains Plain 16 Change Printer font Dialoginputplains Plains 100 Change Change size of fonts listed above by points Figure 19 5 4 Click OK to store the new value Fonts Dialogs Icons lenu font Dialog plain Plain 20 Change Dialog window font Dialog plain Plain 16 Change Command line font Dialog plain Plain 20 Change Status line fant Dialog plain Plain 20 Change Printer font Dialoginput plain Plain 10 Change Change size of fonts listed above by points lo Figure 19 6 Fig 19 6 shows the same part of the Preferences dialog box dialog box after the change of fonts Note that e The value all four font entries has been increased by 4 e The font of the dialog box itself is larger e The change size has been reset to 0 How to Change the Font of the TOPSPIN menu To change the font of the TOPSPIN menu 1 Click Options Preferences set User Preferences 323 2 Click Fonts Dialogs Icons in the left part of the dialog box 3 Click the Change button to the right of the Menu font object Menu font dialog Plainf16 Change 4 Select the desired name style and or size in the appearing dialog box 5 Click OK to store the new font 6 Click Apply The default menu font is Dialog Plain 18 and looks like this File Edit View Spectrometer Processing After changing the font to for instance to Serif Italic 18 the me
178. inux or inspect the contents of the file corba conf Note that the firewall must be configured for TOPSPIN e spectrometer control e remote access TOPSPIN can be used for processing analysis on a local datastation even if it 1s not registered on the firewall However you will get a few Security Alert messages during startup 1 During TOPSPIN installation you can choose to automatically configure the firewall or not PC s delivered by Bruker Germany always have the firewall configured for TOPSPIN 308 Remote Control 18 3 How to Make a Remote Connection without a Local License TOPSPIN requires a license to operate on your local computer However you can make a remote connection without a local license To do this you have to start TOPSPIN as follows 1 Open a Windows Command Prompt or Linux Shell 2 Go to the TOPSPIN installation directory 3 Enter topspin client 4 TOPSPIN will start up and show an empty data field but no browser Before startup you will get the error message The program failed to com municate with local Just click OK to continue 5 Click Options Remote connection and establish a remote connection as described in chapter 18 2 Note that without a local license e TOPSPIN on the remote system must run with a licence e Local data cannot be accessed 18 4 Security of Remote Connections All data transferred during a remote control session is by default encrypted This e
179. ion Getting Started 25 c Select the desired LAYOUT for plotting d Click OK EN proci d Press OF to process J plot the selected dataset using the enabled options The command procid y will process data without this dialog using the last settings Exponential Multiply Cet LE Hz 4 I Fourier Transform CH Auto Phasing tapk Set Spectrum Reference sret Auto Baseline Correction fabs Plot autoplot LAYOUT 1D_H wp Figure 1 1 1 13 How to Archive Data TOPSPIN 2 1 provides the following methods for data archiving e Automatic archiving of raw data after the acquisition as defined in the User preferences click Options Preferences Acquisition Configure e Copying a dataset to a desired destination directory which could for instance be located on a server Type wrpa click File Save or type Ctrl1 s e Saving a dataset in a ZIP file A standard Bruker dataset is a directory tree which contains several files Zipping a dataset stores the entire data direc tory tree into a single file with the extension bnmr zip To zip a dataset type tozip click File Save or type Ct r1 s To unpack and display a 26 Getting Started Zipped dataset enter fromzip Note that bnmr zip files are fully com patible with the well known PC zip format and can be unpacked with any common unzip utility Zipping can be applied to 1D 2D 3D and 4D d
180. ion Mode us Click the Processing Window Multiplication wm enable Manual win dow adjustment in the appearing dialog and click OK Or rs Enter winf on the command line The Tab bar of the active data window will be replaced by a toolbar see Fig 11 2 and the data window itself will be divided into three parts e aparameter part at the left 182 1D Interactive Manipulation e a spectrum part at the upper right e a FID part at the lower right examid 1H 1 1 Cobio guest winfune Parameters WY indo function type Line broadening LE Gaussian max position O GR 1 D gt Sine bell shitt SSB 1 2 3 4 5 Figure 11 1 t Show both spectrum and FID Iw Show FID only uhl Show spectrum only i Switch cursor information on off toggle EL Save windows settings to source 2D dataset and return 1 2D data from which current 1D dataset was extracted e g with rser 1D Interactive Manipulation 183 H Save window settings and return Return without save You can perform interactive window manipulation as follow 1 Select the window function parameter WDW 2 Set the corresponding parameter s e g e LB for exponential e LB and GB for Gaussian e SSB for sine bell and squared sine The displayed spectrum and or FID will be automatically adjusted as you change the window function and parameters 3 Click H to store the window settings and return Now you can perform further p
181. ion to be defined move the mouse to draw a box around that region and release the mouse 2 Choose one of the following options from the appearing popup menu Integrate a to add up all intensities in the region Integrate to add up all positive intensities in the region Integrate to add up all negative intensities in the region Integrate a to add up all intensities in the region and store separate en tries for all positive and negative intensities Integrate a to add up all intensities in the region and store separate en tries for all and positive intensities Integrate a to add up all intensities in the region and store separate entries for all and negative intensities Integrate to add up all intensities in the region and store separate en tries for positive and negative intensities The integral regions will be displayed along with their storage numbers and 2D Interactive Manipulation 223 modes see Fig 12 8 Pxam d HC 3 1 Cobio guest TH xan col 7 154 ppu 7 3577 739 Hz row 6 5 ppm 017 5 Hz Define new region a Drag with left mouse button 5 utii tas 6 Dalf ie ee 7a 8 4 5 F2 ppm Figure 12 8 3 Click the I button and choose Integrate current regions from the pull down menu to integrate the defined regions 4 Click the I button again and choose List integral values from the pull down menu to show the list of integrals
182. irectory hierarchy e Last50 list of the 50 last open datasets e Groups list of user defined groups of datasets e Alias list of user defined alias name The browser appears at the left of the TOPSPIN window and can be shown hidden with Ctrl1 d or by clicking the arrow buttons at the upper right of the browser The Browser tab The browser shows data directory trees and allows you to expand collapse their elements Figure 4 1 shows the browser with three top level data directories and one dataset fully expanded 54 Dataset Handling Browser Last50 Groups Alias E H CBio 9 guest exanitd_13 E 9 exantd_1H a O4 zg E exam2d_CH Gly 1 hxcogt i 1 CH CO Cyclosporin __ exam2d_HC E exam2d_HH B examid fy hechdigpad E Chiot 9 Cts2 0 Figure 4 1 The dimensionality of the data is indicated with different colors e black for 1D data e blue for 2D data e magenta for 3D data Furthermore the browser shows e the pulse program with the dataset EXPNO e g 1 hxcogf in Fig 4 1 e the title with the dataset PROCNO e g CH CO Cyclosporin in Fig 4 1 Note that the displayed pulse program is the e status pulse program if an acquisition has been done raw data exist e setup pulse program if no acquisition has been done raw data do not exist The display of title and pulse program can be switched of see Fig 4 2 Dataset Handling 55 Display Display in Mew vviridovy Display
183. ist r Click Options gt Comment on off in the AU program dialog box A comment is a short description of the AU program which is also part of the AU program header 17 1 17 1 1 Chapter 17 Regulatory Compliance TopSpin complies with the FDA 21 CFR Part 11 regulations Please read the accessible under Help gt Manuals Good Laboratory Practice 217 CFR Part 11 compliance This chapter describes the respective functionalities provided by TOPSPIN in detail Audit Trails A TOPSPIN data set consists of acquisition raw data and processed data These are stored in a directory tree with the following structure lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt The acquisition data are stored in the expno sub directory and the processed data are stored in the procno subdirectory The raw data audit trail Each expno sub directory contains a text file audita txt the audit trail of the raw data This reflects the acquisition state of the raw data and contains a checksum for the file itself audita txt and one for the raw data file fid or ser The latter links the audit file with the raw data By means of the checksums any illegal manipulation of the audit file or the raw data file can be detected using the TOP SPIN commands audit or auditcheck Whenever an acquisition is started the 290 Regulatory Compliance 17 1 2 17 1 3 possibly existing audit file is overwritten by a
184. ithout save 12 3 2D Multiple Display and Row Column Handling 2D multiple display shows a 2D spectrum with an arbitrary number of 1D and or 2D spectra superimposed Spectra are ppm aligned or Hz aligned according to the selected axis unit A superimposed 1D spectrum is automatically displayed in the direction of the matching nucleus for a hetero nuclear 2D or in the F2 direction for a homo nuclear 2D Although multiple display is normally used for spectra with matching nuclei it allows you to superimposed spectra with non matching nuclei You will get a warning that the nuclei do not match Just just click OK to continue How Switch to Multiple Display mode and Read Multiple Spectra Switching to multiple display and reading multiple spectra can be done in two different ways e Read a 2D dataset and click to switch to multiple display mode Then add 1D and or 2D spectra e g from the browser or with re Or e Select multiple spectra in the browser right click one of them and click Display For a more detailed description of reading multiple data in multiple display mode see chapter 11 5 In multiple display mode the Tab bar of the active data window is replaced by 2D Interactive Manipulation 229 a toolbar see Fig 12 9 exam2d HC 3 1 Cobio guest Sele Fag R t Al B E E Ei ts te hjt 4 wt dhl gt F2 ppm Figure 12 9 Multiple display with two 2D spectra superimpo
185. ition status bar Include spooler Include time Include sample temperature Include acquisition status Include acquisition indicator Include lock signal Include MAS Spinning rate Include peak power check POCHKA indicator H O O O K O e SIO Include sample state Figure 15 5 Acquisition 267 3 Check the desired entries To switch the acquisition status bar on w Click Spectrometer Acquisition Status Bar On Off or n Right click in the status line at the bottom of the TOPSPIN window and choose the popup menu Acquisition Status Bar On Off With the entries selected above the right part of the status bar will look like this Acquisition information Fid Flash Sample Time Spooler Scar 2 16 10 49 running O residual time 1m27s tm 1 queued 0 experiments 1 1 SUE a aes The acquisition status bar not only displays information it also allows you to per form various actions e g e Double click the Time field to view detailed time and date information e Double click the Lock field to open the lock display e Double click the Fid Flash field to open the wobble display e Right click the Fid Flash field to switch on off FID flashing e Right click the Acquisition information field to open the following popup menu show acquisition display Start rga Start acquisition Start wobble start qs stop acquisition from this menu you can start various acquisition commands 268 Acquisition e Right cli
186. ity 300008 7 22 ZeSS8ller009 sIr 7S 008 10 000s Peek 3 20 98C TOUS 2 9056eEr00 7 8 000s TAAL TT sooZcoet00s 6 46l6er007 5 000s Tanz dk LO 269 F009 L si 0Let00s Print Export of Copy the Fitting Results To print the fitting curve t Click File Print To export the fitting curve as a graphics file us Click File Export To copy the fitting curve to the Windows Clipboard us Click Edit gt Copy Chapter 15 Acquisition This chapter describes TOPSPIN acquisition as far as the interface 1s concerned Individual acquisition command are described in the Acquisition Reference man ual 15 1 Acquisition Guide If you are a new or occasional user we recommend you to acquire your data with the TOPSPIN Acquisition Guide This will guide you through the typical sequence of acquisition steps To start the Acquisition Guide click Spectrometer Acquist tion Guide 262 Acquisition MMF Data Acquisition Guide at e ES Mew Experiment HU i i Frequency Routing HE Lock Prozol Pars 4 K E Temperature Receiver Gain Probe Match Tune Start Acquisition F Sample Rotation To Processing Figure 15 1 Close Automatic mode In Automatic mode the Acquisition Guide will simply execute each command when you click the respective button This requires the acquisition parameters to be set correctly In interactive mode Automatic mode unchecked the Acquisition Guide will
187. ize and orientation How to Switch Depth Cueing on off 1 Right click inside the data window 2 Choose Depth Cueing On off see Fig 10 4 Depth cueing makes data points which are closer to the viewer appear brighter and those that are further away appear dimmer This increases the depth effect of the 3D image Larger Smaller Default View Depth Cueing Onta Figure 10 4 How to Display a Cube Front or Side view Click one the following buttons 12 Show F1 F2 plane 23 Show F2 F3 plane 31 Show F3 F1 plane 10 3 nD parameter display TOPSPIN 2 1 and newer support parameter display of up to 8D data To show processing parameters t click the ProcPars tab of the data window 176 nD Display Or 1S enter edp on the command line Parameters of each direction are shown in a separate column Fig 10 5 shows the examad 1 1 Cobio guest Reference F3 Fi F1 vin ow FY Reference Phase Baseline a e SF MHz 600 1300000 Peak OFFSET ppm 5 11956 Automation SR Hz ewe Miscellaneous H pPT Hz User AQORDER F Window function Figure 10 5 processing parameter display of a 3D dataset To show acquisition parameters t click the AcquPars tab of the data window Or 1 amp 7 enter eda on the command line nD Display 177 Parameters of each direction are shown in a separate column Fig 10 5 shows the examsad 1 1 Cobio guest
188. l specifications such as PAN_BUTTONS PAN_COLORS etc must have this number of members otherwise you will get some kind of TOPSPIN error Please insert the separator to make sure the item count is correct 20 6 Adding User Defined Buttons to the Toolbars The upper and lower toolbar at the top of the TOPSPIN window can be extended with user defined buttons They can be assigned to any TOPSPIN command macro AU program or Python program To create a user defined button take the following steps 1 Right click at an empty area of the toolbar 2 In the appearing popup menu click Add User Defined Button Reactivate All Invisibleinactive Buttons Add User Defined Button Change Icon Size Change Toolbar Offset Hide Toolbars type SHIFT ESC to reset 3 In the appearing dialog box see Fig 20 3 340 User Extensions a Choose between the options text label or icon The corresponding parameters are enable disabled b Enter the command name the tool tip and the label text or icon file pathname c For a text label set its font text color and background color d For an icon label specify the icon image filename e Set the separator flag to yes or no and select the data dimension s for which the button must appear For an icon label you must stored the icon image file in one of the following direc tories lt user home gt topspin lt hostname gt prop userdefined only available for this us
189. level distance increment leaving the base level the same r Click hold the g button and move the mouse How to Display a Contour Levels Bar in the Data Window 1 Right click in the data window and choose Display Properties dopt 2 Check Contour Levels Bar in the appearing dialog box and click OK see Fig 9 2 152 2D Display Pxam2d HC 1 1 CABRIO guest Spectrum ProcPars AcquPars Title PulseProg Peaks Integrals Sample Structure Fia I EL ra mr qm LL o co o Lm q F2 ppm Figure 9 2 How to Switch on off Square 2D layout Right click inside the data field and click Square Layout On Off E exam2d_Hc 1 1 Cbio guest BHA Spectrum ProcPars AcquPars Title PulsePrag Peaks Integrals Sample Structure Fiq ACEL 120 80 F1 ppm 8 6 F2 ppm Figure 9 3 The F2 scaling will be adjusted to reach a square display 2D Display 153 How to Zoom a 2D spectrum in out r Click one of the following buttons 1 Zoom in to the center spectrum or left edge FID of the displayed re gion increasing the horizontal scaling zi Zoom out from the center spectrum or left edge FID of the displayed region decreasing horizontal scaling zo El Perform an exact zoom via a dialog box zx Ey exacizoom Please enter the exact coordinates of the desired expansion
190. lly using the audit command This will generate a regular entry the comment will appear under the WHAT section and is preceded by the tag user comment You may also add a comment to the raw data or processed data audit trail from an AU program using the macros AUDITCOMMENTA comment or AUDITCOM MENTP comment respectively Alternatively you can store the comment in a file auditc txt in the expno or procno directory and use the macros GDCHECK_RAW or GDCHECK Auditing user defined data manipulations When manipulating a data file with a user defined algorithm e g by means of an AU program or external program the data file and the respective audit trail become inconsistent detectable with the command auditcheck and the data set is no longer compatible with regulations In order to solve this problem TOP SPIN provides a function CheckSumFile which adds the correct data checksum to the audit trails and a function AuditAppend for additional text an alternative to the comment function described above These functions are described in the AU man ual which can be opened by clicking Help Manuals gt Programming Manu als AU programming 294 Regulatory Compliance 17 1 7 Audit Trails in JCAMP DX and ZIP archives The TOPSPIN commands tojdx and tozip allow you to store a data set into a single file in the internationally standardized ASCII type JCAMP DX format or in the well known ZIP format respectively Both stor
191. me gt lt expno gt pdata lt procno gt where lt user gt is the current internal Topspin user This copy can be processed deleted or overwritten even if the original dataset is write protected The origi Dataset Handling 71 nal data set is left unchanged How to Open Special Format Data Apart from the standard Bruker data format TOPSPIN is able to read and display various other formats To do this us Click File gt Open open Ctr1 o select the option Open NMR data stored in special formats select the desired file type see Fig 4 18 and click OK A dialog will appear which depends on the chosen file type Just follow the in structions on the screen The following file types are supported JCAMP DX Bruker TOPSPIN data stored in JCAMP DX format Zipped TOPSPIN Bruker TOPSPIN data stored in ZIP format WINNMR Bruker WINNMR data A3000 Bruker Aspect 3000 data VNMR data acquired on a Varian spectrometer JNMR data acquired on a Jeol spectrometer Felix 1D data FID or spectrum which are stored in FELIX format Note that in all cases the data are stored in a single data file which is un packed converted to standard Bruker format 1 e to a data directory tree 1 Note that the TOPSPIN data format is identical to the XWIN NMR data format 72 Dataset Handling 3 Open fromjdx Options O Open MMF data stored in standard Bruker format OQ Open other file Required parameters Fil
192. meter Handling Note that the command dpp opens the parameter editor and automatically shows the status parameters How to Switch to Maxent parameters r Click the following button MI Switch to Maxent parameters How to Change Processed Data Dimensionality r Click the following button 42 Change data dimensionality This changes the number of parameter columns and value of the processing pa rameter PPARMOD TOPSPIN 2 1 and newer support data dimensionalities up to 8D The parameter editor does not allow you to modify status parameters Processing status parameters reflect the status of the processed data and are used for further processing display or plotting Changing them can make the dataset inconsistent In rare cases however it can be useful to change a status parameter and TOPSPIN allows you to do that from the command line If for instance you want to change the F1 status parameter MC2 of a 2D dataset you have to enter smc2 Note that the command s is used for 1D 2D and 3D dataset TOPSPIN automati cally recognizes the dimensionality of the data and displays the parameter in all relevant dimensions Note that for example the parameter MC2 only exists in F1 5 2 Acquisition Parameters How to Set Acquisition Parameters Acquisition parameters can be set changed as follows e from the parameter editor click the AcquPars tab or enter eda e from the command line e g enter td e from the interactive parameter
193. meter Handling 87 At the left of the parameter editor window you will see a list of parameter sec tions The processing parameter editor supports the following functions r Collapse expand a parameter section by clicking the button Note that the section Window function in Fig 5 1 1s collapsed r Collapse expand all parameter sections by clicking the large button of the data window toolbar us Enter part of a parameter name in the search field and click amp r Click a parameter section e g Phase at the left of the dialog box The sec tion becomes highlighted and the corresponding parameters will appear in the right part of the dialog box ns Click in a parameter field e g PHCO to set the parameter value r Click the button to the right of parameters like AUNMP to open a list of the corresponding programs lists r Right click the E button to the right of parameters like AUNMP to open the current program list with an editor r Hit the Tab key to jump to the next parameter field o gt Hit Shift Tab to jump to the previous parameter field r Use the scroll bar at the right of the dialog box to move to parameters fur ther up or down in the dialog box How to Undo the Last Processing Parameter Change r Click the following button 1 Undo last parameter change How to Display Processing Status Parameters r Click the following button S Show processing status parameters 88 Para
194. meter adjustment dialog see Fig 15 11 0 2 04 06 08 10 12 1 4 5 Figure 15 10 The buttons of the FID display are the same as for the acquisition command zg see paragraph Fig 15 10 The GS parameter adjustment dialog offers tabs at the top of the window to select power frequency delay etc The selected parameter is shown in the middle of the window The slider at the right of the window allows you to change the selected parameter The current value can be viewed and modified in the field below the slider The sensitivity of the slider can be set in the field Sensitivity above the 274 Acquisition squarePower Frequency l Delay Receiver RetPhase Offset Pulse ey sensitivity a 1 r adjust max 3138 51 Offzet Oi Hz min 3038 51 3088 51 DAYE Save all Restore Restore all stop s ME Figure 15 11 slider The effect of the change can be viewed in the FID display the right part of the window This can be manipulated with the FID display buttons as described in chapter 15 10 At the bottom of the window you find the following buttons e Save Save the value of the current parameter Acquisition 275 e Save all Save the values of all changed parameters Restore Restore the value of the current parameter e Restore all Restore the value of all changed parameters e Stop Stop the acquisition and quit the GS window 15 10 Running an Acquisition A typical acquisitio
195. n The following dialog box will appear EA calibrate Spectrum calibration frequency Cursor frequency in ppr Note that the units Hz or ppm correspond to the axis units of the display 3 Enter the frequency you want to assign to the reference peak 198 1D Interactive Manipulation 4 Click OK The spectrum will be calibrated and re displayed TOPSPIN will automatically leave calibration mode 11 5 1D Multiple Display The multiple display mode allows you to display multiple superimposed spec tra The spectra will be ppm aligned or Hz aligned according to the selected axis unit Each spectrum can be individually shifted and scaled allowing exact align ment of corresponding peaks in different spectra The number of superimposed spectra is unlimited Although multiple display is normally used for spectra with matching nuclei it allows you to superimposed spectra with non matching nuclei You will get a warning that the nuclei do not match Just just click OK to continue How Switch to Multiple Display Mode and Read Multiple Spectra One way to superimpose data in multiple display is to read one dataset switch to multiple display mode and add other datasets 1 2 Read a 1D dataset Click the button in the upper toolbar or type md on the command line The data window will switch to multiple display mode Add a dataset as follows t Left click hold the dataset in the browser and drag it into th
196. n is performed as follows 1 Create a new dataset a Click File New new Ctrl1 n Prepare for a new experiment by creating a new data set and initializing its MMR parameters according to the selected experiment type MAME EXPN PROCNO 1 DIR Cibin USER guest Solvent CDCI3 v Experiment Use current params TITLE Figure 15 12 b Specify the datapath variables name expno procno dir and user select the desired Solvent and Experiment enter the Title and click OK The dataset will appear in the data field with no raw and no processed data 276 Acquisition available 2 Click the AcquPars tab to display the acquisition parameters protona 1 1 CABO guest Spectrum ProcPars AcguPars Title PulseProg Peaks Integrals Sample Structure Fid Acgqu va YF Experiment PLLPROG zo LL Current pusepr Att mod Acquisition mace TD Size of fid MS Number of scan DS Mumber of durrirr TOO Loop count for t Width F Receiver RG Receiver gain Civ us 53 Dwell tire hs we Tras ee ed ot ri s gt Figure 15 13 a Optionally click 7 to show the pulse program parameters only b Click the yl button to read the prosol parameters or Set the relevant parameters manually As an alternative to step 2 you can set the acquisition parameters interactive ly in the GS window see par 15 9 3 To start the acquisition e Click p in
197. n started Egh 2 13 15 36 16 145 2256 Corserver js running ai 213 15 5616 145 2320 java virtual machine started i 2 1 3 15 36 16 145 O current data examad 1 1 Cubio guest nmr mi 2 1 3 15 36 16 155 jbrowseDataTree ltl abi soontinste FILE 6 terms a wii 2 13 1556 20 671 jbrowseDataTree lbioldata DIRECTORY 2 terms ok 2 13 15 356 26 500 brov seDataTres C bio datafquestnnr DIRECTOR 12 tems crid brow se_dispdata_newy ai 2 13 15 36 29 173 browseDataTree C bio datafquestnimriexaml d_13C DIRECTORY 9 tems mi 2 13 15 36 29 173 browseDataTree C bioidataiguestnrmnuexami d 13C pedata DIRECTORY i 2 13 15 356 29 1535 browseDataTree C bioidataiguestnrmnuexami d_13C i ipdata DIRECTORY fea 2 13 15 36 29 195 browseDataTree C bio dataiquestnmrfexarm d_1SC Sipdata DIRECTORY f 2 13 15 36 29 224 browseDataTree Cbio dataiquestnmriexarmn d_13C M4 indata DIRECTORY wii 2 13 15 36 29 244 9 brow seDataTree Cbio dataiquestnmriexarmn d_13Cindata DIRECTORY ok 2 13 15 36 29 274 brow seDataTree Cbio dataiquestnmriexarmn d_13Ceindata DIRECTORY wii 2 13 15 36 29 264 brovseDataTree Cbio dataiquestnmriexarn d 130r indata DIRECTORY lk 2 13 15 36 29 504 brovwseDataTree C bio dataiquestnmriexarmn d_13Coindata DIRECTORY ai 2 13 15 36 29 514 browseDataTree C bio dataiquestnmriexarn d_13C indata DIRECTORY a 2 13 15 36 29 594 getDiscFuncEy dent T hioi
198. n the Command Prompt a Entercd lt tshome gt b Enter topspin where lt tshome gt is the directory where TOPSPIN is installed Under Linux 1 Open a Linux Shell or Terminal Window 2 In the Shell Terminal a Enter cd lt tshome gt b Enter topspin where lt tshome gt is the directory where TOPSPIN is installed Startup TOPSPIN specifying dataset Topspin can be started with a dataset option 1 Open a Windows Command Prompt or Linux Shell 2 Enter topspin j TOP_DATA lt dataset path gt The specified dataset is automatically displayed after startup Examples topspin j TOP_DATA c bio data guest nmr exam1d_1H 1 pdata 1 topspin j TOP_DATA c bio data guest nmr exam1d_1H 1 pdata l Ir topspin j TOP_DATA c jcamp dx topspin j TOP_DATA c data archive zip Getting Started 19 1 5 1 6 Configuration After the installation of TOPSPIN it must be configured once TOPSPIN may be used in two different ways on a computer which controls a spectrometer The command cf must be executed once to configure the spectrometer hard ware Just type this command and follow the instructions on the screen At the end of the dialog further configuration commands like expinstal1I are of fered and can be started from there on a computer which is used as datastation The only configuration command to be executed is expinstal1l1 This allows you to install pulse programs AU programs lists etc Just type this command and f
199. nd Data You can find TOPSPIN data according to various criteria To start searching do the following 1 Click Edit gt Find data Ctr1 f find to open the Find data window see Fig 4 22 EN Find data Searching will be performed in all data directories marked inthe data directories list below The checkboxes at the right will enforce exact matching if enabled MAMIE EXPNO PROCNG USER Title Pulse Frog Dimension Data type Date fram minds Date till mirria yy Data directories Figure 4 22 Dataset Handling 79 2 Enter the search items in the upper part of the dialog Note that e There will be searched for items containing the specified string e Exact matching is performed for dataset variables NAME EXPNO PROCNO and USER if the checkboxes at the right are enabled e The search is restricted to data created between the specified dates Note that this refers to the acquisition date e The Reset mask button allows you to reset the default criteria 3 Select the Data directories to be searched in the lower part of the dialog If no directories are selected all will be searched 4 Click OK to start the search A list of data that fulfil the defined criteria will appear see Fig 4 23 ee Search result examid 130 1 1 Cobia quest zgpgq30 examid_ 13c imac exami d_ 130 dept 35 2004 03 30 11 18 36 exami d_13C dept4s 2004 03 30 11 53 06 examid 130 deptgo 2004 03 30 12 27 39 exami
200. nd ppm Axis Units Click the following toggle button in the upper toolbar ha Toggle between Hz and ppm axis units hz How to Switch on off the Spectrum Overview display The spectrum overview shows the entire spectrum at the top of the data window It is useful when only a certain region of the spectrum is displayed In the over view the displayed region is marked as a green area To switch on the spectrum overview click the following toggle button in the upper toolbar ull Switch the spectrum overview display on off ov To shift the displayed region simply click hold the green area in the overview spectrum and move the mouse see Fig 8 13 How to Switch Y axis Display Click the following toggle button in the upper toolbar EM Switch the y axis display between abs rel off y Fig 8 13 shows a data window with the spectrum overview on ppm axis units and 140 1D Display absolute y axis display examid 1H 1 1 Cobio guest Figure 8 13 8 6 Show Display Properties Regions Files If you right click inside the data window the following popup menu will appear Display Properties Save Display Region To Restore Display Region From Params F172 File Properties Files If you choose Display Properties a dialog box see Fig 8 14 will appear 1D Di
201. nd specify the Menu Name in the appearing dialog b Click Add Menu Item and specify the Menu Item name and the corre sponding Command in the appearing dialog c Click Apply Ey User Defined Menus Menu term l Cormmand Figure 20 5 The new menu will appear in the menubar Furthermore the dialog box in Fig 20 5 contains the following buttons e Remove Remove menu names and or menu items e Apply Close Apply any changes and close the dialog box e Up Down Move up down the menu name list 344 User Extensions 20 8 e Cancel Close the dialog box discarding any changes User defined menu definitions are stored in the file umbar_menubarild prop umbar_menubar2d prop or umbar_menubar3d prop depending on the data dimensionality These files resides in the subdirectory userdefined of the user properties directory To locate this directory enter the TOPSPIN command hist Adding User Defined Guides TOPSPIN offers several guides like the Acquisition Guide command aqguide the Processing Guide command prguide and the T1 T2 Guide command t1guide You can set up your own guides which can be adaptations of Bruker guides or new written ones In order to do that you must edit the file toolbar_user prop and cmdtab_user prop in the directory lt user properties directory gt userdefined To identify this directory enter the command hist in TOPSPIN The file toolbar_user prop contains the guide definition If the f
202. nds to be executed automatically after startup To do that 1 Click Options Administration Edit Startup File 2 Enter the desired startup command s in the appearing editor for example re examld_13C 1 1 c bio guest efp apk abs The above lines would cause TOPSPIN to display the dataset C bio data guest nmr exam1 d_13C 1 pdata 1 and execute the command efp apk and abs on it Note that you can use a single forward slash or a double backslash as path separator Note that in TOPSPIN 2 1 and newer the file autostart mac is a regular Top spin macro In older versions however the file autostart prop was used with a different format How to Define Auto Termination after Idle Time TOPSPIN can be configured to be terminated after a user specified idle time To do that 1 Click Options Preferences set 2 Click the Change button to the right of the object Automatic termination of TOPSPIN when idle time has exceeded enter the NMR Administration password as requested and enter the number of minutes of allowed idle time 3 Click OK to close the dialog click OK to close the Preferences dialog 4 Restart TOPSPIN to activate the change User Preferences 315 If the user does not execute any commands from the command line menu or tool buttons a dialog will appear with an OK button to terminate immediately and or Cancel button to continue Automatic termination frees the license used by this
203. ne to the bottom of the data field sd For more information on display options please refer to chapter 8 5 1D data and 9 5 2D data 2 2 Command Line Usage How to Put the Focus in the Command Line In order to enter a command on the command line the focus must be there Note that for example selecting a dataset from the browser puts the focus in the browser To put the focus on the command line r Hit the Esc key or n Click inside the command line How to Retrieve Previously Entered Commands All commands that have been entered on the command line since TOPSPIN was started are stored and can be retrieved To do that Hit the T Up Arrow key on the keyboard By hitting this key repeatedly you can go back as far as you want in retrieving previously entered commands After that you can go forward to more recently en tered commands as follows t Hit the Down Arrow key on the keyboard How to Change Previously Entered Commands 1 Hit the Left Arrow or gt Right Arrow key to move the cursor 2 Add characters or hit the Backspace key to remove characters 3 Mark characters and use Backspace or Delete to delete them Ctrl c to copy them or Ctr1 v to paste them In combination with the arrow up down keys you can edit previously entered commands 36 The TOPSPIN Interface How to Enter a Series of Commands If you want to execute a series of commands on a dataset you can enter the com mands
204. ng with TopSpin at the top of the dialog click Save Close and restart TOPSPIN After the restart a login prompt will be displayed and TOPSPIN cannot be used without entering an internal user and his password To log off the internal user r enter logoff on the command line Or us Click Options gt Administration Log off and enter the user name and password as requested If TOPSPIN internal user is not mandatory 1 e the entry Enforce login for working with TopSpin is disabled you are not prompted to login after TOPSPIN startup You can however still login as internal user with the command login Locking TOPSPIN s Graphical User Interface TOPSPIN can be blocked such that it does no longer accept user input via mouse or keyboard To do that i gt enter Lockgui on the command line Or 0s Click Options Administration Lock TopSpin user interface A window will appear see Fig 17 6 indicating the locked status and offering but 300 Regulatory Compliance tons to unlock TopSpin locked by user carol at Wed Jul 13 16 53 52 BST 2005 Please press a button to unlock carol to unlock MMF administrator to unlock Figure 17 6 Only the current user or the NMR Administrator can unlock the user interface While TOPSPIN is locked all background activity such as data acquisition and processing continue For safety reasons TOPSPIN can be forced to execute Lockgui automatically when no commands from the c
205. nnection is supported Pocket PC Internet Explorer is also sup ported for full spectrometer control via Windows Mobile 2003 TM or equivalent PDF files of spectra may also be viewed on this platform making the mobile pocket spectrometer a reality The configuration of ICON NMR web interface is described in the ICON NMR man ual accessible Help gt Manuals Automation and Plotting IconNmr Auto mation Interface Note that ICON NMR remote control does not require and is fully independent of TOPSPIN remote control Chapter 19 User Preferences 19 1 User Preferences TOPSPIN can be tailored to your preference in many respects This ranges from star tup options to spectrum objects menu settings remote connections etc Every standard user can create his her own set of preferences To set user preferences e Click Options Preferences set A dialog box will appear with at the left side the categories that can be tailored 312 User Preferences see Fig 19 1 Ey User preferences Administration terns Administration terns oll spectrum Auto apen last used dataset when restarting TopSpin C Contour plot Show Topspin data examples directory in data browser C spectrum title Spectrum cursor Setup Users for TopSpin internal laginfagott and esign Spectrum parameters Automatic termination of TopSpin when idle time exceeded Printer Automatic locking of TopSpin when idle time exceeded change
206. nsures that nobody can see data or commands by observing and recording your network traffic TOPSPIN uses the Secure Socket Layer SSL technology for encryption which is also used for secure web sites SSL needs digital certificates on both sides of a connection to achieve a valid authentication After a TOPSPIN installation default certificate files are provided to secured connections There is a chance however small such connections are attacked by a malicious person who also has the same default certificate files If for this reason you want to create your own set of certificate files you can do this by executing a script that is installed in lt t shome gt prog server make_new_certificates and follow the instructions given there To start a remote connection the new certifi cate files must be installed on BOTH machines Remote Control 309 18 5 How to Access ICON NMR from a Remote Web Browser In TOPSPIN 1 3 and newer ICON NMR is web enabled The standard Bruker Auto mation Software now provides a built in website which can be activated to allow remote access to ICON NMR from any web browser which is networked to the spectrometer workstation Experiments may be cancelled submitted the run may be paused or halted and spectra in PDF format are available from the browser win dow No added software apart from ICON NMR is required and configuration is performed via the standard ICON NMR Configuration window For security a SSL HTTPS co
207. ntegration Line shape analysis of solids spectra Data acquisition with Bruker Avance type spectrometers Supporting automated and walk up spectrometers ICON NMR Remote spectrometer control including web enabled ICON NMR Adding user defined functionalities to TOPSPIN AU programs Macros and Python programs Getting Started 17 Available Documentation In TOPSPIN 2 0 and newer the Help Manuals submenu contains list of availa ble manuals for the following items General Beginners Guides Acquisition Users Guides Acquisition Application Manuals Acquisition amp Processing Reference Automation and Plotting Analysis and Simulation Programming Manuals Technical Manuals Installation Guides Good Laboratory Practice Each document is listed with a short description of its contents 1 3 TOPSPIN license TOPSPIN requires a license for startup A license can be ordered online from www bruker biospin de NMR nmrsoftw licenses index html If your PC controls a spectrometer TOPSPIN will start up without a license Fur thermore you can use TOPSPIN for developer purposes with restricted functional ity In this case you have to start it from a Windows Command prompt or Linux shell as follows topspin developer 18 Getting Started 1 4 Startup TOPSPIN Under Windows r Click the TOPSPIN icon on the desktop or r Start TOPSPIN from a Command Prompt as follows 1 Click Start Run enter cmd and click OK 2 I
208. ntry to open the popup menu see Fig 8 4 3 Click Copy to copy the selected peaks to the Clipboard Print the peak List To print the peaklist 0S Right click a peak entry and choose Print Or r Enter print on the command line Or t Press Ctrl p c All actions will print the entire peaklist To preview a print c Right click a peak entry and choose Print preview IS Import a peak List A peak list from a different dataset or program can be imported as follows 124 1D Display 1 Right click an entry to open the popup menu see Fig 8 4 2 Click Import 3 In the appearing dialog box navigate to the directory where the list resides and select the peak list choosing from Auremol peaklist ml MULABEL peak list labels TOPSPIN peak list xml XEASY peak list peaks XWIN NMR peak list txt As such you can import a peak list from a different dataset or program or a pre viously exported list from the current dataset Note that peak picking com mands store the peak list in the processed data directory under the name peak xml1 TOPSPIN 2 1 or newer or peak txt XWIN NMR and TOPSPIN 2 0 or older Shortcuts Double click a peak zoom into spectrum i e show region around that peak Enter key zoom into spectrum i e show region around selected peak s Delete key delete the selected peak s from the peak list Ctrl c copy selected peaks to the Clipboard Ctrl a select all peaks
209. nu looks like this File Edit View Spectrometer Processing A change in menu font also affects all sub menus and popup menus How to Change the Font of the Tab bar Click Options Preferences set Click Fonts Dialogs Icons in the left part of the dialog box Click the Change button to the right of the Dialog window font object Select the desired name style and or size in the appearing dialog box Click OK to store the new font Click Apply Non bk WwW NH Fig 19 7 and Fig 19 8 shows a Tab bar with font size 10 and 14 respectively Spectrum ProcPars AcquPars Title PulseProg Peale Integrals Sample Structure Fid Figure 19 7 Tab bar with font size 10 324 User Preferences spectrum ProcPars AcquPars Title PulseProg Peaks Integrals Sample Struct Figure 19 8 Tab bar with font size 14 How to Change the Font of Dialog Boxes Click Options Preferences set Click Fonts Dialogs Icons in the left part of the dialog box Click the Change button to the right of the Dialog window font object Select the desired name style and or size in the appearing dialog box Click OK to store the new font 6 Click Apply Fig 19 9 shows an example of a dialog box with the font Times New Roman Italic nan amp WwW N Options E Display data in same window Display data in newe window MAME EXPHO PROCMO OIR USER Figure 19 9 How to Change the Font of the
210. o OQ ALU program O Python program CO Pulse program O Parameter list O Mizcellaneous file Required parameters Mame Data directory User Figure 4 20 1 Select a data type option For each option the corresponding command appears in the title of the dialog box These commands can also be used to delete data from the command line 2 Specify the Required parameters Note that you can use the wildcards e Asterix for any character and any number of characters Dataset Handling JI e Question mark for any single character 3 Click OK A dialog box will appear showing the matching datasets For example if you se lect the option An entire dataset 1 Select dataset entries for deletion selected entries are highlighted To select multiple entries click them holding the Shift or Ctrl key 2 Click Delete to delete the entire data directory If you select the option Acquisition data or Processed data you can choose be tween deleting the data files only and deleting the entire expno or procno direc tory respectively see Fig 4 21 Data directory Chio User quest Mame 13 Cptians Delete the selected EXPNOs with all their PROCMOs O Delete the raw data files of the selected EXPOS HAME EXPHO 4COU DATA to ft iD UD eet Poet TS _ _ i i TETA i a up F J E F Figure 4 21 Dataset Handling 4 7 Searching Finding Data How to Fi
211. o Create AU automation Programs 00005 21 How to Create Python Programs 0 0 0 cece eens 28 1 18 How to Automate Data Acquisition 0 0 0 0 cee cee eee 28 The TOPSPIN Intertacesis6s hanced tacts a a S 29 21 The Topspin Window 5424 kae Midaw ead 28 books EE 29 Chapter 3 Chapter 4 How to Use Multiple Data Windows 0 0 00 30 How to Use the Menu Dat 5 icacdu seo eyes Beene ase E eur as 31 How to Use the Upper Toolbar 1D data 31 How to Use the Lower Toolbar 1D data 0 0 33 22 gt Command Line Usa tose on oem a ada eee cere Rae eee es 35 How to Put the Focus in the Command Line 35 How to Retrieve Previously Entered Commands 35 How to Change Previously Entered Commands 35 How to Enter a Series of Commands 00 cee eee eee 36 23 Command Line History c20c24uos casei eka At oer paosea evens 36 2 4 Starting TOPSPIN commands from a Command Prompt 37 2 5 Function Keys and Control Keys 0 0 0 cece eee ees 38 20 Help INCLOpPSPIN 2 sire e cS Os be ee aa oa ea cs Be sae 4 How to Open Online Help documents 00000 42 Howto Get TOPS s eeitcy eit a a E ace ehG oe ae dees 42 How to Get Help on Individual Commands 42 How to Use the Command Index 0 eee eee 43 2 7 User Defined Functions Keys ec
212. o be defined 4 Click the green button to leave the Define peaks mode How to Pick Peaks Semi Automatically 1 Click the following button button turns green il Define peaks semi automatically 2 Move the cursor into the data window 3 Put the cursor line near the desired peak 4 Left click to pick forward or Right click to pick backward see Fig 11 18 A red cursor line will appear at the nearest peak whose intensity is between MI and MAXI 5 Right click to add the selected peak to the peak list see Fig 11 18 Add Peak To List Pick Backward Figure 11 18 The peak label will appear at the top of the data window 6 Click the green button to leave the define peaks semi automatically mode How to Delete Peaks from the Peak List To delete a specific peak 1 Right click on a defined peak 214 1D Interactive Manipulation 2 Choose Delete peak under cursor from the popup menu see Fig 11 19 Delete All Peaks Delete Peak Under Cursor Delete All Regions Delete Region Under Cursor Pick Peaks On Ranges show Peak List Set tll Set Wax Figure 11 19 To delete all peaks r Click the t amp button in the data window toolbar Or n Right click in the data field and click Delete All Peaks in the popup menu How to Return from Peak Picking Mode with without Save To return while saving the peak list and peak ranges r Click the following button J Save the Peak Region and Peak List
213. o status pulse program E Show the pulse program in an external editor Tl Start the graphical pulse program display nmrs im gay Search in the pulse program i Search for more info in the knowledge base How to Display the Peak list Click the Peaks tab 120 1D Display Pxamid 1H 1 1 Cibio guest Oo oc 4 A th amp ww BI Index F173 195699 209299 1320 4 21603 2170 1 1947 5 227658 2 26579 26615 4 3 8319 ala eg 3 1900 3 0861 3 0452 2 9601 2 6994 1 2614 1 2465 Intensity Sity abs 114 F2505 70 1249544509 13371661 03 1 26R S022 3 13175965459 13733719 44 13251595 75 15909545 56 13604594 47 Figure 8 3 Integrals Intensity rel 11 04 11 95 12 67 12 03 12 36 12 93 12 46 15 00 12 95 Sample otructur H a If wj g ji H p H m 0 0044 0 0037 0 0037 0 0040 0 0037 0 0033 0 0040 0 0059 0 0077 This displays the peak list By default the peak list shows the following entries Peak the peak number v F1 ppm the chemical shift Intensity abs the absolute peak intensity Intensity rel the relative peak intensity Half width ppm the peak width at half height Display the spectral region around a peak 0S Right click the desired peak this will open the popup menu shown in Fig 8 4 1D Display 121 Show spectrum e Expand spectrum d In current window Delete In correlated window Edit annotation Remove b Define a reference I
214. olbar see Fig 11 3 The first button define integrals is automatically activated is green examid_1H 1 1 Cibo guest Sl x Mouse Sensitivity 1 0 0 99 ppm 493 42 Hz DEFINE REGION MODE Define Drag using left mouse button Return Left click highlighted icon Figure 11 3 Data window in integration mode ae The yellow button indicates that the data window is in integration mode Some buttons will turn green when they are clicked As long as a button is green it 1s active If integral regions have already been determined for example with abs or witha previous interactive integration these regions are displayed in the data window along with the integral values You can remove them change them or add to them as described below 188 1D Interactive Manipulation How to Define Integral Regions To define integral regions interactively 1 Click the following button button turns green 4 Define integral region interactively Note that the define integrals button is automatically activated on entering the integrals mode 2 Put the red cursor line at one edge of a peak or multiplet 3 Left click hold and drag the cursor line to the other edge of the peak or mul tiplet 4 Do step 2 and 3 for all regions to be defined 5 Click the green button to leave the define region mode button turns grey To define integral regions via a dialog box 1 Click the following button d Define region via dialog
215. ollow the instructions on the screen selecting Installation for Datastation default Note that the commands cf and expinstal1l1 can be started from the command line or from the Options or Spectrometer menu However the latter menu is only available after c f has been performed once choosing Installation for spectrome ter After the configuration has finished TOPSPIN is ready to be used The configura tion only needs to be repeated when you have installed a new version of TOPSPIN or if your spectrometer hardware has changed More details on configuration can be found in chapter 16 2 and the descriptions of cf and expinstall in the Acquisition Reference Manual How to Display Spectra In this chapter opening data in standard Bruker format is described Opening other data formats is described in chapter 4 Please note that a standard Bruker dataset is a directory tree rather than a single file lt dir gt data lt user gt nmr lt dataset name gt lt expno gt pdata lt procno gt e g 20 Getting Started c bruker topspin data guest nmr exam1d_13C 1I pdata 1 How to Open Data from the Menu Open the File menu and click Open A dialog box appears Select the first op tion the Browser type File Chooser and click OK A file browser appears Navi gate to your data directory and expand it to the level of names expnos or procnos double click a directory to expand it Select the desired item and click Display The
216. om the screen Regions which are saved on disk in the int rng file are not affected How to Scale Selected Integrals Integral scaling only manipulates selected integrals However if no integrals are selected it works on all integrals r Click one of the following buttons gt Scale up selected integrals by a factor of 2 f2 Scale down selected integrals by a factor of 2 Scale selected integrals up down smoothly al To scale up down integrals by a factor entered via a dialog 1 Click the following button Scale integrals via a dialog 194 1D Interactive Manipulation 2 Enter a scaling factor e g 2 5 in the appearing dialog amp calib 3 Click OK to apply this factor To scale all integrals to the same height r Click the following button Scale unscale all integrals to the same height The individual scaling factor for each region is displayed above the integral Clicking this button again rescales all integrals to their original height How to Move the Integral Trails Up Down To move the integrals selected and unselected up or down r Click one of the following buttons 4 The left edge of the selected integral is put just above the baseline If no integral is selected the lowest integral is used The right edge of the selected integral is put at 3 4 of the window height If no integral 1s selected the highest integral is used Shift all integral trails up down smoothly How to Cut
217. ommand line menus or tool buttons have been entered for a certain period of time for instance because the current user has left In order to enable automatic locking 1 Click Options Preferences set 2 Click Administration Items in the left part of the dialog box 3 Click the Change button to the right of the object Automatic locking of TopSpin when idle time exceeded 4 Enter the maximum allowed idle time in minutes in the dialog and click OK Chapter 18 Remote Control 18 1 Remote control TOPSPIN supports remote control This means for example that you can control your spectrometer from any PC in the laboratory network or over the internet from your PC at home Using your local TOPSPIN interface you have access to the remote data directories and remotely running TOPSPIN commands Furthermore in TOPSPIN 1 3 and newer ICON NMR is web enabled which means it can be control led from any web browser which is networked to the spectrometer Note that remote access is operating system independent 18 2 How to Establish a Remote Connection from your PC In order to establish a remote connection you have to perform a few steps both on the local and on the remote system Note that the local system is the computer you are sitting at and the remote system is the computer you are connecting to Up to 5 local systems can connect to TOPSPIN on a remote system 18 2 1 Setup the remote system The remote system must be enable
218. on in the upper toolbar or enter md on the com mand line When you open a dataset now for example drag one from the browser it will be superimposed on the current spectrum rather than replacing it Several multiple display functions are available now in the data window toolbar Most importantly you can scale and shift each spectrum individually This allows exact Getting Started 23 alignment of corresponding peaks of different spectra Multiple display mode is supported for 1D and 2D spectra In 2D you can super impose an arbitrary number of 1D or 2D spectra 1 11 How to Print or Export the Contents of a Data Window How to Print Data A TOPSPIN data window may contain various objects like an fid a spectrum ex pansions of a spectrum superimposed spectra spectrum components such as pa rameters peaks integrals cross sections etc Whatever the content of the data window is it can be printed as follows type Ctr1 p or click File Print se lect Print active window in the appearing dialog box and click OK The other options in this dialog box enable you to use or create plot layouts De tails on this can be found in the Plot Editor manual to be found under Help gt Manuals Automation and Plotting TopSPin Plotting The colors of the printed data can be chosen in the User Preferences dialog box Just enter the command set or click Options Preferences and click Printer in the left part of the dialog box
219. on the command line separated by semicolons e g em ft apk If you intend to use the series regularly you can store it in a macro as follows c right click in the command line and choose Save as macro 2 3 Command Line History TOPSPIN allows you to easily view and reuse all commands which were previously entered on the command line To open a command history control window click View gt Command Line History or right click in the command line and choose Command Line History or enter the command cmdhist see Fig 2 2 EY Command History cmadhist Figure 2 2 It shows all commands that have been entered on the command line since TOPSPIN was started You can select one or more commands and apply one of the following functions Execute Execute the selected command s Append Append the first selected command to the command line The appended The TOPSPIN Interface 37 command can be edited and executed Useful for commands with many arguments such as re Save as The selected command s are stored as a macro You will be prompted for the macro name To edit this macro enter edmac lt macro name gt To ex ecute it just enter its name on the command line 2 4 Starting TOPSPIN commands from a Command Prompt TOPSPIN commands can be executed outside of the TOPSPIN interface from a Win dows Command Prompt or Linux Shell Under Windows 1 Open a Windows Command Prompt 2 Enter a TOPSPIN command in
220. ook seeus 263 Do Data window Toolbat 14 55 3 35250 koa bs ehh E Ses 265 15 4 Acquisition Status Bar nes 266 15 5 Command Queuing and Scheduling 0 000000 008 268 15 6 Tuning and Matching the Probehead 00 0000 269 B LORIS 26a sae 6 ins ca ek ee n Re ee ee ee ee 270 Chapter 16 Chapter 17 Chapter 18 Chapter 19 15 8 BSMS Control Panel 6 0 05 eee si ae cs Se ew ee Sew vee ke wee eee 271 15 9 Interactive Parameter Adjustment GS 0 0 00 cee aes 273 IIO Running an Acquisition 20225 50206 4 d40 2aceee ee aN T aes 4 215 OSD 100s anaa area Swe a Geos E EE 279 Configuration Automation ssssssssoosesesesessosoo 281 16 1 NMR Superuser and NMR Administration password 281 How to Change the NMR Administration Password 282 162 SCOMMSUTAUON 262 4 Rate See eee e Penh Rae RR Raa Eee 282 How to Perform a Default Configuration on a Datastation 283 How to Perform a Customized Configuration on a Datastation 283 16 3 ParameterSelconversion suiutis eel teaws aa eed Aa a a 284 IGA Automato 2 2 c5 c0 Boao s Seon Sema eRe Rae eee Saye Bae 284 How to Install AU Programs 1 0 0 ccc cee ns 284 How to Open the AU Program Dialog Box 284 How to Switch to the List of User defined AU Programs 286 How to Switch to the List of Bruker defined AU Programs 286 How to Define the AU Programs Source Director
221. or the chemical shift v F2 ppm the chemical shift in the F2 direction v F1 ppm the chemical shift in the F1 direction Furthermore a stored or exported 2D integral list can be imported as follows 1 Right click an entry to open the popup menu 2 Click Import 3 In the appearing dialog box navigate to the directory where the list resides and select the integral list As such you can import an integral list from a different dataset or a previously exported list from the current dataset Note that integration commands store the integral list in the processed data directory under the name inte grals txt Exported integrals are stored in the files lt name gt txt and lt name gt reg where lt name gt is the name specified by the user How to Display the FID t Click the Fid tab fid 2D Display 161 2D raw data consist of a series of FIDs which are displayed in a row Individual FIDs can be displayed by zooming in To do that click EI repeatedly Now you can shift and zoom in out the data to display different FIDs see Fig 9 11 Pxam d HC 1 1 Cobio guest Spectrum ProcPars AcquPars Title PulseProg Peaks Integrals Sample Structure Fid Acgu Figure 9 11 9 5 2D Display Options How to Switch between Hertz and ppm Axis Units in F2 and F1 r Click the following multi state button in the upper toolbar ha Switch between Hz and ppm axis units in F2 and F1 hz How to Switch on off the
222. ored by automatic in tegration command abs or by a previous interactive integration To read integrals 1 Click the following button 4 Read integral regions The following popup menu will appear Read intng Read inttng Mo Slope amp Bias Corr Read intrng Use Last Slope amp bias impart intrng trom Relaxation Experiment Edit intrig Figure 11 5 2 From the popup menu choose one of the following entries Read intrng to read the last saved integral regions and apply the saved slope and bias correction values e Read intrng no slope amp bias corr to read the last saved integral regions but do not apply the saved slope and bias correction values e Read intrng use last slope amp bias to read the last saved integral regions applying the last slope and bias correction values 1D Interactive Manipulation 191 Read intrng from Relaxation Experiment to read the last stored integral regions of the T1 T2 relaxation experi ment e kdit intrng to edit the file i nt rng that contains the integral regions and slope and bias correction values Changes in this file are automatically shown on the screen How to Perform Interactive Bias and Slope Correction To perform interactive bias correction 1 Select the integral s that you want to correct right click in the region If no integral is selected bias correction will work on all integrals 2 Click hold the
223. orting Data How to Store Export a Data Window as Graphics File The clipboard and metafile formats are resizable vector formats In addition to this TOPSPIN allows you to save the contents of a data window in a graphics file of selectable type Supported formats are png jpg Jpeg bmp emf wmf and pdf To do that 1 Click File gt Export exportfile 2 Navigate to the storage folder 3 Enter the destination filename and extension 4 Click Export The resolution of such a screen dump equals the resolution of your screen When you import a graphics file into an other program you may loose information when resizing the graphics Note that exporting a data window to PDF format is only supported in TOPSPIN 2 1 and newer Chapter 8 1D Display 8 1 The 1D Data Window The 1D data window consists of a data field a title bar a Tab bar and buttons Fig 8 1 shows a data window with a 1D spectrum 110 1D Display maximize data button field ae ee minimize close Tab bar button button examid 1H 1 1 C bio quest MBX Spectrum ProcPars AcguPars Title PulseProg Peaks Integrals Sample Structure Fid Accu Figure 8 1 8 2 Displaying one Dataset in Multiple windows TOPSPIN allows you to display one dataset in multiple data windows This is for example convenient to view various regions or various object
224. overs 171 How to Switch to 2D Plane Display 0 0 0 172 How to Display various Plane Orientations 172 How to Display various Plane Positions numbers 173 102 3D Cube Display Mode 25 vec ntenee a aoe Rekahe E ens 174 Howto Display the SJD Cube ic sc0i wane tendetaceae ahs ac aes 174 How to Rotate the 3D Cube sinis hash ond eta as Fes thd ed 174 How to Scale Up Down the 3D Cube 000 175 How to Reset the Cube Size and Orientation 175 How to Switch Depth Cueing on off 0 0 0 0c eee 175 How to Display a Cube Front or Side view 000008 175 10 3 nD parameter display 0 cw hoses dee ee bo hee ba eee eee ee 175 IOA mDBid Display lt 4vae2seeodiarti hea end teri sused i acekenees 177 10 5 nD Peak and Integral Display 0 0 00 cece eee 178 Chapter 11 1D Interactive Manipulation cccccccccccecs 181 11 1 1D Interactive Window multiplication 0 000002 aee 181 How to Switch to Window Multiplication Mode 181 11 2 1D Interactive Phase Correction ipese eniri aE E AE ees 183 How to Switch to Phase Correction Mode 00000 183 How to Perform a Typical 1D Interactive Phase Correction 184 How to Set the Phase Pivot Point 0 0 0 0 cee eee 184 How to Perform Default Zero Order Phase Correction 185 How to Perform Interactiv
225. owing features The viewer displays the structure file that resides in the expno of the current dataset If this does not exist the structure file defined by the acquisition parameter CHEMSTR is displayed CHEMSTR can define a full pathname or a filename In the latter case the file is searched for in the directory defined in the User Preferences To set this directory click Options Pref erences select Directory path names enter a directory and click OK If no structure file is found you can open one by clicking File Open in the Molecule Viewer The following structure file types are supported xyz mol pdb CMe OU Es MMI py reSy Cif OD Nay WO Secondary structure elements of proteins backbone cartoons ribbons can be displayed in selectable sizes and colors Mouse button effects Rotate a molecule around the x and y axis by pressing the left mouse button and moving the mouse left right or up down respectively Rotate a molecule around the z axis by pressing the middle mouse button and moving the mouse left right Zoom in or out a molecule by pressing the middle mouse button and moving the mouse up or down RASmol command scripts are supported To send a RASmol command to the currently displayed molecule enter Jmol lt RASmol command gt Here are some example isjmol zoom 400 isejmol ribbon 200 Jmol color ribbon yellow You may create TOPSPIN macros containing RASmol commands Just enter
226. parameter sets for conversion of the basic frequency BF from the list on the right Use the checkboxes to select bruker or user definedparameter sets Use the match field to apply wildcards to the list of parameter sets Use cf to set the basic frequency BF Current basic frequency 300 15 MHZ Bruker defined parameter sets F User defined parameter sets Match PROT ase Insensitive match Figure 16 1 Available parameter sets PROT VT PROTON PROTONI 26 PROTOM256 PROTOMCOMLF PROTOMEXP PROTOMLF PROTOMLFEAP PROTOMMR PROTONMREXP PROTOMMRLF PROTOMT1 PROTOMinto 286 Configuration Automation PY AU Programs my au nya E Figure 16 2 List with two User defined AU programs Note that Bruker AU programs are only shown if the command expinstall has been executed once after the installation of TOPSPIN How to Switch to the List of User defined AU Programs t Click Options User defined in the AU program dialog box How to Switch to the List of Bruker defined AU Programs w Click Options Bruker defined in the AU program dialog box How to Define the AU Programs Source Directory 1 Click Options gt Manage Source Directories in the AU program dialog box 2 In the field AU Programs Add or modify AU program source directories How to Create an AU P
227. pectively of all ranges How to Change Peak Picking Ranges 1 Click the following button button turns green im Change peak picking ranges 2 Put the cursor on one of the edges of the peak picking range The cursor turns into a double headed arrow 3 Left click hold and drag the peak range edge to its new position 4 Optionally repeat step 2 and 3 for the other edge and for other peak ranges 5 Click the green button to leave the Change peak picking range mode How to Pick Peaks in Peak Picking Ranges only Peaks in a peak range are automatically picked when the range is defined If peaks have been deleted from a rang they can be picked again as follows 1 Right click in the data field 2 Choose Pick Peaks On Ranges from the popup menu Alternatively you can enter pp1 on the command line This command can be en tered in Interactive peak picking mode or in the normal display mode How to Delete all Peak Picking Ranges r Click the button in the data window toolbar Or r Right click in the data field and click Delete All Ranges in the popup menu 1D Interactive Manipulation 213 How to Define Peaks Manually 1 Click the following button button turns green ii Define peaks manually A red vertical line will appear in the data window 2 Put the red cursor line at the desired peak and click the left mouse button The peak label will appear at the top of the data window 3 Repeat step 2 for each peak t
228. played in that window Or r Hit the F6 key to activate the next window Repeat that until the desired window is the active window How to Open a New empty Data Window r Click Window New window A1 t w n The new data window will become the active window and will by default cover the entire data area hiding possible existing data windows To open a dataset in the new window drag a dataset from the browser or from the Windows Explorer into the new window or click File gt Open see also chapter 4 3 How to Arrange Data Windows If the data area contains multiple data windows you can arrange them in various ways All the arrange commands arrange the windows left to right and or top to bottom in the order in which the windows have been active The currently active data window will therefore be positioned at the top and or left of the data area To arrange the data windows as a grid 0s Click Window Arrange as a Grid Depending on the number of windows they will be arranged vertically and or horizontally see Fig 13 3 Data Window Handling 243 O x Spectrum ProcPars AcquPars Title PulsFrog Peaks Pojexami1d_13C 2 1 Cobo guest Fajexam2d_HC 1 el ES Fcjexamid_1H 2 0 M pele Spectrum ProcPars n 1j Integrals Molecule Fidi 2 Figure 13 3 To arrange data windows in stack see Fig 13 4 r Click Window Arrange in Stack Fcjexamid_1H 2 1 Clbid gue Title PulsFrog
229. pop up This is a short explanation of the buttons function For example if you hold the cursor over the interactive phase correction button you will see the following A eee Interactive phase correction ph The corresponding command line command in this case ph is indicated be tween square brackets Note that the tooltip also appears in the status bar at the bottom of the TOPSPIN window How to Get Help on Individual Commands To get help on an individual command for example ft The TOPSPIN Interface 43 r Enter ft or r Enter help ft In both cases the HTML page with a description of the command will be opened Note that some commands open a dialog box with a Help button Clicking this button will show the same description as using the help command For example entering re and clicking the Help button in the appearing dialog box Options E Display data in same window Display data in newe window MAMIE exam ad 130 EXPHO PROMO DIF USER opens the same HTML file as entering help re or re How to Use the Command Index To open the TOPSPIN command index rs Enter cmdindex or t Click Help gt Command Index From there you can search for and click any command and jump to the corre sponding help page The TOPSPIN Interface 2 7 User Defined Functions Keys The default assignment of functions keys is described in chapter 2 5 and in the document us Click Help Manuals
230. pup menu offers entries to display the dataset list its prop erties and print the full dataset specification Dataset Handling 6l 4 2 Creating Data How to Create a New Dataset 1 Click File gt New new Ctrl n or Click the button in the upper toolbar Specify the dataset name expno procno dir and user in the appearing dia log box If one or more datasets are open the fields are initialized with the current dataset see Fig 4 10 Click the down arrow of the Solvent box and choose a solvent from the list or type a solvent name Click the down arrow of the Experiment box and choose a parameter set from the list or type a parameter set name 5 Type the dataset title in the TITLE box 6 Click OK 62 Dataset Handling Prepare for a new experiment by creating a new data set and Intializing ts MMR parameters according to the selected experiment type MAME EXPNO PROCNO DIR LISER i Solvent CDCI Experiment Hee current parame TITLE AsliAy AY 300 Automation Cholesterylacetate Figure 4 10 A dataset will be created and initialized with the parameters of the chosen exper iment No fid or spectrum are available yet They can be created by data acquisi tion and data processing respectively 4 3 Opening Data TOPSPIN allows you to open data in several ways from the browser the menu the Windows Explorer or the command line Furthermore data c
231. rent position and geometry e Ifa window type is defined in the layout but not displayed the layout definition is ignored e Multiple data windows are arbitrarily assigned to the available data window definitions How to Swap Data Windows Within a certain layout you can easily swap two TOPSPIN windows with the com mand swin If the data area contains exactly two windows swin simple swaps their position and geometry If it contains more than two data windows swin opens a list from which you can select any window to be swapped with the cur rently selected active window Swapping windows can also be executed from the Window menu Chapter 14 Analysis 14 1 Introduction TOPSPIN offers various data analysis methods including chemical shift measure ment signal to noise calculation and T1 T2 relaxation analysis as described in this chapter Furthermore it offers the following structure analysis tools Multiplet Analysis This allows you to easily define multiplets and deduce chemical shifts cou pling constants multiplicities and connections Daisy TOPSPIN 2 0 and newer This allows you to simulate spectra based on chemical shifts and coupling constants Solids Line Shape Analysis This allows you to simulate and fit calculated spectra to various experimen tal 1D solid NMR spectra Jmol A 3D Structure Viewer for displaying chemical structures 2D molecule structure editor A program for drawing chemical structures
232. respect to a reference integral To do that 1 Right click the reference integral and choose Define as reference from the popup menu This will determine the calibration constant 2 Right click any integral and choose Calibrate by reference This will divide all integrals by the calibration constant setting the refer ence integral to 1 0 Now you can read any other spectrum and calibrate its integrals with respect to the reference integral defined above To do that 1 Read the spectrum 2 Enter int to define the integral ranges if this has not been done yet 3 Click the Integrals tab 4 Right click any integral in the list and choose Calibrate by reference from the popup menu Note that the calibration constant is lost when TOPSPIN is restarted Display the integral list with peaks The integral list in Fig 8 7 shows only integrals However if peak picking has been done the integral list also shows the peaks within each integral range see Fig 8 9 132 1D Display examid_1H 1 1 C bio guest 1 el FES Spectrum ProcPars AcquPars Title PulsProg Peaks Integrals Sample Structure Fia amp Object Integral abs Integra aks Rang Fang F1 porn Intensity HHntegral 1 21807940 16 1 6664 4 rora 860s EHintegral i 20864697 285 1 5943 4 r410 7 ar0 Peak 5 Peak 6 L Peaks EHntegral 4 45009321 70 3 5005 1 F056 7 408 Ed jexamid_1H 1 1 Cibio guest 8
233. rious ways Just right click in side the data window and choose one of the options from the appearing popup menu see Fig 9 16 170 2D Display Larger Smaller Default View From Top From Front F2 From right F 1 shitt To Center Shift To Bottom Properties Files Figure 9 16 How to Rotate a 2D Spectrum in Oblique Mode Click hold one of the following button and move the mouse up down Rotate around x axis amp Rotate around y axis How to Switch between Displaying Positive and Negative levels Click the following multi state button in the lower toolbar 4 Switch between positive negative and both contours 1t Chapter 10 nD Display 10 1 Display Planes of 3D Data 3D data can be displayed as 2D planes or as a 3D cube By default the first F3 F1 plane is displayed see Fig 10 1 The plane orientation and number is shown The cube in the lower left corner graphically indicates which plane is displayed The full 2D display functionality is available see chapter 9 172 nD Display gui l o x M ezam3d 1 1 Cibio guest i 4 F1 ppm 2 Plane 5 4 3 2 F3 ppm Figure 10 1 How to Switch to 2D Plane Display If the 3D cube is displayed you can switch to 2D plane display by clicking one of the following buttons Switch to 2D contour display Switch to 2D image display A Switch to 2D oblique display How to Display various Plane Orientations Click one of the following bu
234. rocessing steps like Fourier transform phase cor rection etc 11 2 1D Interactive Phase Correction Manually acquired spectra can be phased corrected automatically with commands like apk or apks or interactively in phase correction mode 11 2 1 1D Interactive Phase Correction Procedure How to Switch to Phase Correction Mode Click the indicated button in the upper toolbar 2d 3d 4 AMO Tjian or enter ph on the command line The Tab bar of the active data window will be replaced by a toolbar see Fig 11 2 1D Interactive Manipulation 184 examid 1H 1 1 Cobia quest k l O x Ajo 1 R mwas gA a EE 0 00 pivot 1 4508 ppm Phase increment 0 20 ph 0 00 phl Set Pivot Point 10 rel Calculate pho O 5 Figure 11 2 Data window in phase correction mode ae The yellow button indicates that you are in phase correction mode Some buttons will turn green when they are clicked As long as a button is green it is active How to Perform a Typical 1D Interactive Phase Correction For a typical 1D phase correction take the following steps 1 Click hold the button 0 and move the mouse until the until the reference peak is exactly in absorption mode 2 Click hold the button 1 and move the mouse until the entire spectrum is exactly in absorption mode 3 Click the button bij to save and execute the phase correction and return 11 2 2 1D Interactive Phase Correction Details How to Set the Ph
235. rogram 1 Click File New in the AU program dialog box 2 Enter the AU program lines in the edit field of the appearing dialog box 3 Click Save as to store the AU program under a new name 4 You will be prompted to compile the AU program click OK Alternatively you can enter edau lt name gt on the command line to create the AU program lt name gt Configuration Automation 287 How to Edit an Existing AU Program 1 Double click the AU program name in the AU program dialog box or Click the Edit button to edit the highlighted AU program 2 Modify the AU program according to you wishes 3 Click Save to store the AU program under the name shown in the title bar 4 You will be prompted to compile the AU program click OK Alternatively you can enter edau lt name gt on the command line to edit the AU program lt name gt How to Execute an AU Program 1 Select the AU program in the AU program dialog box 2 Click the Execute button Alternatively you can enter lt name gt or xau lt name gt on the command line to execute the AU program lt name gt If the AU program has not been compiled compilation is automatically per formed before the execution starts How to Delete an AU Program 1 Select the AU program in the AU program dialog box 2 Click File Delete or click the Delete button How to Show Comments short descriptions in the AU Program List To switch on off the comments in the AU program l
236. rom the portfolio stored in this dataset Override Plotter saved in Plot Editor If enabled the plotter defined in the Plot Editor layout will be overridden by de plotter defined by the processing parameter CURPLOT How to Plot Data from the Processing guide Printing plotting data can be done from the Processing guide by clicking the Plot Print button If Automatic mode is checked the active data window will be printed as it appears in the screen If Automatic mode is unchecked you will get the dialog box as displayed in Fig 7 1 How to Plot Data with the Plot Editor The Plot Editor can be started from the Plot Editor or from the command line command plot The Plot Editor allows you to create layouts and plot data The complete functionality is described in the online manual which can be opened as 106 Printing Exporting Data follows t Click Help gt Manuals Automation and Plotting TopSpin Plotting How to Print the Integral list 1 Click the Integrals tab of the data window see Fig 7 2 2 Enter print or Ctrl1 p to print it examid 1H 1 1 Cobia quest l 2 x Spectrum ProcPars AcquPars Title PulsProg Peaks Integrals Sample ad amp Object Integral abs Integral rel i Fange Fi from Fange F1 to m integral 1 21786348 44 1 6650 0 Tarz 8 603 Integral 2 20849330 78 1 5934 0 r 410 rari Hntegral 3 45796921 97 3 5000 r056 r405 integral 4 131363188 00 10 0393 0 4 491 6
237. roup Add a new empty dataset group to the list Chose All Group Windows Close all data windows of selected group Process selected Datasets Process selected dataset with serial processing File Properties Show file properties of selected dataset Files Show file list of selected dataset Copy Copy pathnames of selected data to clipboard Figure 4 5 Note that a group not only defines the datasets involved but also their data win dow positions and dimensions and the displayed region of each spectrum The entry Update window bounds amp display regions Dataset Handling 57 The Alias tab Clicking the Alias tab displays the list of user defined alias names for datasets Just right click any entry to define remove or interpret alias names Browser LastS0 Groups Alias s ramicidine taxy Menthial 1H Menthol inadequat Strychnine C1 3 strychnine Cl Sdeptgo Figure 4 6 Define Alias For Data In Selected Window define alias for data in selected window List Selected Alias Show selected data name expno etc List All Aliases Show all data names expnos etc Remove Selected Aliases Remove selected aliases from list List Available Alias Commands Show available alias commands Figure 4 7 How to Open the Browser in a separate window The browser can be opened in a separate window as follows r Click Options Preferences set click Window settings and c
238. rrent dataset 1S em TE apk sref auEODOLoL All entries in a macro file must be written in lower case letters In TOPSPIN 1 3 and newer a macro may contain Python commands Any line in a macro that starts with py executes a Python command An example of such a macro is re examid 13C 1 1 Cibio guest efp PY gt NEWWIN open new window re examia 1H T 1 CHDIO guest efp py gt x INPUT_DIALOG py gt if x None EXIT py gt y 2 int x 0 py gt MSG done y str y Note that commands like NEWWIN INPUT_DIALOG MSG and EXIT are Bruker defined whereas x and if are original Python commands Once created a macro can be executed by entering its name on the command line AU Programs An AU program may contain TOPSPIN commands AU macros and C language statements It can be created with the command edau A simple AU program which performs the e fp command on a series of dataset expno s is include lt lib util h gt User Extensions 335 int first max char string 80 first expno GETINT Enter first expno to process first max 10 GETINT Enter number of expnos max WPAR tmpmefp proc expno first TIMES max RPAR tmpmefp proc EFP IEXPNO END DEXPNO DELPAR tmpmefp QUITMSG multiefp finished Note that TOPSPIN commands like EFP and RPAR and AU macros like IEXPNO are written in upper case letters whereas C language statemen
239. rver export conf Now a running TOPSPIN on this system can be accessed from any computer in the network Identify the port number To identify the TCP IP port number used by TOPSPIN 304 Remote Control 1 Start TOPSPIN 2 Enter hist 3 Look for the line To connect to this TOPSPIN use host lt xxxx gt port lt yyyy gt in the upper part of the dialog window The number at the end of this line lt yyyy is the desired port number which must be used to set up the local system see chapter 18 2 2 By default this 1s port number 5500 Only if this port is already used by a program other than TOPSPIN a different port is used Export data directories 1 Log in on the remote system as Administrator windows or root Linux 2 Edit the file lt t shome gt prog server export conf By default this file contains the lines EXPORTMODE ALL SXWINNMRHOME This first entry should be left as it is The second entry exports the data direc tory lt tshome gt data for remote access By default that this is the directory that contains the Bruker example datasets 3 Add the data directories that you want to export for remote access e g CEDO D nmr for the directories C bio dataandD nmr dat a respectively Please use a separate line for each entry 4 Save the file export conf and close the editor 18 2 2 Setup the local system Define the remote system 1 Log in on the local system 2 Start TOPSPIN 3 Cli
240. s Table header Column header foreground Column header background P Foreground P Background F Selection Restore detaults Figure 19 4 Set the desired colours and spacings 4 Click OK Note that table colours and spacings can also be change from a table To do that right click any table entry and choose Table properties User Preferences 321 19 1 4 Changing Lines How to Create Thick Lines on the Screen To create thick double width lines for high resolution display or screendumps 1 Click Options Preferences set 2 Click Spectrum in the left part of the dialog box 3 Enable the entry Use thick lines 4 Click OK How to Create Thick Lines on the Printer To create thick double width lines for high resolution display or screendumps 1 Click Options Preferences set 2 Click Printer in the left part of the dialog box 3 Enable the entry Use thick lines 4 Click OK 19 1 5 Changing Fonts How to Change All Fonts of the Topspin Interface 1 Click Options Preferences set 2 Click Fonts Dialogs Icons in the left part of the dialog box 3 Set the entry Change size fonts listed above by points You can enter a positive or negative number 322 User Preferences Fig 19 5 shows an example of increasing the font sizes by 4 points Fonts Dialogs fleons Menu font Dialog plains Plain 16 Change Dialog window tont Dialog plains Plain 12 Change Command l
241. s spectrum fid parameters etc of the same dataset How to Reopen a Dataset in a Second Third etc Window 1 Select activate the desired dataset 2 Click File Reopen reopen Multiple data windows with the same dataset are indicated with a number in square brackets e g 1 in the title bar see Fig 8 2 1D Display 111 examid_1H 1 1 Cibio guest 7 o x Spectrum ProcPars AcquPars Title PulsProg Peaks integ ij gt examid_1H 1 1 Cibio guest 2 spectrum ProcPars AcquPars Title PulsProg Peaks integ j gt o x Spectrum ProcPars AcquPars Title PulsProg Peaks Inte cs 4 gt oE 23 oa 4 iIndow function LEB Hz 0 30 Feference l C njirinr i E H jl p Figure 8 2 How to Rescale or Shift one Dataset in Multiple windows Display buttons like and only work on the active data window The same counts for the keys Alt PageUP and Alt PageDown However when used with the control key they work on all windows for example o gt Hit Ctrl 7 Ctrl1 Alt PageUp or Ctr1 Alt PageDown 112 1D Display 8 3 Changing the Display of a 1D Spectrum or FID TOPSPIN offers buttons to scale or shift the spectrum vertically and horizontally How to Change the Vertical Scaling of the FID or Spectrum r Hit one of the following the keys e Alt Page
242. s it along with the 2D spectrum Clicking Baseline at Bottom or Baseline at Center allows you to put the projec tion baseline at the respective positions Alternative ways to calculate display projections are 0S Right click on a 1D dataset in the browser and choose Display As 2D Projection or r Click Processing Calculate projections proj This will open the dialog box shown in Fig 9 12 164 2D Display amp f2projp Options O Calculate positive projection CO Calculate negative projection Calculate Sumi O Calculate disco sur Read positive projection Read negative projection CO Update rowsicols fram display Required parameters Projection sum af Display projection First row col Last rowcol Destination PROMO Figure 9 12 From here you can calculate positive negative sum and disco projections and either show them with the 2D spectrum or display them in separate data window as a 1D data For more details on the corresponding commands as shown in the header of the dialog box please refer to the Processing Refer ence Manual How to Switch on off the Grid display r Click the following multi state button in the upper toolbar HH Switch between no grid axis aligned grid and fixed grid gr Fig 9 13 shows an example of axis aligned grid display 2D Display 165 exam2d_HC 1 1 Cibio guest Sle Spectrum ProcPars ACGUP ars Title PulseProg
243. s it can be useful to sent Bruker a stack trace about a possible cause You can create a stack trace as follows 1 Move the cursor into the TOPSPIN startup window 2 Under Windows hit Ctrl Break Ctrl1 Pause Under Linux hit Ctr1 Control backslash 3 Copy the appearing text into a text file Trouble Shooting 51 3 2 5 Store complete log A complete set of TOPSPIN and ICON NMR log files can be made This contains all possible log files and is the most complete debugging information 3 2 6 Under Windows 1 Double click the Utilities icon on the desktop 2 In the appearing window 3 Double click the Miscellaneous folder icon 4 Under Windows double click the savelogs command Under Linux hit Ctr1 Control backslash 5 Send the file Llogfiles tar gz as attachment to the Bruker Service 3 3 How to Show or Kill TOPSPIN processes To show the currently running TOPSPIN processes enter the command show or kill on the command line A list of processes will appear showing the process command dataset etc ie Active commands and processes x Command Data Module Process Id examed HO11 2220 lead Details sort modules Kill Close Figure 3 2 Fig 3 2 shows a list with one process command xfb To kill a process select it in the list and click the button Kill The command show all or kill all work like show and kill except that they also show TOPSPIN system processes Note that killin
244. s the spectrum 22 Getting Started 2 Right click and choose Display Properties in the popup menu 3 Check the desired items and click OK Please note that the selected items are only shown 1f they are available For exam ple peaks and integrals are only shown if peak picking and integration have been performed respectively see also chapter 11 The number of displayed digits for the integral and peak labels can be set in the User Preferences click Options Preferences Spectrum 1 9 How to Display Projections 1D Spectra with 2D Spectra To display projections or 1D spectra in tandem with a 2D spectrum 1 Open a 2D spectrum 2 If no projections are shown click the 3 button in the upper toolbar or enter pr on the command line 3 Move the cursor into the F1 or F2 projection area 4 Right click and choose one of the options With External Projection an existing 1D spectrum can be read This can be a regular 1D spectrum or a 2D projection that was stored as a 1D spectrum With Internal Projection the positive projection can be calculated and displayed Alternate way to calculate projections 1s the following us Click Processing Display Projections projd or 0S Right click on a 1D dataset in the browser and choose Display As 2D Projection 1 10 How to Superimpose Spectra in Multiple Display TOPSPIN allows you to compare multiple spectra in Multiple Display mode To enter this mode click the i butt
245. se and allow you to execute TOPSPIN commands handle NMR data and parameters generate graphics and interact with the TOPSPIN user interface via di alogs windows etc To create a Python program enter the command edpy select a file and insert your Python statements Graphics and interface features pro grammed in Python look and work the same as regular TOPSPIN features For details on Python programming click Help gt Manuals Programming Manuals Python Programming The examples mentioned there like pycmd1 are delivered with TOPSPIN Just enter their names on the command line to execute them The Python dialog window is also available from the TOPSPIN menu us Click File gt Open and select Open other file Python program 1 18 How to Automate Data Acquisition TOPSPIN provides special user interfaces for automation walk up bio molecular experiments etc To open these interfaces t Type iconnmr or click Spectrometer gt ICONNMR Chapter 2 The TOPSPIN Interface 2 1 The Topspin Window The TOPSPIN window consists of a data area a data browser toolbars and a menu bar Note that the browser can be inactive hit Ctr1 d or displayed as a separate window Fig 2 1 shows the Topspin window with two data windows in the data area and the browser as an integral part 30 The TOPSPIN Interface l minimize maximize title bar button button menu aum bar FA Bruker TOPSPIN 2 0 on NMR datastation as Jos van
246. sed examed HO 3 1 Cobia quest Sele SHE S Rae t 4 AL E E E Ei 7 Ss ts dy Blut A Mt i gt F2 ppm Figure 12 10 Multiple display with a 1D spectrum superimposed on a 2D spectrum 230 2D Interactive Manipulation a The yellow button indicates that the data window is in multiple display mode a Some buttons will turn green when they are clicked As long as a button is green it is active The browser in multiple display is split in two parts see Fig 12 11 The addition al lower part shows e which datasets are displayed in the active data window e which datasets are selected they are highlighted Y exarn2d_ H A og a E Ej E B exam2d_CH 1 1 Cibio guest IJ exam2d_HC 1 1 Cibio guest Figure 12 11 How to Align Multiple 2D Spectra 2D spectra in multiple display can be individually shifted To do that 1 Select one of the spectra in the lower part of the browser 2 Click hold the f button and move the mouse Fig 12 12 shows a region of two comparable 1H 13C inverse 2D datasets which are shifted relative to each other Clicking the KE button resets individual scaling and shifting 2D Interactive Manipulation 231 exam2d HC 3 1 Cobio guest i R it 4A BE E Eil 4 ts fo Hat 4S AB F2 ppm
247. selected dataset replaces the contents of the currently selected active win dow If no data window was displayed a new one will be created Alternatively you can first create a new window by clicking Window New Window Al t w n and then open a dataset from the file browser in that window The file browser can also be opened by entering reb on the command line How to Open Data from the Browser TOPSPIN has data browser which by default displays the top level data directory lt dir gt with Bruker example data You can add your own data directories local or remote as follows 1 Move the cursor into the browser area 2 Right click and choose Add New Data Dir in the popup menu 3 Enter the desired data directory lt dir gt and click OK Your data directory will now appear in the browser In order to display data from the Browser proceed as follows 1 Expand your top level directory lt dir gt in the browser to the level of the data name expno or procno 2 Select the desired item and drag it into the data area How to Define Alias Names for Data 1 Open the dataset for which you want to define an alias name 2 Click the Alias tab at the top of the data browser 3 Right click in the browser and choose Define alias for data in selected window Alternatively you can enter the command dalias on the command line Getting Started 21 How to Open Data in Archive Data Directories Topspin 2 0 and newer allows
248. splay 141 Please selectthe components to be displayed together with the spectrum cif availabley x Cursor information Title Status parameters Acquisition parameters integrals x integral labels x Feak labels k Feak annotations Multi plets Show data points Electronic Signature h Molecular Structure Figure 8 14 Here you can check or uncheck the spectrum components that you want to be dis played in the data window Note that the Display Properties dialog box can also be opened from the View menu How to Superimpose the Cursor Information To superimpose the cursor information on the spectrum 142 1D Display 1 Right click in the data window and choose Display Properties dopt 2 Check Cursor information in the appearing dialog box and click OK How to Superimpose the Title on the Spectrum 1 Right click in the data window and choose Display Properties dopt 2 Check Title in the appearing dialog box and click OK How to Superimpose the main Status Parameters on the Spectrum i 1 Right click in the data window and choose Display Properties dopt 2 Check Status parameters in the appearing dialog box and click OK How to Superimpose the Integral Trails Labels on the Spectrum 1 Right click in the data window and choose Display Properties dopt 2 Check Integrals and if desired Integral labels in the appearing dialog bo
249. splay 155 appear Display Properti Edit Contour Levels Save Display Region To Restore Display Region From Params Fi File Properties Square Layout Omnia Files Figure 9 4 Here you can select various display properties region setting and file properties If you choose Display Properties a dialog box see Fig 9 5 will appear 156 2D Display Please select the components to be displayed together with the spectrum if available Cursor information Title Status parameters Acquistion parameters Integrals Integral labels Peak labels Contour levels bar Show projections Electronic Signature Molecular Structure Visible projections CFA O F2 Figure 9 5 d b b bh b amp O b O K F1 F2 Here you can set various display options including parameter integrals peaks contours projections and electronic signature The number of displayed digits for the integral and peak labels can be set in the User Preferences click Options gt Preferences Spectrum 2D Display 157 9 4 Using the Tab bar The 2D data window is a tabbed pane This means its contents depends on the cur rently active tab in the Tab bar The individual tabs are basically the same as for 1D display see chapter 8 4 There are however some differences which are dis cussed below How to Set Processing Parameters us Click the ProcPars tab edp The 2D processing parameter editor
250. square 2D layout 152 square brackets 31 42 110 115 sref command 93 97 196 235 stacked multiple display 202 Start button 68 startup actions 311 status line font 325 Status parameter change 88 display 91 142 display 1D 116 117 stop an acquisition 264 stop command 264 266 277 store 2D contour levels 167 structure file 137 Structure tab 136 sum spectrum in multiple display 201 superimpose 1D spectra 198 cursor information 141 electronic signature 143 integral trails labels 142 main status parameters 142 peak labels 142 spectra 22 title of a dataset 142 SW parameter 265 swap data windows 247 sweep width 265 swin command 247 switch to the last 2D data 32 to the last 3D data 32 T T1 calculation 16 T1 T2 Relaxation 253 tl guide command 253 T2 calculation 16 Tab bar 1D 110 115 2D 150 157 configuration 115 316 font 323 usage 115 Tab key 87 91 tabbed pane 157 316 TCP IP port 303 temperature unit window 246 Terminal Window 18 time domain signal 27 title bar 109 110 149 240 241 244 245 246 287 title file 118 title of a dataset 21 58 61 118 142 275 318 Title tab 118 tojdx command 26 74 toolbar 1D 181 2D 215 configuration 328 extension 339 for acquisition 263 icons 340 342 of the data window 22 138 of the FID display window 277 tips 42 usage 31 tooltips 41 42 top level directory 20 53 60 Topspin color schemes 319 data area 69 72 fonts 322 help 41 installation 283 installation
251. ss 13C DEPTIS5 AY 300 Automation Cholesterylacetate dept45 13C DEPT45 Av 300 Automation Cholesterylacetate deptgo 13C DEPTSO AY 300 Automation Cholesterylacetate Fqigs0 WsCl gt AY 300 Automation Cholesterylacetate Figure 4 13 Note that the command re1 also opens the dialog shown in Fig 4 13 showing the available EXPNO s under the current dataset Similarly rep1 shows the available PROCNO s under the current dataset EXPNO How to Open Data from the Topspin menu 1 To open a dataset us Click the lt j button in the upper toolbar Or us Click File Open open Ctr1 o see Fig 4 14 Dataset Handling 67 File Edit View Processing Analysis Mew Ctrl M Oper Ctrl O Reopen Close Ctrl Y Close All Save Ctrl 5 Print Ctrl F Export gend To Run Delete Figure 4 14 2 In the appearing dialog box see Fig 4 15 amp Open re Options Open NMR data stored in special formats OQ Open other file Required parameters Browser type RE Dialog ve Figure 4 15 a Select the option Open NMR data stored in standard Bruker format b Select the browser type RE Dialog c Click OK 68 Dataset Handling 3 In the appearing dialog box see Fig 4 16 Options Display data in same window O Display data in new window MAME examid_ Tac EXPMO PROC DIR USER Figure 4 16 a Specify the dataset name expno etc b Cl
252. tal scaling to full spectrum hr Al Display the entire spectrum baseline position and intensity scaling are adjusted if necessary a11 1 Zoom in to the center spectrum or left edge FID of the displayed re 34 The TOPSPIN Interface gion increasing the horizontal scaling zi Zoom in out smoothly Zoom out from the center spectrum or left edge FID of the displayed region decreasing horizontal scaling zo iE Exact zoom via dialog box zx l Toggle interactive zoom mode When switched off interactive zoom ing only selects a horizontal region baseline position and intensity scaling remain the same When switched on interactive zooming draws a box selecting the corresponding area Undo last zoom 21 il Retain horizontal and vertical scaling when modifying dataset or changing to different dataset Global button for all data windows keep Buttons for horizontal shifting e e Shift to the left half of the displayed region s1 Smoothly shift to the left or to the right gt Shift to the right half of the displayed region sr W Shift to the extreme left edge of the spectrum s10 Shift to the extreme right edge of the spectrum sro Buttons for vertical shifting f f 4 Shift the spectrum baseline to the middle of the data field su Smoothly shift the spectrum baseline up or down The TOPSPIN Interface 35 4 Shift the spectrum baseli
253. talic ProcPars menus buttons icons to be clicked are in times bold italic fid filenames are in courier name any name which is not a filename is in times italic File directory Conventions lt tshome gt the TOPSPIN installation home directory User Action Conventions r a single user action 1 the first action of a sequence 2 the second action of a sequence De CLC a the first action of a sub sequence 16 Getting Started b the second action of a sub sequence C etc 1 2 TOPSPIN Overview Functionality TOPSPIN is an integrated software package for Displaying NMR spectra Printing and plotting spectra Exporting displays and plots in various graphics and metafile formats Importing NMR data from files of various formats Archiving spectra in various formats such as JCAMP DX and ZIP E mailing data Processing 1D 6D fids and spectra window multiplication various trans forms Fourier Hilbert DOSY phase correction baseline correction inte gration peak picking linear prediction smoothing adding spectra etc Displaying multiple superimposed spectra 1D and 2D Simulating 1D and multi dimensional fids given a pulse program and a spin system virtual spectrometer nmr sim Calculating T1 T2 relaxation times Fitting peaks with Lorentzian and Gaussian line shape models deconvolve overlapping peaks Multiplet analysis Automatic 1D 2D and 3D peak picking Automatic 1D 2D and 3D i
254. tches to interactive integration or peak picking mode as chosen above Here 256 Analysis you can define the ranges or peaks to be included in the relaxation analysis Then use button to export regions peaks to Relaxation Module and quit the inter active mode Relaxation Window Switches the 1D data window to relaxation analysis mode see Fig 14 6 Relaxation titest 1 1 Chiodi jos is e l s 00m OP taxol i Peak iat e227 ppm Current Peak Pra 4s tort 19 4 3 Peak at 7 221 ppr P 2 211e 000 0 1 216e 000 Ti 194672 3 692e 003 Figure 14 6 and performs a default fitting By default this is one component T1 intensity fitting Function type uxnmrt for peak 1 If the dataset was already fitted the previous type of fitting is performed The fitting curve is displayed in the data section and a Brief Report is shown in the parameter section If this default fit ting is appropriate you can view interpret and print the results as described be low If not you can perform the desired fitting as described below Perform Fitting and Calculate the Relaxation Time Analysis 25 Depending on the experiment you can perform the appropriate fitting as fol lows 1 Select a Fitting type Intensity or Area Either every point reflects the intensity of the biggest peak in the defined integral range or the integral itself Both of them can be used but depending on the experiment one of them usually give a
255. ters 116 117 peak list and peak ranges 214 phase correction 2D 219 222 228 processed data 74 processed data as pseudo raw data 74 pulse program 119 136 sum or difference spectrum 201 title of a dataset 118 scale 1D integrals 193 1D spectrum 112 2D spectrum 150 3D cube 175 individual spectra in multiple display 22 198 202 row column in 2D phase 220 scaling factor of integrals 194 scan planes of 3D data 173 rows columns in 2D 231 screen dump 23 108 screenDump wmf file 107 scroll bar 87 91 search criteria 78 data 78 field in the parameter editor 87 90 result window 79 select AU program 287 color scheme 319 data 53 data in multiple display 199 200 data window 241 default printer 283 expno procno combination 65 first expno procno 65 folders in the browser 57 I 13 font 323 324 325 integral regions 188 191 lock signal color 318 multiple datasets 65 multiple folders 57 58 peaks in 2D phase correction 216 plot layout 104 printer 104 remote system 305 row column in 2D phase 219 spectra in 2D multiple display 230 spectrum color 317 spectrum print color 318 Topspin window 247 selective excitation 27 semi automatic peak picking 213 processing 94 sensitivity of the GS slider 273 of the mouse 185 191 208 221 serial command 98 serial processing 98 Server ID 305 set 1D acquisition parameters 117 2D acquisition parameters 157 2D processing parameters 157 colors for multiple display 205 contour levels 1
256. text Print by the following lt html gt lt font size 10 gt lt font color O00BFO0 gt Print lt br gt Now lt font gt lt html gt then the new text Print Now is displayed in green the color to be specified in RGB hex code with 10 points font size Also Now is display below Print due to the html lt br gt break line tag Note that e The Close button and Tips switch are automatically created You don t need to specify them e The TOGGLE button is typically but not necessarily used to call another button panel In this example it calls the panel bproc2d If TOGGLE_BUTTON is specified without a value 1 e the entry is User Extensions 339 TOGGLE_BUTTONE instead of TOGGLE_BUTTON lt action text the corresponding button is not shown in the panel e Items must be separated with the character button items with e A V followed by end of line continues an item on the next line e Tooltips may use html tags for text formatting e Commands may be specified as single commands like em or as composite commands like em nft npk Note that in the latter case the commands must be separated by n e When the bpan lt name gt command comes up with an error message care fully check the syntax of your cmdpanel file A common mistake is to spec ify the button items incorrectly With the keyword PAN_LAYOUT you define the number of rows and columns and the number of items will become rows cols Al
257. the entry Show ased parameter selection with eda and click OK How to Display Acquisition Status Parameters r Click the following button S Show acquisition status parameters Note that the command dpa opens the acquisition parameter editor and automat ically shows the status parameters How to Get Probehead Solvent dependent Parameters r Click the following button lg Set probehead solvent dependant parameters getprosol1 Probehead and solvent dependant parameters can be set up with the command edprosol 92 Parameter Handling How to Change Acquisition Data Dimensionality r Click the following button 123 Change data dimensionality This changes the number of parameter columns and value of the acquisition pa rameter PARMODE How to Set Lock Parameters Enter the command edlock and set the lock parameters in the appearing dialog box For a detailed description of edlock please refer to the Acquisition Refer ence manual or enter edlock on the command line How to Set Routing Parameters Enter the command edasp and set the routing parameters in the appearing dialog box For a detailed description of edasp please refer to the Acquisition Refer ence manual or enter edasp on the command line Chapter 6 Data Processing 6 1 Interactive Processing Interactive processing allows full control over the processing sequence However it requires detailed knowledge about the required parameters see chapter 5 1 an
258. the fractions of the maximum windows sizes In the respective dimension Width of window Height of window offset to previous window Y offset to previous window Figure 4 12 5 Here you can specify the data window sizes and offsets as fractions of the maximum window sizes 6 Click OK to close the dialog box How to Open Data from the Browser In the browser r Left click hold a data name expno or procno and drag it into the data area The data will be displayed in a new data window or Left click hold a data name expno or procno and drag it into an open data window The data will replace the currently displayed data or Left click hold a data name expno or procno and drag it into an empty data window created with Alt w n or Left click hold a data name expno or procno and drag it into a multiple dis play data window The data will be superimposed on the currently dis played data or Right click a data name expno or procno and choose Display from the pop up menu the data will be displayed in the current data window or Right click a data name expno or procno and choose Display in new win Dataset Handling 65 dow from the popup menu the dataset will be displayed in a new data win dow or Hold the Ctrl key and left click several datasets to select them or hold the Shift key and left click two datasets to select these two and all in be tween Then right click one of the selected datasets and c
259. ties Files If the spectrum is displayed the files in the procno subdirectory are shown If the Fid is displayed the files in the expno subdirectory are shown r Select a file and click Open to view its contents Note that this only makes sense for ascii files How to List Open the current Dataset Files in the Windows Explorer To list the current dataset files in the Windows Explorer 1 Click Files gt Run 2 Select Open file explorer exp1 in the appearing dialog box see Fig 4 25 3 Click OK Alternatively you can enter the command exp on the command line The Win dows Explorer will be opened showing the processed data files the files in the procno directory of the current dataset Under Linux a Web browser like KDE Konqueror or Gnome Mozilla will be opened To open a file t Double click the file or right click the folder icon and choose Open Dataset Handling 83 Options O Open File Explorer OQ Open Command Prompt Shell O Serial Processing CO Execute AU Program O Execute Python Program O Execute Macra Start TopSpin Text Editor Figure 4 25 If TOPSPIN data area contains no datasets the exp1 command opens the Explorer showing the users home directory When entered on the command line exp1 can also be used with the argument top to open the TOPSPIN installation directory home to open user home directory or with an absolute pathname to open that di rectory Chapter 5 Parameter H
260. tive Reactivate All Invisiblesnactive Buttons Change Icon Size Change Toolbar Offset Hide Toolbars type SHIFT ESC to reset Print Seso0ciated Command Figure 20 4 The button definitions are stored in the file toolbar_user prop which resides in the subdirectory userde fined of the user properties directory To locate this directory enter the TOPSPIN command hist A dialog box will show the contents of the history file Near the top of this file you will see an entry User properties directory For icon image buttons the formats gif jpg jpeg and png are sup ported Standard TOPSPIN toolbar icons have a size of 16 16 pixels If your own icons have a different size they are automatically rescaled and displayed at the standard size Adding User Defined Menus to the Menubar The menubar at the top of the TOPSPIN window can be extended with user defined menus They can be assigned to any TOPSPIN command macro AU program or Python program They are specific for the dimensionality of the active dataset To create a user defined menu take the following steps 1 Open a dataset of the desired dimensionality 2 Right click at an empty area of the menubar User Extensions 343 3 In the appearing popup menu click User_defined Menus User Defined Menus Change Wenu Font Define Right Click Action Hide Wenubar type SHIFT ES to reset 4 In the appearing dialog box see Fig 20 5 a Click Add Menu a
261. tive PIOcessin erie Rolie dhe de SAR Saree Sheed e ae es 93 How to Process Data with Single Commands 93 How to Process data with Composite Commands 94 6 2 SemiaautomiaticxProcessing 5 ud oa eWs wanes Setee tae ae he a 94 How to Use the 1D Processing Dialog 2 000005 94 How to Use the Processing Guide in Automatic mode 95 How to Use the Processing Guide in Interactive mode 97 6 3 Processing Data with AU programs 2 0 0 0 0 ccc eee ees 97 6 4 Serial Processing using Python programs 0000s 98 Printing Exporting Data s i4 a6 ise obec toe be oe eee Jase 84 6 103 hr Pun ng plottins Datisrersdiess serenan ee dawa tei odeae ates 103 How to Print Plot from the Menu 0 0 0 eee eee 103 How to Plot Data from the Processing guide 04 105 How to Plot Data with the Plot Editor 284 105 How to Print the Integral list 0 0 0 0 00 eee eee ee 106 Howto Print the Peak SEa oa ecc cohen baw tee eh eee eee 106 dee Eponos Datas 0aradeans rre ead ou Se owen eee eee 107 How to Copy data to Other Applications 000 107 How to Store Export a Data Window as Graphics File 108 TD DISD Ay 3 256 855 kot eR auiiele eto hap ws Ae eee S 109 Sh TEID Data WindOws cos oon oie nd s eaen Bees ou eae sheets o on 109 8 2 Displaying one Dataset in Multiple windows
262. trometers 16 283 axis units 33 139 161 197 236 B background of a data window 319 Backspace key 35 backward peak picking 213 baseline correction 1D 93 205 mode 32 205 bem command 208 bias correction 190 191 bio molecular experiments 28 bnmr command 336 bnmrsel command 336 bpan command 337 browser 29 30 38 53 64 font 324 in multiple display mode 200 230 Bruker AU programs 27 286 data format 19 25 26 67 71 81 example datasets 20 60 BSMS control panel 271 BSMS display window 246 bsmsdisp command 271 C calibration 93 1D interactive 196 2D interactive 235 mode 32 196 235 cf command 19 47 281 282 283 chemical shift 202 chemical shift distance 1D 250 2D 237 CHEMSTR parameter 137 C language 27 97 334 335 clevels file 168 clipboard 23 38 close active data window 245 lock display window 271 the active data window 38 close command 38 cmdhist command 36 cmdindex command 43 cmdtab_user prop file 44 collapse a data directory 53 58 color scheme 318 colors of data objects 317 of the lock display 318 on the printer 318 command definition 44 dialog box 85 help 41 index 43 line 35 36 326 command line commands 264 focus 35 38 font 325 history 35 36 preferences 326 resize 327 usage 35 Command Prompt 18 282 compile AU program 286 287 components of a spectrum 23 composite commands 94 configuration commands 19 customized 283 default 283 directory 283
263. ts like are written in lowercase letters Once created an AU program can be executed by entering its name on the command line For more information on writing AU programs t Click Help gt Manuals Programming Manuals AU programming 20 4 Python Programs A Python program may contain TOPSPIN commands User Interface functions and Graphic functions It is created with edpy The Python program below reads a region of the real part of a spectrum and the corresponding region of the imaginary part and displays both The simplest form of DISPLAY_DATALIST is used from TopCmds import import math region 80 72 define region in ppm open testdata don t display testdata exam1d_13C 1 1 c Bruker topspin guest 336 User Extensions RE testdata n read real and imaginary points of the region reals GETPROCDATA region 0 region 1 imags GETPROCDATA region 0 region 1 data const PROCDATA_IMAG if reals None or imags None EXITQ set up list of data to be displayed and respective axis info list dataList reals imags display the data in the list DISPLAY_DATALIST dataList For more information on writing Python program r Click Help gt Manuals gt Programming Manuals Python programming 20 5 Button Panels A button panel is a window with user defined buttons for executing TOPSPIN com mands AU programs Python programs or macros It appears as an integral p
264. ttons 12 Show F1 F2 planes nD Display 173 23 Show F2 F3 planes 31 Show F3 F1 planes How to Display various Plane Positions numbers Click one of the following buttons Show the next plane Show the previous plane t Scan planes smoothly E Enter the exact plane number This will open the dialog shown in Fig 10 2 Here you can specify the desired plane number as well as switch to a different plane orientation Valid plane indexes F3 1 2048 4H 6 120 111 ppm F2 1 128 413C 56 91 17 09 pom F1 1 256 14H 5 12 0 11 pom Selectthe visible plane C F2 F3 rn F1 F3 F2 1 O F1 F2 Fa ooo Use pom for plane selection Figure 10 2 174 nD Display 10 2 3D Cube Display Mode How to Display the 3D Cube Click the following button ql Show 3d cube see Fig 10 3 E exams 2 1 Cibo guest Sele Spectrum ProcPars AcquPars Title PulseProg Peaks Integrals Sample Structure Fid Acqu F3 ppm Figure 10 3 How to Rotate the 3D Cube Click hold one the following buttons and move the mouse up down a Rotate cube around x axis Rotate cube around y axis 7 Rotate cube around z axis nD Display 175 How to Scale Up Down the 3D Cube 1 Right click inside the data window 2 Choose Larger or Smaller from the popup menu see Fig 10 4 How to Reset the Cube Size and Orientation Click the following button R Reset to default s
265. ttons Menus and Commands 327 How to Hide the Upper and Lower Toolbars 327 How tozHide the Menubat e esns renye San Rost hae eee eee seek 328 How to Disable Remove Toolbar Buttons 0 0 328 How to Disable Remove Menus or Commands 329 How to Re enable a disabled Command Menu 331 How to Re enable All Commands Menus 04 331 19 4 Resizing Shifting Toolbar Icons 0 eee eee 331 How to Change the Toolbar Icon Size 00000005 331 How to Shift Toolbar Icons to the Right 331 19 5 Defining Source Directory for Programs Lists etc 332 User Extensions lt iii20 2 a 4c cs tot aws Rear ieaa swat wedi 333 20 User NOteDOOK Sotabturs dis oa dts ee dwetee een nee enes cet eeeos 333 2023 MICOS i oA te Sire acs ee a ia eth aia lec a ete greeter a ae eA aah Bene ee 334 20 3 ACPO MS og iG ate nase ape is ahs 4 eR ee ea oe 334 204 Python Programs s esperen ba pao a ee ek ho ada 335 20S Buton anelss d a setae eet eat outs mes aM r eae at aha 336 20 6 Adding User Defined Buttons to the Toolbars 339 20 7 Adding User Defined Menus to the Menubar 342 20 8 Adding User Defined Guides 0 0 0 0 cece es 344 Chapter Getting Started 1 1 Document Conventions Font Conventions abs commands to be entered on the command line are in courier bold i
266. tus parameters 87 91 sum difference spectrum 201 superimposed 1D spectra 198 I 6 superimposed 2D spectra 228 y axis 33 139 zipped data 25 display properties 22 distance measurement 1D 250 2D 237 mode 32 double headed arrow 240 251 Down Arrow key 35 39 dpa command 117 dpp command 88 91 116 drag amp drop data 69 72 E eda command 88 89 117 157 edasp command 92 117 edau command 27 98 284 286 334 edcpul command 119 edit AU program 287 commands 35 contour levels 166 integral ranges 191 pulse program 119 signal noise regions 252 title of a dataset 118 Edit menu 31 edlev command 150 166 edlock command 92 edmac command 27 334 edp command 24 85 86 116 157 edprosol command 91 edpy command 28 335 edti command 118 ef command 94 97 efp command 94 278 em command 24 93 email data 26 empty data window 64 enable disabled commands 331 menus commands 327 Enter key 39 55 equidistant sequence of levels 166 Esc key 35 execute AU program 284 287 macro 27 334 Python program 28 exit command 38 45 expand a data directory 39 data directory 20 53 data directory in the browser 58 individual spectra in multiple display 203 spectrum 26 expand a region 21 experiment time 265 expinstall command 19 47 264 281 282 283 284 expl command 68 82 83 146 Explorer 68 82 146 expno 61 65 68 74 144 exponential baseline correction 207 window multiplication 93 94 export data 23 108 expt command
267. uttons Buttons of the upper or lower toolbar can be disabled or removed as follows 1 Right click a toolbar button 2 Choose one of the entries t Make this button invisible to remove the button from the toolbar t Make this button inactive to disable the button it will appear greyed To restore the complete toolbars click t Reactivate all invisible or inactive buttons to restore the default toolbar How to Disable Remove Menus or Commands By default all existing TOPSPIN commands can entered from the menu and or from the command line You can however selectively disable remove commands or menus This is typically done by system administrators who want to disable certain functions for standard users Open the Menu Configuration table as follows 1 Click Options Preferences set 2 Click Fonts Dialogs Icons in the left part of the dialog box 3 Click the Change button of the entry Disable Enable menus and commands The table consists of the following columns You can disable remove e Menus e g Options to be found in the column Menu e Sub menus e g Options gt Administration tools to be found in the column Menu e Menu entries e g Options Preferences to be found in the column Description e Commands e g set to be found in the column Command Note that in this configuration table each menu entry corresponds to a certain command In the TOPSPIN menu most commands are indicated in square brackets beh
268. ve the mouse until the red line coincides with the first point of the spectrum 3 Repeat step 2 with the buttons B C and D until the red line coincides with the entire baseline of the spectrum How to Perform Exponential Baseline Correction 1 Click the following button button turns green Perform exponential baseline correction A red horizontal line will appear as well as the equation describing the ex ponential function f x A B exp C x 2 Click hold button A and move the mouse until the red line coincides with the first point of the spectrum 3 Repeat step 2 with the buttons B and C until the red line coincides with the entire baseline of the spectrum How to Preview the Baseline Corrected Spectrum Before actually performing the baseline correction you can preview the result by displaying the difference between the uncorrected spectrum and the red correction line To do that 1 Click the following button button turns green i Preview corrected spectrum show difference The corrected spectrum will be displayed in red 2 If the baseline is correct click the HI button to save the correction If fur ther correction is needed click the rag button to show the original spectrum and the red correction line 208 1D Interactive Manipulation How to Reset the Baseline Correction Line 1 Click the following button Reset the red correction line to zero If the difference spectrum is displayed t
269. ween the two different command line sizes as follows e Click View gt Resize command line Or e Right click in the command line and click Resize command line How to Set the Minimum and Maximum Command Line Size By default the size of the command line can be toggled between 1 and 3 You can however change this minimum and maximum value respectively To do that 1 Click Options Preferences set Click Fonts Dialogs Icons in the left part of the dialog box Specify the Minimum visible command lines gt 0 Specify the Maximum visible command lines 2 Minimum visible Click Apply nn amp WwW N 19 3 Disabling Enabling Toolbar Buttons Menus and Commands How to Hide the Upper and Lower Toolbars Right click in an empty area of one of the toolbars and choose Hide the toolbars from the appearing popup menu see Fig 19 12 To restore the toolbars 328 User Preferences r press the keys SHIFT ESC Wake Button Invisible Make Button Inactive Reactivate All Invisible inactive Buttons Add User Defined Button Remove This User Defined Button Change Ilcon Size Change Toolbar Offset Hide Toolbars type SHIFT ESC to reset Print Associated Command Figure 19 12 How to Hide the Menubar Right click in an empty area of the Menubar and choose Hide the menubar from the appearing popup menu To restore the menubar r press the keys SHIFT ESC How to Disable Remove Toolbar B
270. x 3 Click OK If no integrals appear the integral regions have not been determined yet This can be done with the int command How to Superimpose Peak Labels on the Spectrum 1 Right click in the data window and choose Display Properties dopt 2 Check Peak labels in the appearing dialog box and click OK If no peak labels appear peak picking has not been done yet This can be done with the pp command How to Show Peak Annotations on the Spectrum 1 Right click in the data window and choose Display Properties dopt 2 Check Peak labels and Peak Annotations in the appearing dialog box and click OK Peak annotations appear on peaks for which annotations have been defined in stead of regular peak labels showing chemical shift values If no peak labels or annotations appear peak picking has not been done yet This can be done with the 1 These are the status parameters that also appear on the plot 1D Display 143 pp command How to Show Individual Data Points of the Spectrum 1 Right click in the data window and choose Display Properties dopt 2 Check Show data points in the appearing dialog box and click OK 3 Expand the spectral region where you want to see individual points How to Superimpose the Electronic Signature on the Spectrum 1 Right click in the data window and choose Display Properties dopt 2 Check Electronic Signature in the appearing dialog box and click OK The electroni
271. y 286 How to Create an AU Program 0 0 ec eee 286 How to Edit an Existing AU Program 20 0 cece 287 How to Execute an AU Program 0 cc ccc eens 287 How to Delete an AU Program 2 0 ccc nes 287 How to Show Comments short descriptions in the AU Program List 287 Regulatory Compliance cc cece wee c cece cece cence 289 T Adti Seprono ara Se omc Aeeehaaeade ee eee g 289 172 Electronice Signatures serran ck eit sme at ben es a ee ee 294 17 3 Password Controlled Login Identification 00004 297 Remote COmen OD ici 6 scenes 05s 6a ears aalasacane diane Ore are Anwar 301 1S1 REmole controly 23 4454 4 ge ha oe watiaw aAdaaiaetevdvared wana 301 18 2 How to Establish a Remote Connection from your PC 301 18 3 How to Make a Remote Connection without a Local License 308 18 4 Security of Remote Connections 0 0 0 0 eee 308 18 5 How to Access ICON NMR from a Remote Web Browser 309 User Preferences socso enit id se SGA Se WA ewe eG sie s 311 I9 Ust PreicrenCes 4 a4 fa bbe oS tetas are tee Gu ae wt eee ee 311 How to Open the Last Used Dataset on Startup 313 How to Define the Startup Actions 000 cee cee eee 314 How to Define Auto Termination after Idle Time 314 How to Define Auto Locking after Idle Time 315 How to Change the Preferred Editor 20

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