Home

DeepView – The Swiss-PdbViewer User Guide v. 3.7

1. any amino acid Enter here the number of allowed mismatches within fo allowed mismatches the search pattern Cancel z Highlight residues in structure ond Check this item to highlight the residues on the Graphic window Un checking this item will only select the residues Edit gt Find Sequence Find Sequence PROSITE pattern dialog DeepView will then look for this sequence in the currently active layer If the sequence is found this will be selected in the Control Pane Click Edit gt Find Next to find the next sequence of the currently active layer that matches your entered sequence NOTE The current settings for allowed mismatches will also apply for other search functions e g Search for Prosite Patterns 99 e Searching a molecule for all patterns in the PROSITE database Concept The currently active layer is searched for PROSITE patterns that match any fragment of the amino acid sequence Examples of application In homology modeling finding identical PROSITE patterns in the target and the template sequences helps refining their manual alignment see point 132 Procedure Select Edit gt Search for PROSITE pattern DeepView looks for the occurrence of all specific PROSITE patterns An interactive result list is displayed see figure below NOTE PROSITE patterns are defined in the prosite dat file which contains a set of amino acid patterns that define certain features of proteins e g glycosylation si
2. These are two views of the same PDB file showing the atom coordinates of layers ICRNA up and ICRNB down Relative movement of layers implications on the atom coordinates Whenever a layer is moved respect to another layer a matrix is automatically generated to allow resetting the original orientation of the moved layer This matrix is included in the PDB file at the end of each layer ADVANCED DEEPVIEW COMMANDS 67 E C AWWINNTAPrafilesumfh10000VDesktopiviewertdownlo E3 SPDEUT 0000000000 0000000000 0000000000 al SPDEUT 0000000000 0000000000 0000000000 SPDEUT o000000000 oo00000000 0000000000 SPDEUT 0000000000 0000000000 0000000000 SPDEUT SSBS90960689 OesSersos le Goo00nnoOoo j rl Z PDB file of the previous project showing the transformation matrix SPDBVT generated for ICRNA The matrix contains one rotation and two translations The three first lines are used to store a rotation in this example it corresponds to the identity since ICRNA was not rotated The fourth line stores a translation to be applied before the rotation in this example the translation is null The last line contains a translation to be applied after the rotation the values show that 1CRNA was translated along the X and Y axes This translation was used in the former figure steps 7 9 to compute the original atom coordinates Translation matrices generated after a layer has been moved respect to another
3. me C spdbvidownload blast5 tec x BLASTP 0 10 amp ug 26 1999 Eeference Altschul Stephen F Thomas L Madden Alejandro A Schaffer Number of Jinghui shang aheng chang Webb Miller and Dawid J Lipman 11997 Gapped BLAST and PSI ELAST a new generation of protein database search selected aa for the Nucleic Acids Res 25 3389 3402 query 25 Query query 25 letters Searched Database ExNEL 22 969 sequences 5 146 101 total letters database ExNRL ExPDB Searching E Sequences producing significant aliqnmentes hits Value ExNBL LYe le 10 ExNEL 6LYZ le 10 ExNEL ELYT le 10 Ez NEL S5SLYZ le 10 gt Ha Z PDB accession code clicking an AC will import the BLAST scores see PDB file into Deep View Altschul 1990 Edit gt BLAST selection vs ExPDB result list NOTE These functions require network access the DeepView Network Preferences must be set correctly 50 DeepViewManual c Computing commands 101 e Computing H bonds Concept H bonds are computed on the basis of atom distances atom angle and atom types This computation 1s used to give an indication of putative H bonds over prediction being desirable for visual feedback Therefore even when hydrogen atoms are not explicitly present putative H bonds are drawn between H Donor and H Acceptor atoms e Distance constraints H bonds are drawn if a hydrogen atom is within a distance ranging between 1 2 and 2 76
4. 114 e The Alignment window Most advanced functions that are used to work on projects use the Alignment window as an information panel superposing commands or as a working tool alignment commands Click the question mark for getting help FAM U x on the window lt 4 a Bl ihel KF GR List of loaded K WF N molecules with the al ee c 5 5 l l l K l Di E layer in red Click the page icon to display the Field for information on Amino acid sequences of loaded layers alignment in a Text the pointed residue residues are colored as selected in the Control Panel or window with the Color menu see points 81 and 62 66 selected residues appear in inverse video pointing a residue will make it blink on the Graphic Alignment window window a Merging commands 115 e Merging layers Concept Given several loaded molecules selected residues on each layer can be merged in a new layer Examples of application By merging parts of proteins from different molecules you can build a new entity For example given an ExPDB file containing chain A of a dimer you can build the full dimer by 68 DeepViewManual loading twice the ExPDB file containing chain A applying to one of the two layers the matrix that transforms chain A into chain B see point 110 selecting all residues in both layers and merging both layers Procedure e General procedure On the Control Panel select for each layer the gro
5. Saving other states of preferences that might be more proper for specific purposes such as a white background allows easily switching from one state to another by simply opening the corresponding orf file 147 e Resetting default preferences To reset the preferences to their original default state e close DeepView e delete Default prf from the usrstuff directory e restart DeepView 92 Deep ViewManual 148 e Setting preferences Invoking the remaining 20 commands will display a dialog to let you set the following preferences Preferences menu 149 General Features displayed when initiating a DeepView session and upon loading a molecule Loading Protein Appearance of molecules and default scaling for B factor and RMS coloring Appearance of molecules during displacements Speed and extent of automatic rotation around y screen axis Appearance of labels Colors of molecules and background Appearance of ribbons Appearance and type of surfaces Methods and parameters used for electrostatic potential calculations Appearance of Electron Density Maps Energy Minimisation Methods and parameters used for energy minimisations H bond Detection Distance and angle constraints to detect H bonds Threshold Ramachandran Plot window features Alignment window features Swiss Model Web address of Swiss Model server Web address of DeepView file server and local directory for importing files Definition of 3D r
6. Solvent lonic Strength moll 99 000 elece charge in kT Je laga e Z update display every 20 cycles color gradient in this example 1 6 kT e lt 0 0 kT e lt 1 6 kT e red white gt blue these values can also be set on the For setting the Parameters and Surface Preferences dialog see Computation Method see point above 157 Electrostatie Potential dialog for setting the options for computing electrostatic potentials Electrostatic potential maps can also be loaded in two different file formats e maps computed and saved from a previous Deep View session sph e maps computed by external programs such as GRASP or DELPHI phi Nicholls et al 1991 Once an electrostatic potential map is computed or loaded you can visualize it around the molecule on the Graphic window and set its display on the Electron Density Map Parameters dialog and on the EDM Infos window The sigma value of the Electron Density Map Parameters dialog 1s used to set the kT e cutoff NOTE We are aware that setting electrostatic potentials under electron density maps preferences is not very coherent But both electrostatic potentials and electron density maps are grid based and it was faster to implement it this way A specific dialog for setting electrostatic potentials will be provided in the future Swiss PDB Viewer 3 7 b File Edit Select Build Tools Fit Disple erae AL 2 hal The contouring value of the first contour in the E
7. a screen coordinates 0 0 0 along the X Y and Z axes Intensity light intensity from 0 no Position 20 000 20 000 20 000 light to 1 Higher values would saturate Intensity 0 500 g Sedans the colors Enable Light 3 Cast Shadows currently has no effect 102 DeepViewManual 167 e Display window preferences This dialog lets you set several parameters governing the normal and slab display of molecules on the Graphic window Display Window Attributes x Image width pixels 7 Image Height pixels abe M Maintain Width Height ratio Enter a view angle to set the perspective of molecules A 1 degree angle will render flat images with no depth View Angle o 20 appearance Slab depth 4 fi0 000 Enter the slab thickness in A Auto Center Inspect Radius 7 500 Selecting an atom on a PDB file centers the molecule on the atom enter here a radius in to determine the YDW Dot density 1 12 5 extent of molecule that has to be displayed around the Surface Dot density 1 12 selected atom Enter a value from 1 to 12 for the dot density of van der Cancel Waals and Accessible surfaces 168 e Stereoscopic view settings You can select one over four available stereo modes and set several parameters governing the stereoscopic display of molecules on the Graphic window If you select Red Blue Stereo you need to set the Stereoscopic View Settings Fi color of your glasses
8. entered You will be notified when the server starts working on it lt All further communications from SWISS MODEL will come via E mail The following 1 files in total 331205 bytes were successfully received C WINNT Profiles mfh10000 Desktop proj_test pdb 331205 bytes Yqur SWISS MODEL project file can be found in http fwww expasy chiswissmodl C WINNT Profiles mfh10000 Desktop proj_test pdb Manuel C Peitsch Torsten Schwede amp Nicolas Guex Copy paste the file path in the field below or click on the Browse button to select the project J Desktopi pro pdk Browse REQUEST SUMMARY Now BESARAN o EEA Return address merce_ferres hotmail com Title test Output Format Spdbyv R Copy the first line on the text field or click camara Foldrecognition No Browse to select your project PreditProtin No Mail Attachment Yes Document Done EEF s S E Z Document Done Before submitting the modeling project After submitting the modeling project SwissModel gt Submit Modelling Request Swiss Model Optimise Mode 84 DeepViewManual SwissModel requests are submitted to a batch queuing system As soon as the server starts working on your submission depending on the server load normally within some minutes up to some hours you will receive a Welcome e mail from Swiss Model in which you will be given a Process Identification code corresponding to your request for example AA
9. The slab will display or hide an entire group based on the depth of the Ca atoms for amino acids and Cl for nucleotides This prevents an excessive number of unlinked atoms and bonds in the display Atoms from all other groups are clipped independently The slab can be translated along the axis perependicular to the screen by left clicking and dragging the mouse on the Graphic window while holding down Shift The slab mode allows viewing a cross section of specific groups which is very useful for exploring the interior of proteins 86 DeepViewManual I NON STEREOSCOPIC MODES 139 e Normal Display Mode This is the default mode for Mac and Windows It allows a rapid real time display and a high frame rate rendering Therefore it is the most suitable mode for straightforward work This mode lets you apply all DeepView commands including all computing and fitting tools Under the Preferences menu see point 167 you can adjust several options governing the appearance of molecules under normal display 140 e 3D Renderings Two 3D rendering types are available which can be turned on and off by clicking Display gt Use OpenGL Rendering and Display gt Render in solid 3D respectively Use OpenGL Rendering is the default display mode for Linux and Irix Ribbons and molecular surfaces appear in solid 3D whereas backbones and sidechains are shown as show wire frame van der Waals and accessible surfaces are always dotted Thel
10. 162 e Alignment window preferences Set the display of the Alignment window and its associated AlignPrv txt file Alignment display Alignments MALA AITH L Alignment process For Screen Display SIM parameters check these items to F enter a value ideally dissolva black IV Black Background Open Gap Penalty between T ana 90 46 play V Color Sequence Extend Gap Penalty 4 background and to enalize the opening of Selection Color Matrix default txt p p color the sequence gaps and a generally as set on the For Files inferior value to penalize Control Panel Number of AA oneachline 50 extension of gaps Read on the select a matrix of aa vs aa click Selection PAM 200 by default to Color to select a base the alignments on the i Draw a dot for AA identical to reference ea color to highlight V Draw below alignment and for identical similar aa similarity scores between amino acids selected da on the Minimum score needed to be similar fi V Separate chunks of 10 aa by a space matrix Alignment window Include secondary structure alignment AlignPrv txt file fo Define the information of alignment text files 100 DeepViewManual 163 e Swiss Model server settings For using Swiss Model you need to define the following servers Swiss Mudel Settings x Modelling Server http ww espasy cheswisemodcg binesm submit request cgi Your s
11. 468 x 396 Thel 468 x 396 Normal display Wi OpenGL mode TS eo rendering Normal and OpenGL display modes In addition Render in solid 3D will generate solid backbones and sidechains Thel 468 x 396 Thel 468 x 396 Normal display i Solid 3D mode AER rendering Normal and Solid 3D rendering modes SLAB DISPLAY STEREO DISPLAY AND 3D RENDERING 87 The appearance of the different solid objects can be altered under the Preferences menu e Preferences gt Surfaces you can set the color quality and degree of transparency of molecular surfaces see point 156 e Preferences gt Ribbons you can enable the solid 3D rendering of ribbons and adjust their dimensions shape colors and quality see point 155 e Preferences gt 3D Rendering you can set the dimensions colors and smoothness quality of bonds and atoms Increasing the smoothness will divide the atoms spheres and bonds cylinders with more facets improving the look of the image but also dramatically increasing the rendering time see point 165 Note that these preferences are not for setting POV Ray output see point 141 POV Ray rendering Smoothness Number of facets used to Number of facets used to describe one sphere describe one cylinder hel 468 x 396 amp Thel 468 x 396 Smoothness 1 Smoothness 13 for atoms and bonds for atoms and bonds TO Setting the smoothness of atoms and bonds It might be a good
12. Related commands sin asin acos tan atan PI Demonstrated in example script none e delete Deletes selected residues or hydrogens from a layer delete lt selection gt delete in lt layer gt hydrogens delete in lt layer gt molecular surface delete in lt layer gt electrostatic potential Related commands build Demonstrated in example script none e dist Computes the distance between two atoms vectors lt floatvar gt dist lt vector gt lt vector gt Related commands angle get torsion Demonstrated in example script 07 export This command allows saving images or POV Ray scenes export image as lt string gt export stereo image as lt string gt export pov as lt string gt and render ANNEX 2 117 where lt string gt contains the filename with full path Alternately you can save the file in one of the predefined directories usrstuff download temp with the following command export pov in usrstuff download temp as lt string gt and render See save for more explanations about path and filemames Note that the and render option will open the file for rendering on Mac and PC but will automatically launch pov on Unix boxes provided you save the scene in the usrstuff directory Related commands save Demonstrated in example script 09 e fit This command is equivalent to the Fit molecules from selection command under the Fit menu fit lt layer gt onto lt layer gt using lt st
13. 3D structure of the target sequence The following steps need the display of the Alignment window 80 Deep ViewManual 129 e Superposing and aligning all homologous templates If several templates were selected they first of all need to be superposed by doing one of the following e click Fit gt Magic Fit and Fit gt Generate Structural Alignment or e click Fit gt terative Magic Fit the structural alignment will be automatically done For further details on these procedures see points 116 118 2tanb 611x274 Template 1 Before the fit Target sequence MQQPMNYPCPOQOIFWVDSSATSSWAPPGSVFPCPSCGPRGPDQRRPPPPPPPY Target sequence She tee ae pte Woes 16 T DS s oe t TS s t ae KPAAHLI GOPSKONSLLWRANTORAFLOOGFSLSNNSLLYVPTSGI YFVYSQWV TPSOKPVYVAHVVANPOQAEGOLOWLNRRANALLANGYELRONOLVVPSEGLYLI Templates ey Template 2 onto After _ template 1 the fit Target sequence MOO PM YPCPOI FWVOSSATSSWAPPGSVFPCPSC 7 Target sequence KPAAHLI GOPSKONSLLWRANT DRA TPSOKPVAHVVANPQAEGOLOWLNRRANA ANG SONOQLYVPSEGLY Ali gne d templates Templates alignment 130 e Aligning the target sequence onto the templates Click Fit gt Fit Raw Sequence to generate a sequence alignment between the target and the templates This will provide the target with a preliminary 3D structure which is only to help you further adjust a better alignment ADVANCED DEEPVIEW COMMANDS 81 P41047 611 x 274 A provisional 3D structure is generated fo
14. A of a compatible H Acceptor atom When hydrogen atoms are absent H bonds are drawn between H Donor and H Acceptor atoms if the distance H Donor H Acceptor is comprised between 2 35 and 3 2 A H bonds within this distance range are drawn as green dotted lines weaker H bonds extra allowed distance 0 05 A by default appear in gray When a group is at an H bond distance of several other atoms all possible H bonds are drawn with no attempt to choose the best one Distance settings can be modified in the H bonds detection threshold dialog see point 160 Preferences menu e Angle constraints when hydrogen atoms are present H bonds are drawn if the angle H Donor H atom H Acceptor is superior or equal to 120 When hydrogen atoms are absent it is not possible to compute this angle and H bonds are drawn between a H Donor and an H Acceptor atoms if the angle PreviousAtom H Donor H Aceptor or H Donor H Acceptor NextAtom is superior or equal to 90 Distance constraints lt 1 20 lt d lt 2 76 2 35 lt d lt 3 20 H is present H is absent Possible Angle constraints H bonds Possible H bonds H is present H is absent Distance and angle constraints to detect H bonds H hydrogen atom A H Acceptor atom D H Donor atom X any atom 102 ADVANCED DEEPVIEW COMMANDS 51 Examples of application Computing H bonds lets you visualize polar Interactions In the protein When modeling structures thi
15. Electrostatic potential parameters Set various options for computing electrostatic potentials The same dialog is displayed when computing electrostatic potentials as explained in point 103 Electrostatic Potential x Enter the solvent Select Peeters dielectric constant between Dielectric constant solvent 80 000 M Keep Map using charged use only charged residues w Map Potential to Surtace residues or Check Keep Map to display the electric use atomic partial charges Red 1 800 field spreading out into atomic partial l Whit charges te nno the solvent Computation Method Blue i 500 Coulomb Check here to display Select a Poisson Boltzmann the electric charge of the molecular surface computation Dielectric constant protein 1 000 Cancel you must have method Solvent lonic Strength mal 0 000 computed it first Z update display every 20 cycles Enter the cutoff Enter the values of the electric protein charge in kT e to set dielectric the color gradient constant and the solvent ionic strength Computing electrostatic potentials requires several 1 8 kT e lt 0 0 kT e lt 1 8 kT e iterations check this item to refresh the potential red gt white gt blue on the screen which lets you see how the potential can also be entered in the converges Surface Preferences see above 158 e Electron density maps EDM parameters These settings affect 3D contouring of both electro
16. Saves an exact copy of the current Graphic window contents The format depends on the platform Mac saves in PICT format Windows saves simple files in Bitmap format bmp and OpenGL files in Targa format tga Linux and Irix save in Targa format To convert files to other formats use image file converters such as convert name tga name tif Linux and Irix or Graphic Converter Mac Stereo Image Saves two images corresponding to the left and right eye view according to the current stereo settings The file format depends on the platform as described above POV3 Scene Saves object data to a POV Ray formatted file with options for size anti aliasing and for making a stereo pair see point 141 Linux and Irix Files are saved in the directory defined in the environment variable SPDBV_ POV PATH Pressing the Render button will run POV Ray and display the result provided that POV Ray is installed The script defined in the environment variable SPDBV POV is executed Mega POV scene Same as above but with smoother colors for molecular surfaces see point 141 II CLOSING DEEP VIEW 34 e Closing molecular surfaces electrostatic potential maps and electron density maps Point File gt Discard in the associated submenu select the object to be closed which will be removed from the currently active layer This step is useful to free some memory after manipulating big objects 35 e Closing layers Click File gt Close to close on
17. are used to copy the current colors set for one object selected here Sidechain to the object shown in the first line of the Color menu Use this to save a set of colors in a Ribbon Surface property you re not using like surface color and copy it back later Label Color NOTES e Color by CPK is the only coloring command that uses different colors for the different atoms that belong to a group e For colors by CPK by type and by secondary structure default colors can be redefined in Preferences gt Colors see point 154 c Special commands 67 e Viewing PDB files BASIC DEEPVIEW COMMANDS 29 Click the dog eared page icon to open a text window with the content of the original molecular coordinate file of the currently active layer 68 e Navigating in text files Ctr Control clicking the dog eared page icon opens the Select a TEXT file dialog to let you open any text file Very large files are supported which can be visualized this way Many text file elements can be treated as active hyperlinks When they are clicked they produce an action for example e Clicking a SWISS PROT PDB or PROSITE accession number which appear in red in text files downloads the corresponding file automatically e Clicking an ATOM line will center the view of the model on this atom and will display only those residues that are within a certain radius of the atom To edit this radius see point 167 e Clicking any other line containi
18. be sure to configure WinZip so as to keep the directory hierarchy The following steps b f are optional b Download Swiss PdbViewer Loop Database 2 45 Mb This step is useful if you intend to do standalone modeling or for teaching purposes To be able to use the loop database put it into the stuff directory see point 15 c Download the User Guide 740 Kb This step is useful if you want to consult this user guide from a computer not connected to the network To be able to consult the help directly from within DeepView place the content of this folder into the _ stuff directory d Download the Tutorial Material 325 Kb This step is useful to learn how to use DeepView by looking at real examples e Download PROSITE pattern file http www expasy org prosite INSTALLING DEEPVIEW 5 DeepView can search a sequence for PROSITE patterns if you download the pattern file prosite dat into the usrstuff directory f Download and install POV Ray This step is useful only if you intend to make ray traced images from your molecules NOTE e OpenGL is included in all current Windows versions If during installation of DeepView a missing glu dil or missing opengl32 dll error message is displayed this means that OpenGL is not installed correctly on your system Please refer to your graphic card manual or ask your graphic card manufacturer for support Standard OpenGL DLLs are available from the Microsoft web site http www m
19. bonds from selection must have been computed groups with visible H bonds H bonds must have been built To compute H bonds surfaces and forces see points 101 102 and 106 respectively Show commands apply only to the currently active layer except for Show Axis since all layers use the same coordinate system To extend a Show command to all layers select it while holding Shift The most used Show commands are readily available through the Layers Infos window see point 85 58 e Views command This offers a submenu that allows saving a view reseting a previous view and deleting a saved view A view of a molecule is defined by the orientation and perspective of the molecule Display gt Views command Save Prompts a dialog that lets you name a view to save it The name of the saved view is then included in the last line of the submenu NOTE When saving a layer all saved views are stored with the layer Displays the original model view when first loaded Prompts a message reminding how to delete a saved view 1 e by selecting it while holding down Ctrl 59 e View From command Allows rotating the molecule to change the point of view This command is no longer maintained and will be removed in future versions 26 DeepViewManual 60 e Setting the style of the labels placed with the Control Panel Labels for individual groups can be placed by using the tools as explained above or by using the Control Panel see
20. dey Ajisuoq uono lH jO q UeIpueyoeuey SOJU SIOAR T JUSWUSITV U01 99S 99S ysonboy suljapoyy 1ruiqn soydu qpdxq eridoiddv put Asiouyq Surpe lu r Aq 10100 ony MON Avy dsiq Supeo l epdq Ajjeonewoyny Avjdsiq Sumpen 31epdr qof apoypy S ztumdo 348S I PON Areurwutporg pling opoypy Ppwny ouroH ISpoIA JO sanpisay p3199 9S yoru Opop JO s npiIS q p3 J99 9S Yoo Su nbD s MBI olur DINJON YS IAOW INJON YS olur 99u nb s MELI IAOW SU 199J 1 Sp IDAK JUDIINI 19S se 1ous o SONPISOY MPIC SUI OPOW Suunp WV PAPS BN SUI OPOW SULINP VV p9129 9S 1ous Ju uruSiI v WAP OY AeS Ju uruSI V WAP OY peoT JOpoy 0 959u nb s mey peo nusu OPOJA SSIMS ANNEX 2 SCRIPTING LANGUAGE I USING SCRIPTS e Running scripts Scripts can be run with the Run Script item of the File menu and loaded as text files with the Open Text File item of the File menu II SCRIPTING LANGUAGE e Overview The parser of SPDBV scripting language has been generated with flex and yacc whose combination allows building very advanced parsers The scripting language will be quite familiar for persons who know C or perl The scripting language supports variables conditional branching loops arrays and file access Subroutines are also supported but you must be aware that all variables are global Despite this limitation it allows to make the scripts more compact and readable and can also be used to prepare a kind of
21. form server PDB file I SUBMITTING A MODELING PROJECT e Setting your e mail Swiss Model returns constructed 3D structures by e mail Click Preferences gt Swiss Model to set your name and e mail see point 163 e Submitting the request To submit a request click SwissModel gt Submit Modelling Request This will display a Save request as dialog to let you select a name and a destination folder for your modeling project As soon as the project is saved DeepView opens your Web browser at the Swiss Model Optimise Request mode page and loads your project SWISS MODEL Optimise Netscape Upload Finished Netscape File Edit View Go Communicator Help File Edit View Go Communicator Help Z 3 2 2 m lt 3 F 3 2 u g 2 Q ack d Reload Home Search Netscape Print Security Shop itop H Back Forward Reload Home Search Netscape Print Security Shop Stor B Z a Bookmarks J Location ffile C AWINNT Profiles mth1 0000 Desktop test htm gt 7 What s Related Z a Bookmarks Location http www expasy ch swissmod cgi bin sm submit equest cai gt Gal What s Related 3 EJ Welcome to SGI Hotmail The W 7 Welcome to SGI Hotmail The W Upload Finished Optimise Mode Request submission form Your e mail your Please fill these fields name and the eam Lustre project name are SWISS MODEL Submission Fow Nene automatically Request title es Will be ade Your request submission was successful
22. jump table of your favorite functions that can be executed simply by clicking on their name from the SPDBV interface or from added menus The scripts can be stopped at specific points to let users interact with the graphical interface before resuming operation This allows among other things to access commands not directly available from the script take parameters from the user input or execute other script commands not included in the script by typing them directly from the Execute script command item of the Edit menu On Unix systems scripts can be passed as the last parameter of the command line after optional PDB files The place to post and exchange scripts is on the spdbv mailing list maintained by Prof Gale Rhodes at http www usm maine edu rhodes SPVTut text DiscuSPV html As we all like to be polite scripts must start with please do and end with thank you All instructions are terminated with a semicolon All information following a is ignored until the end of the line e Data Types In the manual data types appear between lt gt These means that a value of the mentioned type is expected or returned This value can be obtained from a variable or provided directly ANNEX 2 111 Supported types are Data type Example vector lt 1 0 1 0 1 0 gt string Hello World layer ICRN alternately layers can be referred to by position the first layer loaded is 0 the second 1 etc selection There are tw
23. lt Z Show Log File upon loading Check the first item to be alerted when no Z Show an alert when no CONNECT informations are found CONNECT information is found on a PDB file Check the second item to enable connection of residues with unusual bond length and enter a Distance threshold to connect two atoms 000 distance threshold for these connections Z Reconnect residues with unusual bond length w Show an alert when unknown groups are treated as HETATM Z Show an alert when some sidechains are reconstructed Check these items to scale B factors and or RMS colors between their min and max values Otherwise a default fixed scale is applied for RMS Scale B factors colors so that min dark blue and max red values and B factor values Scale AMS colors so that min dark blue and max red RMS 0 lt 25 lt 50 B factor 0 lt 50 lt 100 Cancel Color dark blue gt green gt red Z Reconstruct sidechains with missing atoms 150 e Loading preferences Set here the default appearance of molecules and enable some automatic processes when a protein is loaded Note that a more advanced treatment can be envisaged by using the scripting language Loading Molecule Preferences x Options to apply alter having loaded a protein Center It Magic Fit onto first protein loaded Check here to apply Generate Structural Alignment these processes to Compute Threading Energy molecules upon loading refer to Ch
24. molecular visualization we would encourage you to refer to the following Tutorials e Gale Rhodes The Molecular Modeling Tutorial for Beginners http www usm maine edu rhodes SPVTut e The DeepView advanced tutorial Structure of this manual This manual has been organized in points describing certain features or functions of DeepView Swiss PdbViewer The first chapters describe simple operations needed to open and display molecular structures while more complex manipulations are provided in later chapters DeepView Swiss PdbViewer has been designed to work under different operating systems Macintosh Windows Linux Irix 6 x 1 e the commands mentioned in this manual apply to all versions of the program However not all functions using the keyboard could be mapped consistently between all different OS e g the ALT CTRL keys In these cases this manual will provide a table of different keyboard settings Legal Disclaimer The authors reserve the right to change without notice the specifications drawings and information contained in this manual While every effort has been made to ensure that the information contained in this manual is correct the authors and GlaxoSmithKline Research and Development S A Geneva herein after called GSK do not assume responsibility for any errors which may appear DeepView the Swiss PdbViewer is provided without warranty of any kind whether express statutory or implie
25. of sidechains even when backbone is hidden This option is automatically checked if the Show Sidechains even when Backbone is Hidden command of the Display menu is enabled the cycling of layers which is achieved with Ctrl Tab Cycling through layers displays the next layer enabled to cycle NOTE To affect all layers hold down the Shift key while selecting an option valid for all platforms 86 e Obtaining help on the Layers Infos window Click the red question mark to obtain help on the Layers Infos window 36 DeepViewManual Advanced DeepView Commands I WORKING ON A LAYER 87 e Classification Advanced commands that can be applied to a single layer can be grouped into four categories MUTATE Mutates amino acids Modifies torsion angles of selected groups i e 0 X1 x5 angles build gt Build Loop Build loops Build gt Scan Loop Database Build gt Find best Fitting Peptides Finds segments of sequence in a poly Ala model matching electron density maps Build gt Break Ligate Backbone Modify the backbone break ligate it alter Build gt Add C terminal oxygen conformational angles add OXT groups Tools gt Set Omega Phi Psi Ramachandran Plot window 88 Modifying commands modify the structure of Build gt Add Remove Add remove structural elements bonds molecules hydrogen atoms H bonds Tools gt Randomize Selected Groups Randomly translates a
26. one of the Color menu functions 63 to color the selected object If a Color command is invoked while holding down the Shift key colors are appplied to all layers If a Color command is invoked while holding down the Ctrl key only selected groups are colored currently this works only when selecting Color gt by CPK or Color gt by Other Color BASIC DEEPVIEW COMMANDS 21 63 Color menu first block Color menu By CPK Colors the selected object by element type using a default standard CPK scheme N blue O red C white H cyan P orange S yellow other gray This command is only effective if backbones and or sidechains are selected for coloring Default colors can be redefined in Preferences gt Colors see point 154 Colors the selected object by residue property Acidic red Basic blue Polar yellow and Non Polar gray Acidic Basic Polar and Non Polar Default colors can be redefined in Preferences gt Colors see point 154 By RMS At least two proteins must have been loaded superposed and structurally aligned see points 127 132 Each residue in the active layer will be colored accordingly to its RMS backbone deviation from the corresponding amino acid of the reference protein the first loaded NOTE Colors are mapped from a fixed linear scale in which dark blue is for RMS 0 A and red is for RMS 5 A A relative scale can be selected in Preferences gt General where the best fit is dark blue and the worst fit is red
27. perform a submission to Swiss Model in the Optimise Project mode which requires going through the following steps by using DeepView Action achieved File gt Import gt Grab from server Load the target sequence to be modeled SwissProt Seq or Loading files SwissModel gt Load Raw Sequence e Edit gt BLAST Selection vs ExPDB or Load homologous template s SwissModel gt Find Appropriate ExPDB Templates Fit gt Magic Fit followed by Only if more than one template were Fit gt Generate Structural Alignment loaded superpose all templates and 129 or generate a structural alignment Fit gt Iterative Magic Fit Generating a modeling project ADVANCED DEEPVIEW COMMANDS 77 Fit gt Fit Raw Sequence Aligns the target sequence onto the template s and displays a preliminary 3D model for the target e Alignment window The sequence alignment can be refined 132 manually e SwissModel gt Homo Multimer Mode Enables the multimer mode optional To be enabled before manually which is useful if the target sequence refining the alignment contains two or more identical chains Submitting a SwissModel gt Submit Modeling Submits a generated modeling project modeling Request to Swiss Model 134 135 project Select gt aa Making Clashes Selects those residues of the modeled molecule whose atoms make clashes Improving a with other residues returned model I I the best rotamer for a selected aa Bu
28. points 78 79 Click Display gt Label Kind and select a submenu to set the display of the labels placed by using the Control Panel Atom Type Set the label Atom type e g C C O N Atom Charge Shey Atom charge e g 0 000 0 380 0 380 0 280 Only valid after an energy computation has been made Atom Code Atom code referring to the GROMOS96 force field e g 12 11 1 5 Only GROMOS 96 valid after an energy computation has been made Selection will apply to all layers 61 e Clearing user s labels Click Display gt Label Kind gt Clear User Labels to clear any label added to the molecule by using the tools Labels added by using the Control Panel will not be cleared see point 78 For explanations on all other commands of the Disp ay menu refer to the given points Display menu Stereo view 142 144 Use OpenGL Rendering Render in solid 3D Color menu The Color menu is used to systematically apply colors to the Backbone Sidechain Ribbon Label and Surface of each group Backbone amp Sidechains can be colored at once Look at the first line of the Color menu This indicates what object Backbone Sidechain Backbone Sidechain Ribbon Label or Surface will be colored by the subsequent coloring operations The object can be selected by using the pop up menu associated to this command or by using the pop up menu under the header col of the Control Panel see point 81 62 e Coloring objects Use
29. residues are selected on the Control Panel and on the Alignment window Deep View looks for alternate superpositions which are displayed on a result list text file named match txt stored in the temp directory see figure below This method is not using any sequence information and is much slower than the two previous ones It is useful to explore local matches in cases of hinge motions for example or to superpose two molecules that have a sequence identity so low that Magic Fit fails Select an alternate superposition from the list to visualize it on the Graphic window For information purposes superposed residues are selected on the Control Panel and on the Alignment window The backbone and sidechains will be colored by RMS Changes occurring on the Graphic window on the Control Panel and on the Alignment window 70 DeepViewManual 1a4fa 596 x 431 B Superposed Before molecule the fit laOva molecule 1aOva 596 x 431 After Magic Fit or NOTE laOvae IS Iterative Magic Fit After Iterative Magic Fit and Explore superimposed Alternate Fits the message space of the onto la4fa Toolbar displays the number of atoms that were adjusted and their RMS 1a0va 596 x 431 Number of residues involved followed by name of the superposed layer After Explore Backbone and Alternate Fits sidechains are colored by RMS here only the backbone is shown for clarity Explor
30. short list with the five recent files coordinate and non coordinate files that were loaded in previous DeepView sessions Other ways to load molecular coordinate files include Platform Load a molecular coordinate file by Windows dragging one or several PDB files onto the Toolbar Only valid for PDB files 10 DeepViewManual dragging one or several PDB file icons onto the Swiss PdbViewer icon Only valid for PDB files Linux and Irix typing a command line argument e g gt spdbv pdb1 pdb NOTE Mac Linux and Irix These actions launch DeepView and load selected files or if DeepView is already running add selected files into the workspace 22 Loading non coordinate files The File menu offers the following commands to load a non coordinate file File menu Open Text File Displays a dialog box that allows opening any text file including scripts Text files are displayed in a simple window with a scrollbar Shortcut Ctrl click icon in the bottom left corner of the Toolbar Run Script Displays a dialog box that allows opening and executing a script file For the use of scripts see Annex 2 Scripting Language Open Surface Allows loading a molecular surface in three different file formats the surface might have been computed and saved from a previous Deep View session sfc or written by MSMS or GRASP Open Electrostatic Allows loading an electrostatic potential map in three different file for
31. sidechain need to be re orientated Click Tools gt Fix Selected Sidechains a submenu allows finding the best rotamers according to the three following techniques Tools gt Fix Selected Sidechains command Quick and Dirty Finds the best direct fit from the rotamer library This often provides a reasonable fit since most residues have a limited number of preferred conformations Exhaustive Search This routine will try to test all reasonable combinations of dihedral angles along the sidechain to find the best fit You cannot select more than 10 amino acids Simulated This method is the most thorough It tries to minimize the energy computed as a Annealing combination of GROMOS96 energy and mutation score H bonds and clashes Not available yet NOTE The quality of fit is determined according to the formula given in Annex 4 96 e Randomly translating all atoms of selected groups Concept 46 DeepViewManual With pedagogic purposes DeepView offers a command that lets you randomly translate all atoms of selected groups Examples of application You can alter the position of all atoms of a molecule in order to see the effects of an RMS computation or an energy minimization Procedure Click Tools gt Randomize Selected Groups to randomly translate all atoms of selected groups on the Control Panel You will be prompted for the translation distance to be entered in A The RMSd Root Mean Squared deviation between the original coord
32. stop pause thank you Demonstrated in example script all e print Prints a value string variable number etc onto stdout or in a DeepView communication dialog print on dialog print on stdout print on lt file gt lt expression gt print lt expression gt where expression is any combination of arithmetic values or concatenation of strings Note that a new line is printed after each print operation You might then need to prepare a string from concatenation before printing Demonstrated in example script 01 02 03 04 06 07 08 11 psi Will get the psi torsion angle for the first selected amino acid found in a selection Returned value is of type lt float gt and is returned in degrees psi lt selection gt ANNEX 2 123 Alternately you can access directly a specific residue from a specific layer which is faster and handy in loops with psi lt layer gt lt int gt Related commands phi omega Demonstrated in example script 03 and 04 e readin Reads the next line from a text file or from a dialog box string _varname readin from file lt file gt string _varname readin from user lt string gt where lt file gt is a file previously open with the open file command and lt string gt is a prompt that will appear in the dialog Related commands open close clear substring Demonstrated in example script 04 and 06 e redraw Will force the main window to be refreshed Only useful in the int
33. surface rk surface Van der Waals oo ae Van der Waals surface surface 3D rendering Thel 438 x 337 Molecular Molecular surface surface Normal display 3D rendering Visualization of Van der Waals accessible and molecular surfaces 81 e Coloring the molecule The col column of the Control Panel allows assigning different colors to the backbone s side chains ribbon s labels and surfaces of individual groups To select the object to be colored In the pop up menu of the col header select the object to be colored i e backbone side chains etc in the next operation Control Panel color header Selected object backbone side i e backbone side chains backbone side i e sidechains surface only valid for molecular surfaces since van der Waals and accessible surfaces will always take the color set for the corresponding atom 34 DeepViewManual To color the selected object e in the col column select the boxes corresponding to the groups for which you want to color the selected object You can either drag your mouse to select several boxes in a row or shift click anywhere in the column to select all boxes e a Color dialog is displayed in which you can select a color To select the CPK colors hit OK Notice that the Cancel button does not work it colors selected residues black This action can be annulled by selecting Color gt By CPK For other ways to color a mol
34. the left which is referenced to as cross eye stereo e Hardware stereo Two modes of stereo hardware are available The first mode is Above Below stereo AB In this mode the screen is vertically divided into two parts Above Below The left image is displayed on the top part of the screen while the right image is displayed on the bottom part of the screen A special hardware device is used to double the vertical synchronization of the screen so that when the first half of the screen left image has been displayed the electron beam goes back to the top of the screen and displays the bottom of the screen the right 90 DeepViewManual image The result is that the left and right images are displayed in alternation on the screen at very high frequency You can use special glasses Crystal Eyes with an LCD shutter that will alternately obscure the left or right eyes at the same frequency as images are displayed on screen The result is that when the left image is displayed the glasses will only let the light pass through the left eye and when the right image is displayed the left eye will be masked The brain will reconstruct a 3D image from the two different images seen through each eye The second mode is true OpenGL Stereo in a window This stereo mode takes advantage of the capability of OpenGL to support different screen buffers for left eye and right eye view Switching between these views is done by the graphic card while sending the
35. typing before the next entered number will deselect the residue to the selection e g 72 85 will select groups 72 and 85 Typing 87 will add group 87 to the selection whereas typing 72 will deselect group 72 77 e Selecting an interval of groups Select an interval of groups by e clicking the first group and dragging up or down to the last group e clicking the first group and pressing Shift while clicking the last group e using the numerical keypad not implemented yet enter the number of the first group type slash and enter the number of the last group e g 72 85 will select groups 72 to 85 NOTES e Selected groups appear red in the Control Panel and the total number of selected groups is displayed in the Layer Infos window see point 84 e For further ways to select groups see points 50 56 78 e Setting the display of a single group Check uncheck the columns after the name of a group to display hide the following objects Column Displayed object for amino acids Displayed object for other groups Control Panel Graphic window Graphic window show Backbone Atom or group of atoms The show column has to be checked to The show column has to be checked to enable the display of sidechains labels enable the display of all other checked and surfaces options no o efe labl Amino acid label See point 60 to select Group label the kind of label NOTE In principle to see the sidechain of a group
36. 0 smooth the Image parameters s oa A check Stay Solid during for setting the Radius solid p 200 A motion to enable a real time visualization H bond radius 0 075 Dotted H bonds display of bonds and Smoothness 1 13 atoms Check Show Atoms to Atoms visualize atoms as spheres Radius u 30 and then select Alpha Carbone size relative to other C 100 z Atom colors if you colored Atoms Smoothness 1 13 2 your backbone by something Spacetiled atoms smoothness 1 13 else than by CPK select same color as bonds for C Select a Show Atoms atoms to apply the backbone background same color as bonds for C atome Z and others color to all C atoms and color this Keep atoms proportions by multiplying atom radius select and others to apply the will apply by 1 1 for H 1 5 for N 1 7 for C 1 4 for 0 1 85 for 5 same color to all atoms to normal Atom sizes check Keep atom display proportions to draw each also Background Color Cancel kind of atom proportional to its size 166 e 3D light settings You can enable the use of up to three sources of light to illuminate 3D images For each source of light you can specify the following parameters Q3D lights a W Enable Light 1 Position 4 20 000 20 000 20 000 Intensity 1 000 Z Cast Shadows Enable Light 2 Position 0 000 20 000 20 000 Position distance in A between the Intensity s source of light and the center of the
37. 2 v A A A A A A A A A A A A A A A A A A A gogogo gt y gt gt E E E P P P PP P PP PP PP P PP P 3 P OOOOOWOOO00OOO bre Hoogu P P P P P PP PP PP P p P P P P P P P P P P imi D 41 HEM142 v Amino acids that fit the static Amino acids witha high RMS Backbone and sidechains are molecule are selected they turn are deselected they turn black colored by RMS according red to the selected solution on the match txt result list Fit gt Magic Fit followed by Iterative Magic Fit followed by Explore Alternate Fits changes occurring on the Control Panel Here the superposed molecule is shown NOTE Applying Iterative Magic Fit is equivalent to applying Magic Fit followed by Improve Fit and Generate Structural Alignment see below 117 e Superposing two molecules based on selected residues Concept You can superpose a selected part of a superposed molecule onto a corresponding selected part of a static molecule Examples of application e By superposing precise domains you can see the relative movement of other specific domains between the two molecules this lets you study hinge motions for example e By superposing e g only the cofactor of two enzymes it is possible to compare the binding sites of otherwise structurally dissimilar proteins Procedure e Based on 3 selected atoms Click the FA icon 11 tool on the message space below the tools you will be prompted to pick t
38. 453 x 368 ITNRA 453 x 368 S f mi Layer B is brought a Layer B f back to its original Fitting superimposed eta an operation onto layer A 4 2TUNA 453 x 368 Reset Orientation Layers A and B are brought every layer follows back to the original e e t ti fl B Fit gt Reset Orientation commands orientation ot layer c Alignment commands 121 e Generating a structural alignment Concept A structural superposition between two molecules is used to find pairs of residues close to each other These are aligned on the Alignment window showing pairs of residues with similar structural roles Procedure Before invoking this tool you should already have done a Magic Fit of two molecules 122 123 74 DeepViewManual Select Fit gt Generate Structural Alignment on the Alignment window residues of the superposed molecule that are spatially close to residues of the static molecule are aligned Appropriate gaps are inserted in the sequences i Alignment ii After Magic Fit GFLEAADR OY m A T WEDI AGAD 1adi ALTESQGAALVES WEEF NANI as N Best matching residues are highlighted i Alignment After Generate B GLSAAUR UYI AATWEO AGAODNGAG Structural igdi GALTESGAALVKS S WEEFNANTP sid Pairs of residues that are spatially close are aligned Appropriate gaps are inserted in the sequences to indicate a lack of structural correspondence Fit gt Magic Fit followed by Fit gt Genera
39. Aa02MdM The modeling results should then follow at maximum within the next 4 hours IV EVALUATING AND IMPROVING THE MODEL The constructed 3D model will be sent to you by e mail as an attached PDB file named as the Process Identification code and containing the submitted alignment t P41047 Si x274 A ribbon representation of the model is colored by the Confidence Factor see annex 4 to let you estimate the quality of the model Regions of the model that appear in red C factor of 99 99 have been completely rebuilt and are to be considered with caution The rest of the residues are colored accordingly to the number of templates used to build the residue using a color gradient from green only one template to seOusLiweairo sari ooo st SNis LL vs blue more templates used Model returned by Swiss Model Depending on the quality of the model you might need to e proceed to a minor adjustment of the structure see point 136 e resubmit a new modeling project after correcting the alignment see point 137 136 e Minor adjustments For minor adjustments of the sidechains you can subsequently apply the two following commands Selects residues with atoms too close to atoms of other residues i e atoms closer than the sum of their van der Waals radii see point 56 A submenu allows finding the best rotamers for previously selected amino acids according to three techniques see point 95 Build gt Bui
40. Bo e 2 2 Around CA limits a volume around the centered aa according to the distances that around CA sn s Fe you enter for each axis 3 around Selected Residues the map is f Display only around Selected Residues slow displayed ee sss i en Z Contour a fi D sigma with Color e Dotted W Contour afso E B sigma with Color i Dotted I You can enable the visualization of two garse Contouring Along contours and set their appearance sigma values el vf 2 TA see below color and doted vs non doted I Draw Unit Cell l Daig Enabling a Coarse Contouring Along the axes speeds up the display during interactive work to the detriment of contouring precision Electron Density Map Parameters dialog Uncheck these items for picture quality ADVANCED DEEPVIEW COMMANDS Fl 474 x 372 e From Section p Im lt 5 A to Section Jaa Elsa s C Around CA e 000 fe 000 ig 000 G Display only around Selected Residues slow E Contour a 2050 sigma wth Dotted m E 500 a with Color T x Thel 474 x 372 PHE 38 E Display I e Display only around Selected Residues slow m Contour a js 500 sigma with Ww 050 sigma with Color weirs Dotted a I Dotted Ess From Section f 24 x to Section u a6 fao Modes 6000 feno so DE 3t Thel 474 x 372 Whole molecule m Display From Section fo fio fo to Section mn fao a C Around CA
41. By B Factor Colors sidechains and backbones independently according to their respective largest B factor per group A color gradient is used In which blue is for B factor 0 A green is for B factor 50 gt and red is for B factor gt 100 A Ribbons take the colors of sidechains and surfaces take the color of the B factor of the nearest atom In the case of a model returned by Swiss Model the B factor column contains the Model Confidence Factor see point 135 NOTE The coloring gradient can be adjusted in Preferences gt General to fit the range of B factor values present in the structure see point 149 By Secondary Colors the selected object according to the three common secondary structure types Structure Helix red Strand yellow and Coil gray Especially useful for coloring ribbon drawings Default colors can be redefined in Preferences gt Colors see point 154 By Secondary Produces a gradient along the polypeptide chain from N terminus blue to the C terminus Struct Success red Each secondary structure element gets a single color and random coils are gray Especially useful for coloring ribbon drawings 64 e Color menu second block Color menu Coloring action By Selection Colors selected residues in cyan and non selected residues in dark gray Useful to quickly find where selected residues are located in the model Default colors can be redefined in Preferences gt Colors see point 154 By Layer Each l
42. DM Infos window is displayed on the Toolbar e g 0 80 kT e Red contour comprises points with kT e values lower than the cutoff i e lt 0 80 kT e Blue contour comprises points with kT e values higher than the cutoff 1 e gt 0 80 kT e Put the cursor on the Graphic window Using the up and down keys of the keyboard will increase or decrease both contouring values and refresh the display of the contours in real time Visualizing electrostatic potentials ADVANCED DEEPVIEW COMMANDS 55 Electron Density Map Parameters x m EDM Infos x EDM viz dot Slqma corxcorYcore cell cs x x 3 300 ladod pot iF iF 3 300 m Infos Unit Cell Size A Cell Angles Nb Sections 7 55 Min Section 2 17 23 1 4 2 5 Max Section 1 Check these items to display the contours Bee 2 Edit here the contouring values From Section f22 17 23 3 Assign a color to each contour a blue positive to Section 37 E a contour and a red negative contour are given by C Around CA 40 000 40 000 default C Display only around Selected Residues slow 4 Ckeck these items to display dotted contours only aroun F Contour 20 sigmawih Color F Dotted plained lines will be used otherwise FZ Contour h 3300 sigmawith Cater FZ Dotted 5 Check these items for a coarse drawing along the x y and z axis this will worsen the visualization Coarse Contouring Along r YF Y 2 of contours but wil
43. DeepView The Swiss Pdb Viewer User Guide v 3 7 DeepView Swiss PdbViewer user guide Since there was a strong demand for a printable version of a DeepView user guide we decided to prepare this manuscript to complements the documentation and tutorial found on the web site We are aware that this user guide is still incomplete in some chapters there are references missing etc Please help us to make this user guide useful for you If you find any errors or inconsistencies or you don t find an important piece of information please let us know The DeepView Team Geneva 13 September 2001 GlaxoSmithKline R amp D World Trade Center I Rte de l A roport 10 1215 Geneva 15 Switzerland Contents II Generating a Modeling Project HI Submitting a Modeling J H DeepViewManual Preface Acknowledgements The following manual has been prepared by Merc Ferres in the Protein Structure Bioinformatics group of GlaxoSmithKline Research and Development S A Geneva with contributions from Nicolas Guex Alexander Diemand and Torsten Schwede We would like to thank all our users who have contributed innumerable suggestions bug reports and new ideas that let to the development of DeepView the Swiss Pdb Viewer in its current form We are especially grateful to Gale Rhodes University of Maine Simon Andrews BBRC and Joe Krahn NIEHS for continuously supporting our efforts To learn more about molecular modeling and
44. E 000 E 000 6 000 C Display only around Selected Residues slow 2 Contour a 2 000 sigma with Color j Contour a 1 500 I so sigma with Color Dotted One contour at 2 05 o is displayed around all atoms within 6 A of the CA of the centered residue PHE 38 One contour at 2 05 o is displayed around all atoms of selected residues PHE 38 and ASN 39 One contour at 2 0 o is displayed around all atoms within a volume limited by the given max and min section numbers Three different displays of electron density maps You can display up to two contours for each map Their appearance sigma contouring value color dotted lines vs solid lines can be set on the Electron Density Map Parameters dialog as explained above and on the EDM Infos window E EDM Infos x EDM visz dot sigma corkcorYcor g cell T7 x 2 000 lhel dne x x 1 500 w ki ki ki Contour colors click a box to change the color Check these items to visualize a contour vis and to represent it with dotted lines dot Check here fora Check here to coarse drawing of visualize the both contours protein unit cell along the x y and z axes Contouring values click here to edit them EDM Infos window 64 DeepViewManual Thel 474 x 372 Electron density map contoured at o 3 0 2 4 and 0 6 II WORKING ON A PROJECT A project consists of a set of layers simultaneously displayed on the Graphic wind
45. Find Sequence Find Next Search for PROSITE pattern BLAST selection vs SwissProt BLAST selection vs ExPDB Assign helix type to selected aa Assign strand type to selected aa Assign coil type to selected aa Select menu The Select menu allows selecting specific groups on the Control Panel on the basis of atom properties residue properties structure properties or other criteria Selected groups appear in red on the Control Panel If several layers are loaded shift clicking a Select option allows extending the selection to all layers 50 e Applying basic selections Use the following commands of the Se ect menu to achieve the following basic selections Select menu Selectmena 5 8 Visible groups Selects those groups for which the backbone the ribbon or both are displayed on the Graphic window Allows selecting groups by picking them on the Graphic window Extend to other When working on a project this command copies selection status from groups in the layers currently active layer to all other layers based on the sequence alignment This command is useful for identifying important counterpart residues for an aligned structure such as active site residues Groups with same Allows picking a residue on the Graphic window and selects all residues with the same color as color BASIC DEEPVIEW COMMANDS 23 51 e Selecting groups by type Click Select gt Group Kind This displays a submenu to select groups b
46. JDIIIS JO SIOQYSION ST Im on n Jol 0 PSULI ISOYM VL MINIONS Jol 0 1e rurtS ve MINIONS Jol o eonuop ve SIOAB T 19970 0 pud x7q se 1o oO owes YM sdnoip BE qISS9939V ainjonng ATepuodas Aytodoig dno pury dnoip Uu 419S UO YI SdNOIS S QISTA 199 UOoT 93 9S OSIOAU V20 IIV 0 0 SuoN nusu JIITOS opjin uo VY Jeqe uo pV uoqqry uo 19y SUIBYDOPIS uo JOV suoqyoeg uo y SUIBYDOPIS ouoqyoeg UO 0V U01 99S 99S puvwiuosqns IO OD joqe y Aq 1o oO ouJin Aq 1o oO uoqqry Aq 1o oO uleysapis Aq IO OD suoqyoeg Aq IO OD J9yIO Aq sut qoid Ulaj01g Aq ASIOUY Poly 9010 4 Aq Asiouq Surpe l1u I Aq AjIfIqissaooy Aq AVISIOAIG 1u ouusrv Aq uorssaoong IMPINS Arepuosas Aq oNN Alepuosas Aq l19 qoO papas uo y nusu 1002 CH9 CE Pilos ur Jopusy E 0 Y1YS sSuupu q TH u do sN spuoq H I qISIA YIM sdnois Aju MOUS uono j s WO spuoq H uO Aous soouR sIp spuoq H Aous d 109 spuog H Aous H4 10 suosoIpAH MoUs S3910 J MOUS IWJINS sjoq MOS u ppiH SI uoq jogg UIM UA SUTeYDOpPIS MOYS sudsAXQ dU0GyoVg MOUS AJUQ S 81 VO MOUS SIxy MOUS LHD MATA 09191S IV qeis sjoqe T Jos AN SOWOUD 9poO woy asiveyy Woy add uuo v SUIPN WOTY SumN dno soyerp Aq jst asueyo yOSay pury qv I WOOL MAAN nusu Avydsiq u0n29S 99S AH209 Aejds q 0313S Aejds q sIysIT q SULIOpUdY AE YyIOMION ISPo A SSIAS sju ouuusirv ueIpueyoewe
47. MS computed value will be displayed on the field for information of the pointed residue see point 114 NOTE Hydrogen atoms are never used for these calculations Set Layer Std Dev This command is useful to analyze molecular dynamic results or NMR files Based on the into B factors alignment the Standard Deviation of each corresponding atom of each residue is computed and assigned to the B factor column of the PDB file Proteins are then accordingly colored with those parts that move the most being highlighted in red NOTE This command requires that all layers have exactly the same sequence e Resetting orientations Concept The orientation of a molecule is brought back to its original position before a fitting operation Procedure ADVANCED DEEPVIEW COMMANDS 73 On the Control Panel make sure that the static molecule is not selected as the currently active layer and then apply one of the two following commands Fit menu Reset Orientation Moves the superposed layer back to it s original position before a fitting operation current layer only Reset Orientation Moves both the superposed layer and all static layers back to the original position of the every layer superposed layer before a fitting operation This is useful to change the coordinates of follows several layers which will be put in the referential of the superposed molecule TTNRA 453 x 368 Reset Orientation current layer only x 3x 1TNRA
48. NTRODUCTION I OVERVIEW DeepView the Swiss PdbViewer or SPDBV is an interactive molecular graphics program for viewing and analyzing protein and nucleic acid structures In combination with Swiss Model a server for automated comparative protein modeling maintained at http www expasy org swissmod new protein structures can also be modeled Annex 5 Glossary provides an extended dictionary for DeepView terminology To facilitate understanding of the following chapters some essential terms are introduced here A molecular coordinate file e g pdb mmCIF etc is a text file containing amongst other information the atom coordinates of one or several molecules It can be opened from a local directory or imported from a remote server by entering its PDB accession code The content of one coordinate file is loaded in one or more layers the first one will be referred to as the reference layer DeepView can simultaneously display several layers and this constitutes a project When working on projects the layer that is currently governed by the Control Panel is called the currently active layer Each molecule is composed of groups which can be amino acids hetero groups water molecules etc and each group is composed of atoms Non coordinate files containin specific information other than atom coordinates Molecular surfaces electrostatic potential maps and electron density maps are examples of non coordinate files whi
49. Protein Science 2 8 1 2 8 17 4 Jackie Neider Tom Davis and Mason Woo Addison Wesley 1993 OpenGL Programming Guide The Official Guide to Learning OpenGL Release 1 OpenGL Architecture Review Board 5 Dong Xu and Ying Xu 2000 Protein Tertiary Structure Prediction Current Protocols in Protein Science 2 7 1 2 7 17
50. adjust the displayed colors to your glass colors under Preferences gt Stereo Display The rotation angle between the two images 2 2 4 by default can also be altered see point 168 e Side by side stereo Two images are displayed side by side on the screen The left image is the control image on which you can click to select any object By default the left image is rotated 2 degrees around the vertical axis and the right image 2 degrees Thel 442 x 396 Side by side stereoscopic view The principle of seeing in stereo is to look at the left image with the left eye and to look at the right image with the right eye As the two images are slightly rotated each eye will see a slightly different side of the object and the brain will combine the two images into a 3D object Two factors which can be adjusted on the Stereoscopic View Settings dialog see point 168 affect the side by side stereo perception e the separation in pixels the further apart the images are the more difficult it is to maintain each eye aimed at the correct image In 3D rendering mode each stereoscopic image is half the width of the Graphic window and their separation cannot be adjusted on the Stereoscopic View Settings dialog However modifying the width of the Graphic window will affect the 3D rendering stereo separation e the rotation angle in degrees a negative rotation angle displays the left image at the right and the right image at
51. aint 160 e H bond detection threshold Fix here the distances and angles between atoms to constrain H bond detection see point 101 H bond detection threshold Fi a aa a FEES Edit here the H bond detection threshold when H are present Min dist 1 200 min H H Acceptor distance 1 20 A by default Max dist 2 760 0 050 A max H H Acceptor distance 2 76 0 05 A by default Min fzo H Donor H H Acceptor angle 120 by default 5 Edit here the H bonds detection threshold when H are absent Mindis 41 min H Donor H Acceptor distance A by default Max dist 3 300 0 050 max H Donor H Acceptor distance 0 050 A by Min 50 000 default Any atom H Donor H Acceptor or H Donor H Acceptor Cancel Any atom angles 90 by default SETTING PREFERENCES 99 161 e Ramachandran Plot preferences You can set the display of the Ramachandran Plot window Ramachandran Plot Preferences FQ General Options IV Black Background Check these items to Ignore GLYs display a black background if the option is not T Ignore PROs checked the background is white ignore GLYs and PROs i e they will no be plotted Save to Disk Options Always save images with a white background Check here to always save Ramachandran plots with a white background independently on whether you did or Cancel did not check the option above
52. amed blast txt see figure below is sent back and stored in your download directory Doing successive BLAST selections will generate new blast txt files which will be named blast2 txt blast3 txt etc These text files contain red hyperlinks that let you import BLAST hits for further comparisons BLAST selection vs ExPDB Depending on the selected command one the following result lists is displayed ADVANCED DEEPVIEW COMMANDS 49 i C spdbvidownloadiblast3 txt x BLASTP 0 10 Aug 26 15955 RFeference Alt chul Stephen F Thomas L Madden Alejandro A Schaffer N b f Jinghui zhang Zheng Zhang Webb Miller and David J Lipman 411997 NUMDET O Gapped BLAST and PSI BLAST a new generation of protein database search selected aa for the programs WMucleic Acids Res 25 3389 3402 query 23 Query query 23 letters Database sp A 55 753 sequences 32 291 714 total letters atabase sp SwissProt Searching E Sequences producing significant alignments hits Value HEE HYLLA Poz025 HEMOGLOBIN BETA CHAIN 3e 07 HEE GORGO DD0202Z41Y HEMOGLOBIN BETA CHAIN Protein 3e 07 HEB HUMAN p02023 HEMOGLOBIN BETA CHAIN a 38 07 HEB PREEN iP02022 HEMOGLOBIN BETA CHAIN description 6e 07 gt x SwissProt SwissProt accession codes clicking an AC BLAST scores see identifier imports the corresponding SwissProt entry Altschul 1990 as a text file Edit gt BLAST selection vs SwissProt result list
53. an only A be used when selected residues are identical the static molecule a involved the static molecule Fit gt Magic Fit Iterative Magic Fit Explore Alternate Fits RMS amp Auto Fit options dialog The following actions can be achieved Magic Fit DeepView compares the primary sequences of the two molecules using a PAM matrix ADVANCED DEEPVIEW COMMANDS 69 Iterative Magic Fit Explore Alternate Fits PAM 200 by default selects the best matching fragments of amino acid pairs and based on them superposes the molecules on the Graphic window This is the quickest way to test if two molecules could fit but it will only work if a reasonable sequence homology is found This fit can usually be improved For information purposes involved residues are selected on the Control Panel and on the Alignment window DeepView starts with an initial superposition as described above Magic Fit Then the fit is optimized by iterating through several Improve Fit cycles see point 118 Finally a structural alignment is generated see point 121 This method is slightly slower than Magic Fit but gives a better global superposition Depending on the option you selected on the RMS amp Auto Fit options dialog the fit is optimized by minimizing the RMS deviation between Ca backbone sidechain or all atoms The RMS deviation for the last cycle is displayed in the tool bar message space For information purposes involved
54. and then strands of less than 3 residues are destroyed e There is a subsequent step of trimming the helices in order to make nicer ribbons This is to avoid the problem when residues could be assigned as both belonging to one helix and one strand HII MUTATIONS ANNEX 2 133 When browsing through rotamer libraries a simple clash score according to the following formula is provided valid for Rotolibl aa and Rotolib2 aa libraries The best rotamer is the one that with the lowest score Clash Score 4 x number of clashes with backbone N CA and C atoms 3 x number of clashes with backbone O atoms 2 x number of clashes with side chains atoms number of H bonds 4x number of SS bonds IV BUILDING LOOPS Similarity score Score sum of amino acid exchange penalty scores for the currently selected alignment matrix Clash score Score see above Angle evaluation Score deviation compared to an ideal closure angle see also RMS Field Force Energy and Threading Energy V MOLECULAR SURFACES Not yet described VI ELECTROSTATIC POTENTIALS Charge Model Currently the protein is assumed to be at pH 7 0 with default protonation state for all residues As default settings only charged residues Arg Lsy Glu Asp are taken into account and the charges are located at the corresponding non H atom positions You may also use the partial charges of the GROMOS 43A1 force field This is much slower as
55. at http imsb au dk mok o The O server http xray bmc uu se usf Uppsala Software Factory e XPLOR maps The Uppsala University is providing an electron density server containing electron density maps for many PDB entries http portray bmc uu se eds NOTE Although DeepView can display electron density maps it has not been designed for crystallographic structure solution i e you will not find elaborated functions for model building or map manipulations VIII SOLVENT ACCESSIBILITY DeepView defines the maximum accessibility as the accessible surface area for residue X in an extended pentapeptide GGXGG The relative accessibility of a residue X is obtained by comparison of the observed accessibility to this reference value of 100 Colors range from dark blue for completely buried amino acids to red for residues with at least 75 of their maximum surface exposure NOTE The numerical values for each residue can be accessed via the scripting language command access ANNEX 2 135 IX MATRICES They are located in the usrstuff matrix directory Standard exchange matrices used by other programs FASTA Blast can be used X THREADING ENERGY MEAN FORCE POTENTIAL PP Not yet described XI FORCE FIELD ENERGY FP Swiss PdbViewer includes a version of the GROMOS 43B1 force field It allows evaluating the energy of a structure as well as repairing distorted geometry through energy minimization In this implementation al
56. ation on current layer 111 62 Deep ViewManual e Using electron density maps Concept Structures derived from X ray crystallography can be displayed together with their corresponding electron density map Examples of application Viewing an X ray derived structure in its corresponding electron density map allows evaluating the local fit of each residue with the experimental data This helps to estimate the accuracy of e g mobile loops or bound inhibitors Procedure First open an X ray derived structure and then load its electron density map by clicking File gt Open Electron Density Map DeepView currently supports three file formats O DN6 CCP4 and X PLOR see Annex 4 Electron density maps The Electron Density Map Parameters dialog lets you adjust the display of the electron density map This field cannot be edited It provides Electron Density Map Parameters Fa information on the unit cell and the loaded Infos ee I s Y z unit cell size along a X b Y c Z Unit Cell Size 2 famo fao unit cell e B y angles number of sections in which the cell is Cell Angles 90 000 90 000 90 000 divided along each axis Mo i fisi 73 range of sections Min to Max covered by the Min Section 2 E BI map Max Section M FE E Select the display of your map see below Displa 1 From Section to Section limits a volume FomSection pe FB according to the number of sections Geada
57. atom C Display only groups that are within Displays groups on the Graphic window that are Scectauupe hai re alih within the entered distance of the picked atom Add to Selection groups that are within Selects groups on the Control Panel window that 6 000 of the picked are within the entered distance of the picked atom Act on all Layers Adds to a previous selection those groups that are Cancel within the entered distance of the picked atom Enter here the distance If more than one layer was loaded the Display Radius dialog box lets you enable disable application of the tool to all layers Display Radius dialog box 48 e Centering the view on a picked atom Button 10 is for centering the display of a molecule on a selected atom Click the button and pick one atom The display jumps to center the molecule on the picked atom For centering a molecule on a specific group by using the Control Panel see point 72 BASIC DEEPVIEW COMMANDS 21 b Using the menus Edit menu 49 e Editing the identification of a molecule The Edit menu offers three commands that allow editing the identification of a molecule Edit menu Rename Current Displays the Rename Layer Components dialog box which allows renaming the currently Layer active layer and changing the chain identifier of selected amino acids as well as renumbering them see figure below Rename Selected Displays the Rename HETATMs dialog box whi
58. ayer gets a single unique color The layers are colored in order from the first as yellow blue green red gray magenta cyan salmon purple light green and brown The color succession is repeated for additional layers Ideal for viewing superposed structures By Chain Colors each chain by a different color yellow blue green red gray magenta cyan salmon purple light green and brown The color succession is repeated for additional chains NOTE Chains are defined in the PDB file a break in the modeled polypeptide chain does not signify a new chain 28 DeepViewManual 65 e Color menu third block Color menu By Alignment At least two proteins must have been loaded superposed and structurally aligned see points Diversity 127 132 Applies a blue to red color gradient to all layers according to the degree of similarity among all aligned residues Blue indicates identical or very similar and red indicates that residues have dissimilar properties see Annex 4 By Accessibility Each group is colored by its relative accessibility see Annex 4 Colors range from dark blue for completely buried amino acids to red for residues with at least 75 of their maximum surface exposure The relative accessibility of a residue X is obtained by comparison to a reference value of 100 accessibility computed in an extended conformation in the pentapeptide GGXGG By Threading Colors each residue of the protein according to its ene
59. ayer has its own associated axis which is displayed on point 0 0 0 of the layer by checking the axis item on the Layers Infos window When several layers are loaded these axes are not necessarily superposed since crystal structures have no reason to share the same referential NOTE When only one layer is loaded it might be more appropriate to use the global axis by checking Display gt Show Axis see point 57 The axis will be displayed on the top left corner of the screen instead of on point 0 0 0 When some layers are allowed to move and others are not the atom coordinates of the moving layers will be changed Follow the steps of the next figure to understand how the atom coordinates are affected 66 DeepViewManual 3 Reopen the project and display its PDB file see point 67 the X Y Z atom coordinates of both layers remain unchanged equal to 1CRN atom coordinates 1 Load 1CRN in two layers and rename them 1CRNA and ICRNB see point 49 x a m C WINNT Profiles mfh10000 Desktop viewer download 1CRN x ATOM 2 CA IEM l 00 10 80 E 1CRNA ATOS 4 O Im 1l 00 3 65 and ATOM 5 CB THR 1 00 13 02 4 1CRNB m C WINNT Profiles mfh 10000 Desktop viewer download 1CRN 2 Click File gt Save gt Project to save ATOM 1 N THR 1 00 13 79 I ATOM z CA THR L 00 10 80 both layers as a project see point ATOM 3 C THR 1 00 9 19 ATOM 4 0 THR ki 00 9 85 31 and close all layers are E EE TE a 00 13 02 These are two v
60. box to the corresponding cavity change the color Shift Ctrl click a line to center and display only Check here to display on the Surface A and volume A the residues surrounding Graphic window the molecular of the molecular surface and the cavity surface and the detected cavities detected cavities Window gt Surface and Cavities window Before you compute a molecular surface its drawing quality can be set on the Surface Preferences dialog by entering a value from 1 worst quality to 6 best quality This is important because areas and volumes of cavities depend on the drawing quality Drawing quality oh oar A 103 ADVANCED DEEPVIEW COMMANDS 53 NOTE Differences in the drawing quality between levels 1 2 3 4 and 5 6 depends on the number of triangles considered The accuracy of the surface and volume computation as well as the cavity detection are also dependent on this value e Computing electrostatic potential maps Concept Protein molecules contain charged groups e g side chains and terminal residues that induce an electrostatic field around the molecule These potentials can be represented as three dimensional electrostatic potential maps DeepView provides two different representations of electrostatic potential maps e three dimensional potential maps showing the electric field spreading out into the solvent A positive value in kT e is used as a cutoff to delimit a blue contour of those grid p
61. c X11 XF86Config as following l The entry in VertRefresh must match your monitor s hardware limits check your hardware manual for correct settings to prevent monitor damage In our example we use VertRefresh 40 120 2 Enter a new modeline with a new screen resolution e g Modeline 1600x1200 135 00 1600 1604 1688 1928 1200 1225 1228 1262 where 1600x1200 is the resolution 135 00 is the pixel clock in MHz the first block of four figures are the horizontal rates and the last four figures are the vertical rates Htotal is 1928 and Vtotal is 1262 You can adjust these settings with the program xvidtune once it is in the config file The total vertical frequency of the mode should not be more than half the maximum your monitor supports You can calculate the vertical refresh frequency in Hz with the formula pixel_clock 1000 1000 htotal vtotal 3 Make the new mode active in your X server s section Screen in the config file Change the line Modes in the subsection Display to contain the previously defined mode e g Modes 1600x1200 1280x1024 We have tested this successfully on a HP vectraVE with a 21 Compaq Qvision210 monitor 131 ANNEX 4 CALCULATIONS I CONNECT DeepView will read the CONECT cards in PDB files and use them to generate bonds provided they are plausible If no CONNECT cards are present DeepView will try to guess the correct molecular structure from the atomic coordinates You can use a text ed
62. carbon CA The group appears in bold in the Control Panel This action is very useful for jumping to a specific group in the model Linux Irix right Alt click the residue using any mouse button Mac option click the group in the Control Panel 73 e Selecting all groups belonging to a chain The first column under the group header is for the protein chains named A B C Click anywhere to select all groups amino acids hetero groups belonging to the selected chain If the model contains no chain identifiers the column is blank and clicking it will select all groups 74 e Selecting all groups belonging to a secondary structure element The second column under the group header is for the protein secondary structures named h s Click anywhere to select all groups amino acids belonging to the selected secondary structure element 75 e Selecting one group only The third column under the group header is for the amino acids identification VAL1 LEU2 see point 46 Clicking a group will select it 76 Selecting several individual groups In the third column under the group header you can select several individual groups by clicking them while holding down Ctrl on PCs or Alt on Mac Linux and Irix BASIC DEEPVIEW COMMANDS 31 Alternatively you can use the numerical keypad not implemented yet e enter the first group number and then e typing before the next entered number will add the residue to the selection e
63. ce Auto Color by Enabling this option colors the residues by threading energy updating the coloring Threading Energy whenever the sequence alignment is edited see point 132 Residues are colored on the Graphic Alignment and Control Panel windows Blue indicates a low energy green 1s for intermediate values and red indicates a high energy 132 e Manually refining the alignment The alignment of the target sequence onto the templates can be manually refined on the Alignment window by translating residue or inserting and removing gaps 82 DeepViewManual imi Alignment Fa D p f H IL mne ED E EN ETT AEE Select an amino acid on the target sequence and use the space bar to insert a gap Select an amino acid on the target sequence and use the backspace key to remove a gap Original gap E Alignment Fi Select one or a group of amino acids on the target sequence and use left right arrow keys to displace the gap V Ql S S Q YP 2tunb TI SRIVVSYOTEI P4047 VAL221 mms 0 000 Procedures to manually adjust an alignment The preliminary 3D structure and the threading energy plot help find the most satisfactory adjustment e Graphic window a gap in the target sequence is represented by a long peptidic bond Its display is updated whenever the gap is adjusted in the alignment window thus letting you assess the 3D quality of your adjustments e Alignment window the threading energy plot and the total threading
64. ch can either be computed by DeepView or loaded from specialized external programs II WORKING ENVIRONMENT DeepView can display up to eight interconnected interactive windows This section presents the general purpose of every DeepView window each of which will be fully described later 1 e Graphic window see 23 167 It is used to visualize loaded molecules which can be rotated translated and zoomed Display of the coordinate axis is optional Molecular surfaces electrostatic potential maps and electron density maps can also be displayed on the Graphic window 2 Control Panel see 70 This table like window is for controlling the visual representation of the currently active layer It lets you enable the display of backbones side chains labels molecular surfaces and ribbons for each group and set the colors for the different objects on display 3 e Toolbar see 38 40 Contains the menus and tools of the program 2 DeepViewManual These let you analyze the loaded molecules and use Swiss Model in combination to model new structures Graphic er saa window F group show side abl ea AE Main windows v v v v v v v v v v v v v v v v v m Alignment YRGYSLGNWYVCAAK Sh DA G5 Y G p NS Rwwe y Y S L G N WS C A A F h L 2 A GS Y G DI NS Riwwe Specific 480 120 60 0 60 120 18 qso windows 180 180 q a gt n wa at gt s lt i L a 180 oo 450 E 120 60 0 60 120 180 t
65. ch allows renaming selected hetero groups HETATMs as well as their atom names see figure below Fix Atoms Checks if amino acids atom names are conform to the IUAPAC standard This is useful Nomenclature since files returned from Swiss Model see chapter on homology modeling or files that have been energy minimized with external force fields see point 107 sometimes contain wrong atom names Rename Layer Components gt Fields for renaming Layer Name thew the layer the chain ID of selected groups Rename Chain of Selected Groups to leave unchanged Field for renumbering selected Renumber Selected Groups from to leave unchanged groups Field for renaming the selected Group Name ATP HETATM Atoms Names PG 01G 02G 036 PB 018 026 O3B L PA 101A 02A 03A OSI CSI CAIO A C3103 C2102 C1N9IC8IN7I I ESICeINSINTICOINSICAT Field for renumbering the e atoms belonging to the selected A HETATM four characters per atom as in PDB files Rename Layer Components and Rename HETATMs dialog boxes In addition to these specific commands the Edit menu includes the following commonly used commands e Undo and Redo which allow undoing and redoing the last action e Cut Copy Paste and Clear not implemented yet 22 DeepViewManual For explanations on all other commands of the Edit menu which consist of advanced commands refer to the following points Edit menu Script Commands
66. cks if a specific residue is selected When lt layer gt is omitted the current active layer is used Returned value is of type lt int gt and is 1 if the is_selected lt layer gt lt int gt is selected lt int gt group is selected and 0 otherwise Related commands select ANNEX 2 Demonstrated in example script 11 e layername Will return the lt string gt value of the layer name lt string_var gt layername of lt int gt where int is the relative position of the layer from the first loaded which is number 0 of course Related commands none Demonstrated in example script none max Will return the max value of two numbers or variables max of lt float gt lt float gt max of lt int gt lt int gt Related commands min Demonstrated in example script none e min Will return the min value of two numbers or variables min of lt float gt lt float gt min of lt int gt lt int gt Related commands max Demonstrated in example script none minimize Performs an energy minimisation using n cycles of steepest descent minimize lt selection gt of lt layer gt with lt int gt cycles Related commands compute Demonstrated in example script 07 move Moves a selection move lt selection gt by lt vector gt where lt vector gt contains the translation in angstroms Related commands zoom rotate Demonstrated in example script 09 e mutate Will mutate an amin
67. corresponding signal to the emitter and this allows to see stereo in a normal window while the rest of the desktop stays the same This means that there is no loss of screen resolution or available screen space This mode is much more convenient than Above Below stereo format AB and is supported by most current stereo ready applications on the market Not all graphic cards support true quad buffered OpenGL Stereo and drivers may be available only for some operating systems Please check carefully with your hardware supplier before buying a card SETTING PREFERENCES I OVERVIEW 145 e Administering your preferences The first block of commands under the Preferences menu is for administering your preferences Preferences menu Modify Last Prefs Recalls your last invoked Preferences command Dialog Save Preferences as Lets you save in a prf file the state of all preferences of your current session Open Preferences Lets you open a prf file This will contain the state of all preferences of a previous session so that you do not have to re enter them again 146 e Default preferences The first time you launch DeepView a Default prf file setting the most appropriate preferences for a smooth and rapid use of DeepView default preferences state is created and stored in the urstuff directory This file will be opened by default each time DeepView is launched The Default prf file is updated at each time a preference is changed
68. ction Returned value is of type lt float gt and is returned in degrees omega lt selection gt Alternately you can access directly a specific residue from a specific layer which is faster and handy in loops with omega lt layer gt lt int gt Related commands phi psi ss Demonstrated in example script none open Loads a pdb file in the workspace next available layer open pdb from disk net lt string gt ANNEX 2 121 To be able to use the net option you have to set the correct server address in Network Preferences Note that it is possible to omit pdb as it is the default value lt string gt contains the full filename see below The filename must be the absolute path of your file Unix users will enderstand what I mean but Mac users might be a little confused Alternately to be cross platform you can also use one of the predetermined directories open pdb from usrstuff lt string gt open pdb from temp lt string gt open pdb from download lt string gt Constructing a full path on a Mac name of disl name of folder name of subfolder name_ of subsubfolder filename For example assume you store your pdb files in a folder named pdb located in the System disk You can access the file lcrn pdb like this System pdb 1crn pdb As you can see Mac uses as separator This is of course different for Unix which uses and from windows which uses V In order to make your scripts as por
69. ctory see point 15 User Defined Links Opens your web browser to the page user htm in your usrstuff directory and lets you set your favorite links to go quickly where you want on the net directly from within DeepView see point 20 30 e Updating the program not implemented yet Under the Help Apple or Info menus according to the platform click Update Swiss PdbViewer the program will look in the server for a new version of DeepView or for updated library files and will automatically download and install them on your computer Ending a Deep View Session During a Deep View session you might have loaded several molecular coordinate files see point 21 displayed objects around them As DeepView will immediately quit when you invoke the Exit command see point 36 before ending your session you might want to e save your data e systematically close your files These actions can be achieved by using the Fi e menu of the Toolbar I SAVING DATA Select File gt Save this command offers a submenu to save data and images 31 e Saving molecular coordinate files File gt Save command Layer Saves the currently active layer in PDB format In addition to atom coordinates saved data include the current Control Panel settings the current view orientation the background color and any added bonds except hydrogen bonds The REMARKs journal references statistics etc from the originally opened PDB file are not inc
70. d including all implied warranties of merchantability and fitness for a particular purpose DeepView Swiss PdbViewer is provided on an as is basis The limited license grant means that you may not do the following with Swiss PdbViewer decompile disassemble reverse engineer modify lease loan sell distribute or create derivative works based upon the Swiss PdbViewer software in whole or in part without written permission of the authors transmit Swiss PdbViewer to any person except if the original package and its whole original content is transmitted and that this person accepts to be bound by the terms and conditions of this software license agreement and warranty Neither the authors nor GSK shall in any event be liable for any direct consequential incidental indirect or special damages even if advised of the possibility of such damages In particular the authors and GSK shall have no liability for any damage loss or corruption of data or programs stored in or used in conjunction with DeepView Swiss PdbViewer nor shall the authors or GSK be liable for the cost of retrieving or replacing damaged lost or corrupted data If for any reason a court of competent jurisdiction finds any provision of this license to be unenforceable the other provisions of this limited warranty and software license agreement shall remain in effect without limitation All products mentioned in this user guide are trademarks of their respective companies I
71. d Linux Related commands open Demonstrated in example script 06 e search ANNEX 2 Allows searching 3D patterns in pdb files NOT yet AVAILABLE search in lt layer gt lt string gt search in lt layer gt lt string gt gt gt lt string gt where the first lt string gt contains the filename of the 3Dsearch pattern description file and the second optional string appends the output to a file that might be worth clearing before with the clear command Demonstrated in example script none e selcount Will return the number of selected groups in a layer Sint_varname selcount of lt layer gt Related commands groupcount Demonstrated in example script 06 e select Allows selecting specific residues and performing logical operations on them This can then be used to color or hide residues among other things lt var gt select in lt layer gt lt selection gt select lt var gt when in lt layer gt is omitted the current active layer is assumed lt var gt must contain a selection and lt selection gt can be any combination of all None Water hoh solvent h2o Strand Helix Het will select all HETATM Aa will select all amino acids nt will select all nucleotides Res lt string gt residue kind example res A C D Name lt string gt residue name example res ALA OXT ATP Chain lt string gt residue chain example chain A Num lt int gt residue number P
72. d is Above Below Open the Monitor and Sounds Control Panel display all resolutions not only the recommended ones and figure out if the monitor supports a resolution with 60Hz or below If this is so there is a good chance that it can support Above Below stereo Note that the stereographics device has to be connected between your monitor and your computer As the cable has an HD15 plug you need to check whether your monitor has an HD15 input This is not likely to be the case on Apple monitors in which case you will need an additional plug Check with your Apple supplier what needs to be done in your case We have tested this successfully on a PowerMac 9600 with a 21 multi synch Apple color monitor and with a SGI 20 color monitor ANNEX 2 PC MS windows Two hardware stereo modes are supported Above Below and OpenGL Stereo DeepView uses Above Below format for all graphic cards that do not support quadbuffer OpenGL Stereo in the current video mode If you activate the Use hardware Stereo Top Bottom option on the Stereoscopic View Settings dialog see point 168 you will see 2 pictures separated on the top and bottom of the screen To get a good stereo perception you may have to adjust the vertical offset of the 2 pictures with the up and down keyboard arrows while in stereo We have tested this mode successfully on an HP Kayak workstation with an HP1100 monitor This mode also supports DimaondFireGL400 video card Make
73. ds will appear in green and steric hindrances in purple provided that the group that makes the contact with the mutated amino acid is visible You can cycle through all available rotamers by hitting the key of the numerical keypad holding Shift while hitting the key will select the previous rotamer instead of the next one or by clicking the little arrows that appear below the Mutate tool ITATE TORS Use these arrows to cycle through the available rotamers Number corresponding to This score is for evaluating the the displayed rotamer 5 rotamer the best rotamer is the over the number of one that totalizes the lowest available rotamers 9 score Mutating an amino acid Clicking once again the Mutate tool ends a mutation You will be prompted for accepting or discarding the mutation Discarding it will restore the original side chain NOTES e The Mutate tool is currently limited to amino acids e The tool was designed not only to mutate a residue but also to provide alternate rotamer conformations that can be easily browsed ADVANCED DEEPVIEW COMMANDS 39 e Two rotamer libraries are available Rotolibl aa and Rotolib2 aa located in the stuff directory A copy of Rotolibl aa named Rotolib aa is loaded at startup to be used by default e Rotolib2 aa is a backbone dependent rotamer library The score is computed as for Rotolibl aa In addition the message space displays the probability from 0 to 1 of find
74. e Control Panel show lt part gt of lt selection gt show in lt layer gt lt part gt of lt selection gt where lt part gt can be any combination of res side label surface ribbon vdw Related commands hide color Demonstrated in example script 06 09 and 13 e silent Can be used in conjunction with the stop command to prevent any feedback of which line the script was stopped silent stop Related commands stop Demonstrated in example script 08 and 10 e sin Computes the sinus of an expression sin lt float gt sin lt int gt This returns the value in radians Related commands asin cos acos tan atan PI Demonstrated in example script none SS Will get the secondary structure assignment of the first selected amino acid found in a selection Returned value is of type lt string gt and is h s or c ss lt selection gt Alternately you can access directly a specific residue from a specific layer which is faster and handy in loops with ss lt layer gt lt int gt Related commands phi psi omega ANNEX 2 127 Demonstrated in example script 11 e stop Will stop the script in a way that it can be continued from the graphical user interface with shift open script Very convenient if you want to interactively inspect a molecule before resuming the script flow sub select_negative silent stop Related commands please do thank you pause silent Demonstrated in example scri
75. e ot HUTHTE T F5SISH Selected tool lt W SEP Wey i FS eo L SY 2 The dihedral angle of four selected atoms is given on the message 46 e Identifying groups and atoms Button 8 allows identifying an atom and the group to which the atom belongs Click the button and pick one atom The atom type CA CB O and the group to which it belongs LYS116 ASN117 are displayed both on the molecule and on the message space In addition the message space gives the x y z atom coordinates and B factor For further ways to label groups on a molecule see point 78 20 DeepViewManual Identification of an atom picked on the Graphic window TS dhew Lr5S1 N D 72Z70 33 095 25510 J3D45 layer amino atom x y z atom atom name acid type coordinates B factor Identification of the same atom on the Toolbar 47 e Displaying selecting groups within a distance of a picked atom Button 9 allows restricting the display of the molecule on the Graphic window or the selection of amino acids on the Control Panel to groups within a distance of a picked atom Click the button and following the instructions that appear in the message space below the toolbar pick one atom The Display Radius dialog box allows entering a distance and choose one of the following options Display Radius x Add to view groups that are within Adds to a previous display those groups that are within the entered distance of the picked
76. e Alternate Fits result list match txt Select one solution to visualize it on the Graphic window and to display on the Toolbar the number of atoms involved and their RMS Fit gt Magic Fit followed by Iterative Magic Fit followed by Explore Alternate Fits changes occurring on the Graphic window ADVANCED DEEPVIEW COMMANDS 71 E Control Panel x V visible Control Panel x can move v 7 visible Control Panel x E Control Panel x JV visible can mowe Z group show side labl ribn col p group show side labl 4 ribn col g group show side labl ribn col p can move 7 can move 7 h SER124 v h LEU125 v h ASP126 v h LYS127 v h PHE128 v h LEU129 v h ALA130 v h SEF131 v h VAL132 v h SEF133 v h THR134 v h VAL135 v Before the fit h SEF124 v h LEU125 v h ASP126 v h LYS127 v h PHE128 v h LEUI29 v h ALA130 v h SER131 v h AL132 v h SER133 v h THR134 v h VAL135 v A h SEF124 v A h LEU125 v A h ASP126 v A h LYS127 v A h PHE128 v A h LEU129 v A h ALA130 v A h SEF131 v A h YAL132 v A h SEF133 v A h THF134 v A h vAL135 v After Explore Alternate Fits h THR134 v h VAL135 v A h LEU136 v A THR137 v A SER138 v A LYS139 v A TYR140 v A HEM142 v h LEU136 v THR137 v h LEU136 v THR137 v h LEU136 v THR137 v SER138 v LYS139 v TYR140 v ARG141 v OXT141 v HEM142 v SER138 v LYS139 v TYR140 v ARG141 v SER138 v LYS139 v TYR140 v ARG141 v OXT141 v HEM14
77. e file 1 e this will be the active layer and select the residues currently alanines for which you want to find the real sidechains Click Build gt Find Best Fitting Peptides DeepView will compute and display a list with the existing polypeptides that would fit onto the backbone fragment that you selected 42 DeepViewManual me CAWINNT Profiles mfh10000 Desktop vie x FFRACHENTS 46 6 FEGATY mismatch WHGEVF mismatch FSCGCLPH mismatch YIGVEA mismatch EH GDTE mismatch Polypeptides fitting ENNCCA mismatch your selection in this ICSCTL mismatch example 6 alanines NNGCAR mismatch VYVIGAGF mismatch were selected VIGSGT mismatch GAGFYG mismatch 1 1 1 1 1 1 1 1 1 1 1 Moe dm d TS q in on oo d n PMH b d q Cn n Cn n Number of mismatching residues Number of atoms inside and Score value outside the electron density Build gt Find Best Fitting Pepetides Result list Results are sorted by a score see Annex 4 Electron density maps Explore the various results by either clicking on the different lines or by using the up and down keyboard arrows while the Result list is the active window You will visualize the result on the Graphic window On the Control Panel the names of the selected alanines will change into the names of the solution residues NOTE If the result list window is not active the up and down keyboard arrows will change the sigma contouring value of the electron d
78. ecking here will only Default Appearance Default Colour points 116 121 and apply the preferences set Carbon C alpha Trace 105 respectively In this dialog to non Backbone CPE Swiss Pdb Viewer files i Backbone Sidechains f Secondary Structure which include any PDB coloring scheme for Select a default t Ribbons f B Factor molecules upon IY Show Hydrogens if any f Threading Energy loading IY Show Solvent if loaded AMS needs Magic Fit file not saved by Deep View Check here to filter all IY Apply default settings only to non Swiss Pdbyiewer files water molecules from the structure they will not be i Z Ignore solvent WAT SOL HOH Cancel displayed nor loaded 94 DeepViewManual 151 e Real time display preferences You can specify how much the display of molecules should be simplified while these are moved The simpler the display and the smoother the handling of real time translations rotations and zooms Thus vartous options to reduce the CPU load are provided Real Time Display Preferences F During real time operations display To allow a finer control of the CPU load you can Harie Nu A oss modify the maximum number of lines to draw If the number of lines to draw exceeds this H Bonds P Label Electron Density threshold value the program will first attempt to draw the molecule without stereo view then Update H bonds and clashes during coord move without hydrogen a
79. ecrease the image size by 10 Related commands rotate move Demonstrated in example script 05 ANNEX 2 129 Annex 3 Hardware Requirements e Hardware Stereo Support DeepView Swiss Pdb Viewer currently supports the following hardware stereo display modes Real OpenGL Above below AB quad buffered frequency doubling z x j gt a a a _ Quad buffered OpenGL Stereo We highly recommend to buy a stereo card that supports quad buffered OpenGL stereo if available for your operating system Please see with your hardware dealer As a starting point see e g Stereo Hardware ttp www stereographics com p www nuvision3d com 0 www 3dlabs com Above Below AB stereo mode The AB hardware stereo mode needs a monitor capable of supporting a vertical synchronization that has been doubled Other monitors might fuse when doubling of frequency is enabled Make sure that you can switch your screen to a 120 Hz refresh rate before buying such hardware This should be true for most of the multi synch monitors but is definitely not the case for old fixed frequency monitors Also consider that the effective resolution of the screen will be halved so a 19 screen is quite recommended All graphic cards will work as all switching 1s done by the external hardware You will also need an emitter and LCD shutter glasses e g CrystalEyes Macintosh The only hardware stereo mode that can be supporte
80. ects 57 58 Display commands select various views for displaying a molecule 59 set the style of labels placed by the Control Panel 60 clear all labels placed by the tools 61 Let you color all or parts of a molecule by different criteria 62 66 Displays PDB files or opens text files Ctrl clicking 67 68 tji Provides help on the Toolbar p69 72 Let you center the model on a specific group Let you select all groups belonging to a chain 73 all groups belonging to a secondary structure 74 vee element Ah ALA 22 one single group s several individual groups an interval of groups show side labl ribn Toggle the display of groups Toggle the display of surfaces col Lets you color a molecule and associated graphic objects ribbon surfaces Toggles on and off the display and movement of layers Provides help on the Control Panel LF Manages the display of projects Provides help on the Layers Infos window 16 DeepViewManual I USING THE TOOLBAR 38 e The Toolbar The Toolbar contains the tool buttons and menus of the program amp Swiss PDB Viewer 3 7 b1 File Edit Select Build Tools Fit Display Color Preferences SwissModel Window Help Move PDB file icon click it to Message space this is for providing Help icon click it to obtain display the PDB file of instructions for the use of the tools as help on the Toolbar the currently active layer well as for displaying information Toolbar contains
81. ecular surface is colored in yellow and different colors of your own choice to a colors are assigned to the cavities inside the protein computed molecular surface Atom Type the surface is assigned the CPK colors of underlying 1 on the surface header select atoms molecular surface Electrostatic Potential a color gradient from blue to white to red 2 select the groups for which you is used to color the molecular surface where blue red and white want to color the surface are for positive negative and neutral potentials respectively 3 on the color header select to color according to the given cutoff values in kT e Note that to apply surfaces and then click col to these colors you first need to compute the electrostatic potential display the color palette where you see point 103 can choose a color Coloring a molecular surface by using the surface preferences and the Control Panel Computing a molecular surface allows identifying internal cavities big enough for a water molecule e on the Surface Preferences dialog see point 156 select the Cavity Default surface Color e compute the molecular surface e display the Surface and Cavities window The first line 1s for the 7 ae B T on 51 Mm Surface and Cavities Colors assigned to Remaining lines are for wis volume c the molecular detected cavities listed by i surface and to the decreasing size click a detected cavities line to center the view on ki Click a
82. ecule see points 62 66 Co or menu 82 e Viewing moving a layer The following commands which are only meaningful when working with projects see chapter on advanced functions section B are located above the column headers of the Control Panel Check them to enable the following actions Control Panel upper header Show hide the whole layer Allows moving the layer 1 e translating and rotating it 83 e Obtaining help on the Control Panel 2 Click on the red question mark to obtain help on the Control Panel III USING THE LAYERS INFOS WINDOW 84 e The Layers Infos window Mm Layers Infos x Click the question mark lt q Layer vis mor axis C H HbndHdst side HOH cyc lern WF WF VF WF to obtain help on this lhet v v v v window lhel v v v v List of all loaded files The For each layer check uncheck Shows the number of currently active layer appears these items to toggle on off the currently selected in red You can select it here display or actions described below groups in each layer Hold down Shift to act on all Layers Infos window layers 85 e Setting the display of layers When several layers are loaded the Layers Infos window lets you independently set the display of each layer by checking unchecking the following items BASIC DEEPVIEW COMMANDS 35 fis uda mor te movement of ayer For e relave movement of yen see pom 0 the dipay ofbackboncowgenstoms SSS the display
83. endering parameters Definition of the position and intensity for three available 3D lights Graphic window features slab depth Definition of stereoscopic view parameters Il SETTING PREFERENCES Each Preferences dialogs comprises a series of items Text fields are for entering specific values of your own choice Items preceded with a square Height 4 J0 400 are for cumulative selections w Use this Top Color W Uze this Side Color Use this Bottom Items preceded with a circle Clicking a Color button are for selecting one amongst displays a standard color various exclusive options palette to let you choose a color for the associated item This chapter goes through all Preferences dialogs Clarifications are limited to the most complex items each dialog being generally enough self explanatory SETTING PREFERENCES 93 149 e General preferences You can enable disable the display of informative and warning messages both on initiating a DeepView session and upon loading a molecule You can also set how DeepView reads PDB files Check here to accept the preferences set G T x appearance of the Graphic window as set under CIPTA eee are Preferences gt Display see below LE Enable this item to get a report of problems found Auto accept display window attributes at startup during loading molecules missing atoms etc Center molecule upon loading Show splash screen at startup
84. energy are also updated whenever the gap is adjusted in the alignment window to let you evaluate the quality of your adjustments Global Threading energy of amino acids flanking a gap threading As no point is above the zero line it indicates energy that no gross alignment errors are detected by the mean force potential in this region 3x P41047 461 x 376 Long bond A7 corresponding to a gap in the Lex target sequence Elements that help find the most satisfactory alignment see example in the figure below 133 134 135 ADVANCED DEEPVIEW COMMANDS 83 e Setting the multimer mode in development If you have to model a symmetric homo oligomeric structure SwisModel gt Homo Multimer Mode enables the multimer modeling mode in which the alignment adjustments manually performed see point 132 on one monomer will be reflected in all the other monomers This requires that all monomers have exactly the same amino acid sequence e open the FASTA file with a text editor and generate the polymer by copying the monomer sequence separating each copy with a semicolon e SwissModel gt Load Raw Sequence to Model opens the FASTA polymer Each monomer will be displayed as a helix and will have its own chain identifier Homologous polymer templates will be PDB files ExPDB files contain only one chain that can be opened from local directories File gt Open PDB File or imported from the PDB server File gt Import gt Grab
85. ensity map 92 e Modifying the backbone Concept DeepView lets you modify the backbone by e breaking ligating it at any selected amino acid e adding a terminal carboxyl group OXT Examples of application e Since a peptide chain is linked altering the structural features of a part of a protein such as modifying the backbone angles of residues will move all N terminal residues of the chain To prevent this the backbone can be broken after the last residue that belongs to the part of the protein to be altered This is particularly useful to alter a loop manually you might want to isolate it from the rest of the protein by breaking the backbone after the last residue belonging to the loop Once satisfied you can ligate the backbone again to restore a peptide bond where the backbone was broken e You might need to add a carboxyl group OXT at the end of a chain in order to make the carboxy terminus of a protein after removing residues see point 94 Note that an OXT 1s automatically added before any energy calculation see points 106 Procedure To break ligate the backbone and to add a terminal carboxyl group use the following commands under the Build menu ADVANCED DEEPVIEW COMMANDS 43 Break Backbone You will be asked to pick either a N atom or a C atom of the backbone which will be broken at this point Ligate Backbone You will be asked to pick an unlinked backbone atom and DeepView will try to ligate it to the followi
86. entage of the helix or strand width and height as set above 156 e Surface preferences Set the appearance and color of molecular surfaces Van der Waals and accessible surfaces are always dotted and that their color can only be modified on the Control Panel Select a color for Surface Preferences x molecular surfaces If you color them General Appearence General Appearence Real Time by their C Dotted Lines fe Not drawn Electrostatic t Plain Lines C Dotted Lines Select the general appearance of molecular surfaces for static and moving Filled Triangles only in 3D mode Plain Lines Potential you need aoleu to compute it first t Filed Triangles and edit here the i Set the surface qualit sigma values for K quem I 1 coarser 6 finer he electr 1 Transparency will show only on SGI or wher ie m Carang Derana A the scene is rendered with POY affects the precision for detecting cavities see point 102 and transparency 0 none 100 full Default surface Color NOTE Coloring a Cavity Ignore Selected Residues molecular surface amp Atom Type for example cofactor by its electrostatic Electrostatic Potential otential is eile Ri as Hi Check here to compute e 1 800 0 000 fi B00 a surface ignoring selected residues useful to compute a surface for one chain only for example electrostatic potential to the surface see next dialog SETTING PREFERENCES 97 157 e
87. eractions or to quickly regularize the geometry of very distorted residues before performing an energy minimisation with all parameters enabled ADVANCED DEEPVIEW COMMANDS 57 E C spdbv temp 1a3od E2 x Computations were done in vacuo with the CROMOS96 43Bl parameters set without reaction field Z Z For more information about GROMOS96 refer to W F van Gunsteren et al 1996 in Biomolecular simulation the GROMOS96 manual and user quide Vdf Hochschulverlaq ETHZ http iqe ethz ch gromos When using those results please mention that energy computations were done with the GROMOS96 f implementation of Swiss PdbViewer z torsion improper nonBonded electrostatic constraint 7 540 0 000 0 00 17 35 0 0000 12 626 9 528 22 41 1093 21 0 0000 10 310 2 653 43 23 17 87 0 0000 3 614 3 765 6 99 6 35 0 0000 Amino acids list FF in kJ mol computed for each considered object Total FF name chain ID in Kj mol number Tools gt Compute Energy Force Field Energy Report The Energy Report like any other text file can be opened with a text editor and printed To display the force graph Click Window gt Alignment to open the Alignment window and click its small arrow next to the red question mark layer name and total E Alignment x molecular FF OF Smooth 1 means that the pir energy of each residue will be the average of itself plus the energy of flanking residue on each side Click smooth t
88. eractive mode superpose Ibhp onto 1Icrn using CA redraw Related commands show Demonstrated in example script 05 and 07 rename Will change the chain name of the selected residues rename chain of lt selection gt as lt string gt Will change the layer name rename lt layer gt as lt string gt Related commands renumber Demonstrated in example script none renumber Will change the residue number of selected residues renumber lt Sselection gt from lt int gt renumber lt selection gt add lt int gt Related commands rename Demonstrated in example script none res Will get the one letter name of the first selected group found in a selection Returned value is of type lt string gt e g A or C or D res lt selection gt Alternately you can access directly a specific residue from a specific layer which is faster and handy in loops with res lt layer gt lt int gt 124DeepViewManual Related commands num name chain ss access Demonstrated in example script 11 e rotate Rotates the view successively around axis x y z rotate lt vector gt where lt vector gt contains rotation angles in degrees This command can also be used to rotate a selection around a specific axis rotate lt selection gt by lt float gt deg rad around axis lt vector gt lt vector gt or to do a torsion rotate atoms downstream a bond around this bond using the following syntax rotate a
89. esidue of the currently active layer is computed using a partial implementation of the GROMOS96 force field Computed FF values can be plotted against the amino acid sequence and on the Graphic window the resulting force at each atom can be displayed Examples of application Both displaying the resulting force at each atom and plotting the FF vs the amino acid sequence will let you quickly visualize parts of the structure with incorrect geometry or too close contacts Procedure Tools gt Compute Energy Force Field a dialog appears in which you can include or exclude following parameters for FF calculations bond lengths torsion energies bond angles improper angles interactions between non bonded atoms and electrostatic interactions On the same dialog check Show Energy Report to display a text file presenting the details of computed FF at each amino acid Once a report has been requested this is stored in the temp directory and can be re opened later by clicking File gt Open Text File Note that the content of the temp directory is deleted when the DeepView session is closed NOTE Force fields are parameterized using all parameters Therefore disabling computation of some parameters is an heresy and although mostly used for didactic considerations it is not encouraged However it might be useful to check and highlight residues on the basis of their bond length and angle deviation only neglecting non bonded and electrostatic int
90. f one of the members is of type lt float gt X lt 1 0 1 0 1 0 gt 3 0 will put lt 3 0 3 0 3 0 gt into X or performs a dot product if the operation involves two vectors The scalar product can be obtained with the X operator X lt 0 0 1 0 0 0 gt X lt 0 0 0 0 1 0 gt Floating point and integer variables can be pre post incremented with lt var gt and lt var gt respectively or pre post decremented with lt var gt and lt var gt respectively This is mainly used for loops The remainder modulo of an integer division can be accessed by the operator as in print 8 3 112DeepViewManual which would give 2 e Commands Available commands are alphabetically access acos angle align align pos asin ask atan build center chain color compute clear close cos delete dist do else export fit get goto groupcount hide if inline is_selected layername max min minimize move mutate name normalize num omega open pause phi Pi please do print psi readln redraw rename renumber res rotate return rms save selcount select set show silent sin ss stop sub substring superpose system tan torsion thank you while zoom NOTES For version 3 7b1 some commands might not be implemented on all platforms More commands will be added as needed You can find several script examples in the scripts directory Script examples are named script01 txt script02 txt etc Scripts are designed to progressively introduce more and more
91. f this server is to make Protein Modelling SWISS MODEL using accessible to all biochemists and molecular biologists World known PDB codes Wide Search the template sequences accessible to The present version of the server is 3 5 and is under constant SWISS MODEL Examples using SWISS MODEL and the Swiss PdbViewer Course on protein improvement and debugging In order to help us refine the sequence analysis and modelling algorithms please report of possible bugs and problems with the modelling procedure HELP Disclaimer Frequently Asked The result of any modelling procedure is NON EXPERIMENTAL Questions and MUST be considered with care This is especially true since Visualising 3D models there is no human intervention during model building e Reliability of models How SWISS MODEL works How ProModII works Document Done Torsten Schwede Manuel C Peitsch amp Nicolas Guex Optimise project mode Instead of using the Web interface requests can be submitted as modeling projects from DeepView This Optimise mode offers a much better control over the whole modeling process since it lets you perform and improve the alignments Oligomer modeling This mode is used to model multimeric proteins Requests must be send from DeepView GPCR mode Models the 7 transmembrane helical part of G protein coupled receptors GPCR 126 e The Optimise project mode The following points explain how to
92. features and an other way to learn this language is to study the scripts starting from script01 txt All example scripts use the network import function to open pdb files If you are working offline you should copy the example files to your local disk e g the spdbv usrstuff directory and change the example scripts accordingly Instead of open pdb from net 1CRN it should then look like open pdb from usrstuff ICRN pdb e Tests conditional execution if expression test expression i else i Where test can be Identity l different gt greater than gt greater than or equal to lt smaller than lt smaller than or equal to Demonstrated in example script 04 06 and 08 e Loops Two kinds of loops are supported that allow to cope with any situation The higher level for statement is not implemented In the following case statements will be executed at least once and more depending on the result of the test do lt note that statements must start on the next line statements j while expression test expression lt note the semicolon In the following case statements may not be executed at all depending on the result of the test while expression test expression statements Demonstrated in example script 01 02 03 04 05 06 07 and 09 ANNEX 2 113 e nternal variables This is the list of recognized internal spdbv variables that can be accessed by the get and se
93. file varname open file lt string gt in usrstuff for appending where lt string gt must ONLY contain the file name no directory no path The open command can also be used to open a text file which is only useful coupled with the graphical user interface open text lt string gt open text lt string gt in usrstuff open seq lt string gt this can be used to load a target sequence to model Sequence must be in format FASTA SWISSPROT or SEQRES Related commands close clear readin inline print save Demonstrated in example script all 122DeepViewManual e pause Will stop the script execution for some seconds pause lt float gt Related commands stop thank you please do Demonstrated in example script 05 06 07 and 09 e phi Will get the phi torsion angle for the first selected amino acid found in a selection Returned value is of type lt float gt and is returned in degrees phi lt selection gt Alternately you can access directly a specific residue from a specific layer which is faster and handy in loops with phi lt layer gt lt int gt Related commands psi omega as Demonstrated in example script 01 02 03 and 04 e PI Returns the value of PI Related commands sin asin cos acos tan atan Demonstrated in example script none e please do Initiates a script and resets all scripts variables Note that this statement must be on the FIRST line of the script Related commands
94. files that help to reliably identify to which known protein family if any a new sequence belongs PDB or Protein Data Bank is an international repository of 3 D protein structures primarily determined by X ray crystallography and solution nuclear magnetic resonance ExPDB is a Swiss Model template database of protein structures containing one entry for each individual protein chain of the PDB proteins Several modeling modes are currently available at the Swiss Model server First Approach mode The primary sequence of a protein to be modeled can be directly submitted to the Swiss Model server in FastA format or even by simply entering its SWISS PROT accession code This First Approach modeling mode is based on a fully automated alignment of template and target sequences 76 DeepViewManual X SWISS MODEL Netscape File Edit View Go Communicator Help 4 L Bookmarks Location http www expasy ora swissmad x EJ A ETA MENU Modelling requests First Approach mode Optimise project mode available Oligomer modelling delin GPCR mode a An Automated Comparative Protein modes Interactive tools Modelling Server T PuovVIEWET a NIN for viewing and manipulating protein structures and models Macintosh PC SGI and SWISS MODEL is an Automated Protein Modelling Server whe the EXPDB developped at the GlaxoSmithKline in Geneva Switzerland template codes accessible to Introduction The purpose o
95. formation Cancel by checking the Apply Reverse Transformation option however this will not let you undo a projection Deep View does not check if the matrix that you Check Act on All Layers to apply the transformation matrix to all loaded layers Tools gt Apply Transformation on Current Layer Transformation dialog box e Building a dimer from a PDB file that contains only one chain 4mdha 466 x 364 E Control Panel Ea 1 Load twice chain A eee 3 Select all of a dimer e g Pan residues of 4mdha pdb 4mdhB A s ILE4 N A s ARGS A s VALG 2 Rename one of the A s LEUT A s VALB two layers e g As 1 A ALA 4mdhB see point eye A GLY13 A h GLN14 A hILE15 A h ALA15 A h TYR17 A h SEF18 A h LEU19 A h LEU20 A h TYR21 A h SER22 QOOOOOOOOOOOOOOOOoOoOooOo 4mdha 466 x 364 Transformation x acer tae pny eee a ca ak 4 Select 5 4mdhB is translated Tools gt Apply according to the Rotation Em com Transformation ye 7 given matrix Y 10 500 x 10 830 Y f 0 248 Z le e a Le 3 A L A n n r hee y Y Ne gt lt gt Z 0 032 x 0 304 y 0 952 a enter the Ct gt RAR a f eee 4mdhB Y j appropriate NAC AMG mwas w matrix to transform chain A into chain B Translation 55 21 4 B 99 e91 33 Apply Reverse Transformation Act on All Layers f te z 77 ema For merging the two layers see point 115 Tools gt Apply Transform
96. g the window NOTE For large loops involving more than eight amino acids this command is much slower than Scan Loop Database see below Scan Loop Database Several loops will be proposed from a database of known loops loopDB stored in the stuff directory A result list will be displayed in a Text window see figure below Accept one loop by selecting it on the list and closing the window ADVANCED DEEPVIEW COMMANDS 41 i C WINNT Profiles mfh10000 Deskt 3 clash score amp ahs eee Evaluation parameters click one to sort C N CA C N C N Cat the loops below according to that parameter 0 14 3 55 8 08 It takes a while 0 34 15 47 14 60 0 04 14 15 1 57 os i a a List of computed loops the first column C N gives the deviation in A to the ideal closure bond length while the next two For the selected loop on the list the evaluation parameters columns CA C N and C N CA give the give f deviation in degrees to the ideal angle clash score an evaluation of contacts closure Selecting a loop will compute and PP pair potential threading energy the lower the better display its evaluation parameters above FF force field energy in kJ the lower the better Select a loop with the mouse or pressing the up and down keys Build gt Build Loop result list NOTES e In both cases once a loop has been selected it is advisable to perform an energy minimization see point 107 of
97. h is faster and handy in loops with access lt layer gt lt int gt Related commands name res ss Demonstrated in example script 11 acos Computes the arc cosine of an expression Values are in radians acos lt float gt Related commands sin asin cos tan atan PI Demonstrated in example script none e angle Computes the angle AOB between three atoms vectors lt floatvar gt angle A O B 114Deep ViewManual where A O and B are lt vector gt values Result is returned in degrees Related commands dist get torsion Demonstrated in example script none e align Will make a primary sequence alignment between layers align lt layer gt onto lt layer gt where lt string gt contains the question to be presented to the user Related commands align_pos Demonstrated in example script none e align pos Will get the position of a residue in an alignment in the Alignment window Returned value is of type lt int gt align pos lt selection gt Alternately you can access directly a specific residue from a specific layer which is faster and handy in loops with align_pos lt layer gt lt int gt Related commands generate structural alignment superpose rms fit Demonstrated in example script none e asin Computes the arc sinus of an expression Values are in radians asin lt float gt Related commands sin cos acos tan atan PI Demonstrated in example script none ask Will make a dial
98. he x HELIX GLY 104 TEP los 5 HELIX VAL 109 ARG 1143 1 HELIX VAL lz ILE lz4 5 PDB file SHEET 3 ALA 42 ASN 46 O0 L L SHEET 3 GLY 49 GLY 54 0 SER s N ASN 46 SHEET 3 LEU 56 SER 60 0 SER 60 N THE 51 Deep View reads the SSBOND cys 127 SSBOND CYS 115 space group of your SSBOND crs 50 SBOND 34 molecule on the CRYSTI CRYST 75 100 795 100 37 500 90 00 90 00 90 00 P 43 21 2 8 Hne ofthe PDB file 4 in order to provide the correct space group as the first choice Click the space group appearing If Deep View cannot 172 1721x 3 442 in red to apply all displayed 1 2 Y 1 2 X 1 4 Z crystallographic operators guess the space group of Lfe M 1724Y 374 7 l7z2 4xX l72 Y 1l 4 2 youto enle yaww X Click a crystallographic operator be prompted for locating I 37 16 8 I422 PBG422 TETRAGONAL to apply 1t it yourself x Y Z N Y E Each transformation will x Y 2 generate a new layer HaIa Tools gt Build Crystallographic Symmetry NOTE Clicking Tools gt Build Crystallographic Symmetry while holding down Ctrl will display a dialog to let you enter a crystallographic operator of your own choice 110 e Applying transformation matrices Concept Applying a transformation matrix see annex 4 transformation matrices will alter the coordinates of all or part of a molecule This can be useful to translate to rotate or more generally to position a molecule in a specific orientation PDB files might include
99. he checkmark of the last item of the Tool menu Move C term part during Phi Psi Changes or by clicking the small box C N on the upper left corner of the Ramachandran Plot window NOTE To make backbone torsional changes that affect only a part of a protein the part to be altered can be disconnected from the rest of the protein Build gt Break Backbone and then reconnected afterwards Build gt Ligate Backbone 94 e Adding removing residues bonds and atoms Concept DeepView offers several commands that allow adding or removing residues bonds H bonds hydrogen atoms and water molecules Examples of application These commands are useful to fine tune an image before a final rendering e g by adding or removing H bonds or to discard a part of a protein to save truncated proteins e g by removing one chain The inverse operation which consists of creating new entities by merging layers is developed in point 115 Procedure Under the Build menu select a command to achieve one of the following actions Build menu Add commands Add Residue Pick a N ora C terminal atom A list with the 20 protein amino acids is displayed select one residue This will be added as a terminal residue This command also lets you insert residues in the protein Add Bond This will add a bond from or within a HETATM You will be prompted for two atoms to be bonded the first one must belong to a HETA TM This function can be useful when no CONECT inf
100. he previously described Display Radius dialog box see point 47 which allows selecting groups on the Control Panel or displaying groups on the Graphic window within a distance that you can specify The dialog lets you extend a selection display around a previous selection display and includes an option to act on all layers Select menu Neighbors of Selects displays groups with at least one atom within the specified distance of any atom of selected aa selected groups Groups close to Selects displays any group that is near any other group with a different chain ID This another chain command is useful to highlight residues at the interface of two chains Groups close to Selects displays any group that is near any other group from a different layer It applies to all another layer layers and is useful when interacting chains have been loaded into separate layers 56 e Selecting groups by structural criteria Finally use the five following commands to select groups according to specific structural criteria Select menu Accessible aa Selects residues with an accessible surface area higher than a given percentage which you will be prompted for in a dialog aa Making Selects residues with atoms too close to atoms of other residues Since van der Waals radii Clashes are not assigned when files are loaded DeepView looks for atoms that are closer than the minimal H bond distance as set in Preferences gt H bond detection threshold w
101. hel Phi Deep View working environment 4 e Layers Infos window see 84 This table like window is for controlling the display of individual layers You can toggle on and off the visualization and movement of layers and enable the display of certain objects e g H bonds or water molecules for each layer 5 e Alignment window see 14 Shows the amino acid sequence of loaded proteins in one letter abbreviations This window is used to compare and to align sequences of two or more proteins During homology modeling it allows correcting the alignment of target sequences onto the templates 6 Ramachandran Plot window see 93 Displays a Ramachandran plot Each dot on the plot gives the 0 and angles of one selected residue of the currently active layer Ramachandran plots are used to judge the quality of a model by finding residues whose conformational angles lie outside allowed regions INTRODUCTION 3 7 Surface and Cavities window see 102 Gives the surface A and volume A of a molecule and its cavities This window can only be displayed if a molecular surface has been computed It is mainly for information purposes but can also be used to center the view on specific cavities 8 e Electron Density Map Infos window see 103 This is a table like window that lets you control the appearance of electron density maps and electrostatic potential maps 9 e Text windows In addition to all previously described windows yo
102. hen no hydrogen atoms are present A finer way to find clashes consists in coloring the molecule by force field energy residues that have a high non bonded energy colored in red are too close to each other aa Making Selects groups with at least one atom too close to the backbone of another group Clashes with Backbone Sidechains Selects those buried residues whose sidechain could make an H bond or a salt bridge but do lacking Proper none see point 101 computing H bonds Few should occur in good structures H bonds Reconstructed Selects residues with reconstructed sidechains These may have been built automatically for BASIC DEEPVIEW COMMANDS 25 amino acids residues with missing atoms which often occurs for highly mobile surface residues Automatic reconstruction can be disabled see point 149 Display menu The Display menu is mainly comprised of Show and View commands These are checkbox commands which turn on and off various viewing options Some of these options are also available through the Layer Infos window 57 e Show commands Show commands consist of self explanatory toggles for showing or hiding the global coordinate system axes the carbon alpha trace backbone oxygens sidechains even when backbone is hidden dot surfaces must have been computed first forces must have been computed first hydrogens H bonds must have been computed first H bond distances must have been calculated H
103. hree atoms on the static and the superposed molecules On the Graphic window the superposed molecule will be superposed onto the static molecule according to the three selected patrs of atoms e Based on a set of selected residues Select on the Control Panel an equal number of residues from the two layers and click Fit gt Fit molecules from selection On the Graphic window selected amino acids of the superposed molecule will be superposed one to one onto selected amino acids of the static molecule This fit is more accurate than the three corresponding atoms superposition described above and can involve more than three residues 118 e Improving a superposition Concept 119 120 72 DeepViewManual Given two similar structures that were previously superposed with a fitting tool Fit gt Magic Fit see point 116 or Fit gt Fit Molecules from Selection see point 117 an improved superposition is done by iterating through 1 Generation of a structural alignment see point 121 to find those pairs of residues that are spatially close to each other These will be added to the previous selection 2 Superposing again the two structures based on the new selection Iterations are done until the RMS cannot be lowered while keeping the number of matching residues as high as possible Procedure On the Control Panel select the superposed molecule second loaded layer by default so that it becomes the currently active layer and then
104. icrosoft com e Windows NT The DeepView root directory and the tree below must not be write protected for the user executing the program because DeepView will create several temp files during runtime 12 e Installing DeepView on Mac DeepView can be downloaded from http www expasy org spdbv or any of the mirror sites mentioned there a Download OpenGL from http www apple com openGL and install it if it is not yet present on your system This step is optional but allows rendering nice images b Download Swiss Pdb Viewer The following steps are optional c Download Swiss PdbViewer Loop Database 3 44 Mb This step is useful if you intend to do standalone modeling or for teaching purposes If you have a program that can expand zip files you can download the zip version which is 2 45Mb To be able to use the loop database put it into the stuff directory see point 15 d Download the User Guide 698 Kb This step is useful if you want to consult this user guide from a computer not connected to the network To be able to consult the help directly from within Swiss PdbViewer place the content of this folder into the stuff directory e Download the Tutorial Material 512 Kb This step is useful to learn how to use DeepView by looking at real examples f Download POV Ray http www povray org This step is useful only if you intend to make ray traced images from your molecules NOTE If your browser starts to dis
105. idea to select a low smoothness to work on scenes and increasing it once everything has been set up A high number of facets is actually not necessary to describe a good looking sphere provided that the Use Meshes option is enabled on the 3D Rendering Parameters dialog Other 3D features that can be set under Preferences gt 3D Renderings include e the use of meshes for drawing solid objects this will render nicer but slower images e the real time display of solid images 141 142 88 DeepViewManual Finally click Preferences gt 3D Light to define the position and Intensity of up to three sources of light to illuminate 3D renderings Current limitations of OpenGL 3D renderings on include e Mac only images appear in 256 colors on screen but they will be always saved in millions of colors You need to allocate enough RAM to the program so that the entire image 24 bits can reside in RAM e Images bigger than the screen cannot be rendered for large images POV Ray must be used e POV Ray rendering To obtain 3D images with a better quality you can save your views to POV Ray formatted files by clicking File gt Save gt Pov3 Scene or File gt Save gt MegaPov scene same as Pov3 Scene but with even smoother colors You will get ray traced quality images which means that you will be able to add reflections refractions transparencies and shadows to your view As POV Ray renders spheres and cylinders as mathematical objects these wil
106. iews of the same PDB file showing the atom coordinates of layers ICRNA up and ICRNB down 6 Reopen the project and display its PDB file the X Y Z atom coordinates of ICRNA have changed those of ICRNB remain unchanged Tern 465 x 380 4 Using the Layers Infos window disable movement of layer 1CRNB and translate layer 1CRNA C WINNT Profiles mfh10000 Desktop viewer clownload 1 CRN Ea CRNB 1CRN 5 Save both layers as a new project and close all layers These are two views of the same PDB file showing the atom coordinates of layers ICRNA up and ICRNB down 9 Reopen the project and display its PDB file The X Y Z atom coordinates of 1CRNA were reset the matrix described on the next page was used to compute the atom coordinates of the TernA 465 x 380 a original file 7 Reset the orientation of ICRNA Fit gt Reset Orientation current layer E E EEE m C WINNT Profiles mfh 10000 Desktop viewer download 1CRN x only see point 120 ATOM 1 N THR 1 00 13 79 ATOM z CA THR 1 00 10 80 ATOM 3 C THP 1 00 9 19 p ATOM 4 THP 1 00 9 85 ICRNA ATOM 5 CB THR L 00 13 02 Y and JE JE r Z ra 1CRNB z m C WINNT Profiles mfh 10000 Desktop viewer download 1CRN x ATOM 1 N THP 1 00 13 79 ATOM z CA THR 1 00 10 80 ATOM 3 C THR 1 00 3 19 8 Save both layers as a new project and a ee aa s close all layers ATOM 5 CB THR 1 00 13 02 Y l mall 14
107. ignment by striping all gaps 123 113 ADVANCED DEEPVIEW COMMANDS 65 Superposing commands Superpose a molecule onto another to let you compare molecular structures This requires fixing a molecule which is called the static molecule whereas the superposed molecule designates the molecule that is moved onto the static one By default the reference layer first loaded layer is the static molecule but the role of molecules can be changed on the RMS amp Auto Fit options dialog see point 116 NOTE Superposing and alignment commands are mostly employed to prepare modeling projects Therefore the use of these commands will be further developed in the next chapter Homology Modeling e Relative movement of layers When working on a project it is possible to apply a movement i e rotation or translation to only some layers of the project Movement of a layer can be enabled or disabled on the Control Panel or on the Layers Infos window Control Panel x Z visible Check uncheck this item to show side labl v ribn ool p enable disable movement of the currently active layer Currently active layer Layers Infos gt Layer vis mov axi CA D H Hbnd dst side HIH eye Sel Loaded layers lhel v v vo v 25 The first layer is the v oD reference layer and the red layer is the i Check uncheck this item to enable disable currently active layer movement of the corresponding layer Each loaded l
108. ild gt Build Loop Computes or loads a sertes of loops Build gt Scan Loop Database connecting two amino acids NOTE The following commands under the SwissModel menu are currently not used or still in development Load FoldFit Alignment Save FoldFit Alignment Ignore Selected AA during modeling Use Selected AA during modeling Draw Residues to Ignore as Set current layer as reference Move raw sequence into structure Move structure into raw sequence Lock Selected Residues of Model Unlock Selected Residues of Model Build Preliminary Model Save Optimize Model Job I LOADING FILES 127 e Loading a target sequence DeepView supports two formats to load a target sequence i e a protein to be modeled FastA and SWISS PROT e The target sequence 1s a FastA file not included in the SWISS PROT database It can be loaded by selecting SwissModel gt Load Raw Sequence The Select a Text File dialog is displayed to let you browse though your computer for the FastA target sequence e The target sequence is a SWISS PROT file It can be loaded by selecting SwissModel gt Load Raw Sequence as explained above or it can be directly imported by clicking File gt Import The Import dialog is displayed enter the SWISS PROT accession code and press the SwissProt seq button see point 21 When a SWISS PROT sequence is imported into DeepView the header information is lost This can be retrieved in a separate window by selecting again File gt I
109. inates and the altered ones will be equal to this value 97 e Altering the visualization of the ribbon secondary structure Concept When a protein is loaded its secondary structure is automatically computed see Annex 4 a sa EP This computation might misinterpret the secondary structure in ambiguous regions or whenever one residue can be considered as belonging to two secondary structure elements at the same time The net result is that the ribbon drawn accordingly to the method of Carson 1987 does not look as nice as it could A set of commands allows altering the ribbon visualization to help making nicer images These commands do not actually modify the structure of molecules and will only affect the rendering note that these modifications are not saved in DeepView files and are lost when Tools gt Detect Secondary Structure 1s applied Examples of application You can try to improve a protein image For example if a strand is directly followed by a helix and an arrow is put at the end of the strand this depends on your ribbon preferences see point 155 it might happen that the arrow is not complete because the last strand residue 1s assigned to the helix To make a nicer image select the last strand residue or the first helix residue and set it as a coil residue Procedure On the Control Panel select the residues to be transformed enable their ribbon visualization on the Graphic window and then do one of the following e U
110. indow the force field graph is plotted see point 106 On the Graphic window the structure of the minimized molecule is updated NOTE Click File gt Save Remote Job to save the coordinates and related command files needed to run one of the three structure refinement packages CHARM AMBER and GROMOS energy minimization jobs You might need to edit the files manually but this 1s a good first approach This option is currently deprecated since the GROMOS96 force field has been implemented in DeepView but it has not been removed as it may be useful to do molecular dynamics d Crystallographic commands e Translating a molecule along its unit cell Concept You can translate a molecule or a copy of the molecule along the axes of its unit cell provided that the currently loaded coordinate file contains the crystallographic unit cell information CRYST record Examples of application Translating copies of molecules in conjunction with applying symmetry operations can be used to examine crystal contacts or to construct biologically active protein assemblies Procedure Click Tools gt Translate Layer along Unit Cell this will open a window providing a list of possible translations 109 ADVANCED DEEPVIEW COMMANDS 59 E C spdbv _stuff_ crystmov bct F Click on the appropriate translation The window provides the sts t har gee following translations The direction of the translation is given along one axis or or ino
111. ing the specific rotamer in the secondary structure for example R 2 5 s 2 p 0 08 h h means that the second rotamer over five scores 2 and has a 0 08 probability to be found in this conformation where the backbone is an helix e To use Rotolib2 aa close DeepView copy Rotolib2 aa as Rotolib aa and restart the program 89 e Applying torsions a Concept Given a molecule you can twist it by modifying e the j and conformational angles of the backbone of a selected amino acid e the yl to y5 dihedral angles of the sidechain of a selected amino acid e any rotational bond angle in hetero groups Examples of application Applying torsions can be useful to explore all orientations of a previously mutated amino acid since the available rotamer library provides only the most commonly observed side chain orientations see above Studying torsions also lets you finely adjust the orientation of side chains during protein modeling Procedure Click the Torsion tool 13 button of the Toolbar and following the instructions appearing in the message space below pick one atom belonging to the group amino acid or hetero group to be twisted e Acting on amino acids A number of little arrows will appear below and at the right of the Torsion tool to let you twist the molecule at the selected residue While changing the 1 y5 angles will only affect the selected side chain changing the backbone dihedral angles Phi Psi will modify the who
112. is performed and you might want to enable the display of H bond length by clicking Display gt Show H bond distances to have a numeric feedback A torsion is ended by clicking once again the Torsion tool You will be prompted for accepting or discarding the torsion Discarding it will restore the initial position of the group If you accept the torsion the amino acid atom names will be updated accordingly to IUPAC nomenclature if necessary 90 e Building loops Concept DeepView can compute or search a series of loops connecting two amino acid anchor points These possible loops are evaluated by the number of clashes by the putative H bonds that they can make and by their GROMOS96 Energy Examples of application Building loops might let you complete a protein that has missing parts refine a protein model returned by Swiss Model if you are not satisfied with its loops or search for the best loop during model building In fact unlike helices and strands which are usually well conserved loops can noticeably vary among similar proteins Procedure Use one of the following commands under the Bui d menu to build a new loop between a pair of amino acids Build menu Build Loop Several possible loops will be computed A result list will be displayed in a Text window see figure below selecting a loop on the list will compute its evaluation parameters and display them on the window accept one loop by selecting it on the list and closin
113. itor to manually add a connection to a PDB file Example to connect a single atom to an amino acid where 2967 is the atom number of the single atom and 58 is the atom number of the amino acid atom that has to be connected to the single atom CONECT 2967 58 Note that if the distance between the two atoms is extravagant will not make the connection when loading the file instead it will prompt a warning message Before editing a PDB file make sure you have a look at the PDB format definition http www rcsb org pdb info html Il SECONDARY STRUCTURE DETECTION Deep View is currently not using the secondary structure described in the PDB file header Instead the secondary structure is newly assigned by the following procedure e if phi lt 20 0 and phi gt 110 0 and if psi lt 15 0 and psi gt 80 0 an alpha helix is temporarily assigned e Only helix nucleation sites of more than 4 residues are kept and elongated in both C and N terminal direction using the H bonding pattern e Long helices are then broken into two helices if they bend too much checking phi psi dihedral angles if phi lt 120 0 or phi gt 0 0 or if psi lt 100 0 or psi gt 10 0 e Then non helical residues are checked for strand using the H bonding pattern again each possible sheet nucleation site two amino acids H bonded possibly forming a sheet are temporarily assigned as a strand They are extended in N and C terminal
114. its backbone must be displayed However see point 57 to see sidechains without backbone 79 e Setting the display of several selected groups Once you have selected several groups in the Control Panel window you can e press Return to hide unselected groups on the Graphic window e set the display of all selected groups at once by checking the Control Panel options as it follows All platforms Left click Shift Left click Click any point in a column Checks unchecks the pointed group Checks unchecks all groups Click the column header Checks selected red groups only Checks selected red groups only If several layers are opened you can extend your check to all layers by Mac Windows Irix Shift Ctrl click Linux shift left Alt click 32 Deep ViewManual 80 e Displaying surfaces DeepView offers three ways to represent a surface oO Accessible surface Molecular surface Rolling solvent molecule Van der Waals surface Molecule Contact surface of each atom based on the Van der Waals radius Accessible Surface described by the center position of a water molecule that would be rolled over the protein This is approximated by rolling a sphere with a 1 4 A radius which is approximately the radius of a water molecule Molecular Area that can be reached with the surface of a solvent molecule 1 4 A rolled over the protein Surface types You can display a surface by e Directly enabling its display
115. k arrows are for displaying pop up menus For selecting a surface type v In the example i e van der Waals see point 80 For selecting the object to be colored R in the example 1 e ribbon see point 81 A A A A A A A A A A A A A A B A B B B A A A B A B B WOOO OOOO lt lt lt lt lt lt lt lt lt 30 DeepViewManual 71 e Changing the currently active layer The Control Panel governs the currently active layer If you are working on a project 1 e several layers are loaded click on the gray bar below the Control Panel title bar a pop up menu with the names of all loaded molecular coordinate files 1s displayed Select one file to make it the currently active layer i Control Panel x v 1ern Click the gray bar to display a pop up menu containing Thew deeds TAD the names of all loaded molecular coordinate files Thel On the pop up menu select a file this will be the currently active layer governed by the Control Panel Selecting the currently active layer on the Control Panel NOTES e The currently active layer can also be selected on the Alignment window see point 114 and on the Layers Infos window see point 84 e Hitting the Tab key while the Control Panel is the active window cycles through all layers 72 Centering the model on a specific group Windows in the Control Panel right click a group to center the view on its alpha
116. l always be perfectly smooth regardless of the smoothness settings that you had defined in the Preference menu Linux and Irix pressing the Render button will run POV Ray and display the result see point 33 Have a look at Armand Tepper s homepage Leiden University for some really breathtaking examples Il STEREOSCOPIC MODES Click Display gt Stereo View this toggles the stereo view on and off Swiss PdbViever supports three distinct stereo modes red and blue side by side and hardware stereo Red and blue and side by side are supported on all machines whereas hardware is only supported on machines equipped with hardware devices e g Stereographics CrystalEyes NuVision Read carefully instructions given in ANNEX 3 HARDWARE REQUIREMENT to prevent any damage to the screen Stereoscopic modes can be selected on the Stereoscopic View Settings dialog which is displayed by clicking Preferences gt Stereo Display see point 168 The default mode is Side by side e Red and blue stereo By default a red and a blue overlapping images are displayed The red image is rotated 2 degrees around the vertical axis and the blue image is rotated 2 degrees laOub 468 x 396 Red and blue stereoscopic view SLAB DISPLAY STEREO DISPLAY AND 3D RENDERING 89 143 144 To see the molecule in real 3D you simply need a pair of glasses with a red left glass and a blue right glass If your glasses have other colors you must
117. l computations are done in vacuo without reaction field GROMOS96 e W F van Gunsteren et al 1996 in Biomolecular simulation the GROMOS96 manual and user guide Vdf Hochschulverlag ETHZ e http igc ethz ch gromos welcome html XII TRANSFORMATION MATRICES Not yet described XU RMSD Not yet described XIV SEQUENCE SIMILARITY Not yet described ANNEX 5 GLOSSARY References Sequence Alignment BLAST Altschul S F Gish W Miller W Myers E W Lipman D J 1990 Basic local alignment search tool J Mol Biol 215 403 410 SIM Huang X and Miller M 1991 A time efficient linear space local similarity algorithm Adv Appl Math 12 337 367 Molecular Graphics RIBBONS Carson M 1987 Ribbon model of macromolecules J Mol Graphics 5 103 106 MSMS Michael F Sanner Olson amp Spehner Biopolymers 1996 38 305 GRASP Anthony Nicholls Kim Sharp and Barry Honig Proteins 1991 11 281 Electrostatics DELPHI GRASP Honig and Nicholls 1995 Classical Electrostatics in Biology and Chemistry Science 268 1144 Anthony Nicholls Kim Sharp and Barry Honig 1991 Proteins 11 281 Klapper I Hagstrom R Fine R Honig B 1986 Focussing of Electric Fields in the Active Site of Cu Zn Superoxide Dismutase Effects of Ionic Strength and Amino Acid Modification Proteins 1 47 59 Homology Modelling DeepView amp SWISS MODEL Peitsch MC and Jongeneel V 1993 A 3 dimensio
118. l refresh them faster whenever Draw Unit Cell the molecule is moved 6 Check this item to display the unit cell not relevant for electrostatic potentials For all other options of the Electron Density Map Setting the display of electrostatic potential maps Parameters dialog see point 158 104 e Triangulating maps Concept Since contours for both electrostatic potential maps see point 103 and electron density maps see point 111 are drawn as plain lines or dotted lines it is not possible to draw them as solid or transparent surface contours unless they are first triangulated 1 e converted into surfaces Examples of application Maps are triangulated mostly to obtain nicer pictures when using POV Ray or OpenGL Note that their real time display will be faster but that in counterpart you will loose the possibility to alter the contouring values Procedure Tools gt Triangulate Map the current contours of an electron density map or an electrostatic potential map are transformed into a surface NOTE Currently each layer can have only one surface object This means that two layers are needed to display a molecular surface and a triangulated map at the same time 105 e Computing pseudo energy mean force potential also pair potential threading energy or PP Concept A mean force potential of each residue of the currently active layer is computed for details on calculations see annex 4 Computed PP values can be p
119. lbar and the Graphic window can be linked by checking Link Toolbar and Graphic Window under the Window menu Both windows will then move together when one of them is moved NOTE Problems were reported when this option is enabled on some Linux and Irix systems 26 e Bringing a Text window to front Click Window gt Text to bring to front the first loaded Text window III OBTAINING HELP According to the platform look under one of the following menus Mac Apple menu These menus contain commands that allow e obtaining information about DeepView e obtaining help in using DeepView e updating the program 12 DeepViewManual 27 e Obtaining information about Deep View About Swiss PdbViewer will display the DeepView splash screen with the current version of the program and a list of authors 28 e Obtaining short help about a particular window Either click its small red question mark or select the window under the Help Apple or Info menus according to the platform 29 e Obtaining detailed help about all DeepView commands Under the Help Apple or Info menus according to the platform click one of the following commands Help Apple or Info menus according to the platform WWW Manual Opens your web browser to the HTML User Guide at the Deep View Home Page Local Manual Opens your web browser to the HTML manual stored on your computer provided that you have downloaded and installed it in your stuff dire
120. ld Loop Loops can also be adjusted by proceeding as explained in point 90 or Build gt Scan Loop Database 137 e Resubmitting the modeling project Wrong alignments and improper placement of gaps insertions are a common reason for bad models or complete failure of the modeling procedure Refine the alignment as explained above see point 132 and resubmit the project see point 134 135 Display Modes DeepView offers three modes to visualize a molecule on the Graphic window Main display features Normal Backbones sidechains ribbons and molecular surfaces are rendered as wire frame Van der Waals and accessible surfaces are dotted This is the fastest rendering mode not available for SGI and Linux versions 3D rendering Renders molecules in solid 3D Two 3D rendering types are available one applies to ribbons and surfaces only and the other renders the whole molecule in solid 3D Stereoscopic Allows visualizing molecules in real 3D Depending on the characteristics of your computer up to three stereoscopic modes might be available 138 e Slab Display Mode Click Display gt Slab this toggles on and off the slab mode which delimits a molecule slab parallel to the screen by removing those groups that reside too far into or out the screen Thel 309 x 302 Thel 309 x 302 Normal Slab display display Normal and slab display The slab depth in A can be adjusted in Preferences gt Display see point 167
121. le protein arrangement By default the C terminal part of the protein will move However you can let move the N terminal part of the protein by removing the checkmark of the last item of the Tool menu Move C term part during Phi Psi Changes or by clicking the small box C N on the upper left corner of the Ramachandran Plot window see point 93 Use the upper and saat lower arrows to ERAR From top to modify 9 and bottom use these E SN arrows to modify l y1 to y5 Torsion tool acting on amino acids NOTE You can use the keyboard instead of clicking an arrow any sidechain dihedral angle y1 to 5 can be rotated by holding down a key from 1 to 5 while clicking and moving the mouse from left to right Key 1 will rotate the CA CB bond key 2 the CB CD bond and so on Alter 0 or angles by holding down the 9 or 0 key respectively This might not work on Linux and Irix e Acting on hetero groups You will be prompted to pick a second atom belonging to the same group The first picked atom will define the fixed point while the second one will be used to define the rotation axis All atoms downstream the second one will move around the bond defined by the two atoms you picked 40 DeepViewManual hk These arrows let you modify the rotation Not used axis defined by picking two atoms Torsion tool acting on heterogroups e In both cases A real time evaluation of clashes and hydrogen bonds
122. left eye and right eye and you can adapt to your sight the Rotation angle item below W Allow Real Time Stereo od Use Red Blue Stereo a Right E ad If you select Side by Side Stereo you can adapt to Use Side by Side Stereo your sight the following parameters s uns He p O00 Rotation angle the left and right images will be Serene on Piwels ho rotated by a half of your entered value positive tereo Separation F izels values are for parallel stereo viewing negative Z Strict Screen Separation of Stereo Pairs values are for cross eye stereo viewing Stereo Separation enter here the distance Use hardware Stereo T op Bottom between the two images Use hardware Stereo in a window check Strict Screen Separation to avoid that both images overlap when zooming Rotation angle deg 4 000 Cancel Stereo Separation Pixels a If you select a Hardware Stereo you can set the rotation angle for Top Bottom and in a window and the stereo separation for Top Bottom only ANNEX 1 LISTOF KEY MODIFIERS AND MENUS I KEY MODIFIERS NOTE Option key in Mac OS corresponds to right mouse in Windows Please note that in this beta version the keys and shortcuts will best match the user guide for the Mac version not for the PC version However the Ctrl key is mapped to the right Alt key The middle mouse button can be used to move the molecule and the right mouse button can be used to zoom in o
123. ll atoms of selected groups Edit gt Assign Helix Strand Coil Type Alter the visualization of the ribbon Tools gt Detect Secondary Structure secondary structure 92 93 97 e Edit gt Find Sequence Search a layer for segments that match a Searching Edi Find Next given amino acid sequence commands dit gt Search for PROSITE pattern Searches a layer for segments that match PROSITE patterns 102 105 106 109 Edit gt BLAST Selection vs SwissProt Search protein databases for homologue Edit gt BLAST Selection vs ExPDB amino acid sequences Tools gt Compute H bonds Computes H bonds Tools gt Compute Molecular Surface Computes molecular surfaces Computing rools gt Compute Electrost Potential Computes electrostatic potential maps commands Tools gt Triangulate Maps Triangulates maps Tools gt Compute Energy Threading Compute energy threading and force Tools gt Compute Energy Force Field field Tools gt Enery Minimisation Performs energy minimisations Tools gt Transl Layer along Unit Cell Translates a molecule along its unit cell Crystallo Tools gt Build Crystallogr Symmetry Applies crystallographic symmetries graphic U commands Tools gt Apply transf on current layer Applies a transformation matrix e File gt Open Electron Density Map Loads and displays electron density maps 38 DeepViewManual NOTES e This action does not actually modify a structure It just alte
124. lotted against the amino acid sequence Examples of application When modeling structures a plot of PP versus the amino acid sequence lets you quickly visualize which region of the alignment might be wrong PP values above zero indicate that this arrangement is not observed in the set of protein structures that was used for the training of the PP 56 DeepViewManual Procedure Tools gt Compute Energy Threading the mean force potential of each residue is computed Click Window gt Alignment to open the Alignment window and display its associated graph by clicking on the small arrow next to the red question mark 5 to display the PP or the gt FF diagrams of the KVFGRCELAAAMKRHGLONYRGYSLGNWVCAAKFESNFNTOATNRNTOGSTOYGILOINSR WwW currently active layer E Alignment Fi layer name and total a molecular PP R e click smooth to select th ias number of previous and following aa whose PP will be averaged for smoothing the curve click default PP to switch from this graph to the FF graph KVFGRCELAAAMKRHGLONYRGYSLGNWYVYCAAKFESNFNTQATNRNTOGSTOYGI The horizontal line is for PP 0 points lying above correspond to amino acids surrounded by an arrangement of residues not frequently observed in the set that was used to derive the potential Tools gt Compute Energy Threading threading energy vs amino acid sequence 106 e Computing energy force field also FF Concept An empirical force field energy of each r
125. luded Other programs should be able to read the atom coordinates saved in this format but will ignore the additional information saved by Deep View Project Saves all layers in a single PDB file see point 113 The saved file contains the same data as above Other programs should be able to read the atom coordinates but will not distinguish the different layers Save Selected Saves the currently selected groups from all layers to a PDB file Residues mmcif Saves a molecular coordinate file to an mmCIF file This format will eventually replace the current PDB format 32 e Saving non coordinate files Saves a surface to a SPDBV surface file sfc Saves a computed electrostatic potential map to an SPDBV potential file Potential Sequence FASTA Saves the sequence of the currently active layer in FASTA format single letter codes Alignment Saves the current sequence alignment formatted exactly as seen by clicking the page icon on the left side of the Align window Ramachandran Plot Saves a simple list of angles for selected residues of the currently active layer You Values must first open the Ramachandran Plot window to calculate the angle values The file contains for each residue the layer name the 3 letter residue name the secondary structure type H S or the peptide dihedral bond angle and the backbone conformational dihedral angles and 14 DeepViewManual 33 e Saving images Image
126. ly active layer This will not apply to HETATM All groups unless you hold the Ctrl key while invoking this command You might need to remove H since DeepView may occasionally miss identify non hydrogen atoms as hydrogens depending on how the individual atoms have been named which is sometimes done incorrectly for two letters element abbreviations i e He Hf Hg and Ho might look like hydrogens Remove Hydrogens Same as before but only for non polar H This produces cleaner pictures of NMR Non Polar structures for example NOTE Add bond and Remove bond functions were designed to modify the connections of e heterogroups wrongly connected in some PDB files e heterogroups badly connected by the automatic reconnection algorithm that Deep View uses when no CONECT cards are present in PDB files 95 e Re orientating sidechains Concept Given a molecule you can select all sidechains of a specific spatial area and explore all rotamers to see which is the best combination Examples of application When modeling a protein structure you can study the different sidechain orientations and optimize them in order to make good contacts If this cannot be achieved it could reflect a misalignment between the protein to be modeled and the template When studying mutations you can see if a specific residue has a chance to fit well in the structure according to its different sidechain orientations Procedure Select the residues whose
127. ly the currently active layer Click File gt Close All Layers to close all layers at once This command is only active if you are working on a project several layers were loaded 36 e Closing the program Click File gt Exit to quit DeepView The next time you use DeepView the program will remember which windows were open and their locations Note that DeepView never asks if you want to save changes in files or projects before closing them nor before quitting the program Basic DeepView Commands 37 e Classification The following basic DeepView commands are mainly for setting the visualization of molecules by selecting displaying and coloring objects as well as for analyzing molecules by measuring distances and angles between atoms They can be grouped according to their location Location Toolbar Control Panel YO O Q N S O N O iS fae O O fae O Translate zoom and rotate molecules S hog Measure dihedral angles 2 Identify groups and atoms Display select groups within a distance of a picked atom Center the model on a picked atom Edit the identification of a molecule apply basic selections 50 select groups by type 51 Select commands select groups by property 52 select groups by secondary structure 53 2 select groups with respect to a reference 54 S select groups by distance 55 gt select groups by structural criteria 56 show hide various obj
128. mats the map Potential Map might have been computed and saved from a previous DeepView session sph or written by external programs phi Open Electron Allows loading electron density maps in either DN6 CCP4 or X PLOR formats dn6 Density Map map txt HII DISPLAYING WINDOWS For an overview of all DeepView windows see points 1 9 23 e Initial windows location The first time you use DeepView and load a molecular coordinate file the program opens the Toolbar the Graphic window and the Control Panel as shown on the figure below When closing DeepView the program remembers which windows were open and their locations So if you already ran the program window locations will be those of your previous session Once a molecule is loaded use the Window menu to manage the display of windows INITIATING A DEEPVIEW SESSION 11 is play Be TXI x Toolbar lt lt Control Panel Graphic window OOOOOOOOOO0000000000000 Initiating a Deep View session displayed windows and their location 24 e Displaying closing a window Under the Window menu click the name of a window to open it or to send it to front An Electron Density Map window or a Cavities window can only be displayed if an electron density map or a molecular surface were loaded or computed see point 102 To close a window follow the normal procedure of the operating system 25 e Linking the Toolbar and the Graphic window The Too
129. measuring distances and angles between atoms Select the font size and color for labeling the amino acids Select the font size number of decimals and color for labeling the distances and angles between atoms 154 e Color settings q Labels Settings gt lt Main Labels Notation Type fe iuys4s LYS 45 Lysd5 Lys 45 45 C K 45 r 45 Default Color Text Size Distances angles lt Test Size E Mb decimals Color 1 3 Cancel 95 Select a notation type for labeling the amino acids Set the colors of various objects by clicking the items of the following dialog which will display a standard color palette to let you choose the colors Molecule Color Settings x CPK atom colors by default C white H cyan N blue O red P orange S yellow Others gray Bond colors by default SS yellow lt Strong H Bond green Weak H Bond dark green Clash purple Background by default black lt Background Amina Acid Kind Acid Basic Polar Mon Polar Structures Helix Strand Other Atoms cfu sj o e one Bonds so Bord Strang H Bond weak H Bond Clash Cancel i Backbone and sidechain colors of amino acids according to four properties by default Acidic red Basic blue Polar yellow Non Polar gray Backbone and sidechain colors of amino acids according to their secondar
130. mes In s usr X11R6 lib libGL so 1 2 0 usr X11R6 lib libMesaGL so 3 In s usr X11R6 lib libGLU so 1 2 0 usr X11R6 lib libMesaGLU so 3 and then run sbin Idconfig to make the system remember this changes This is assuming that the libraries are installed under usr X11R6 lib If this is not correct please adjust the above commands with the correct location 14 e Installing DeepView on Irix DeepView can be downloaded from http www expasy org spdbv or any of the mirror sites mentioned there a Download Swiss PdbViewer v3 7b2 stable Beta version 6 0 Mb b gunzip c spdbv35 IRIX tar gz tar xf c cd SPDBV DISTRIBUTION d install sh Il DEEP VIEW DIRECTORIES Depending on whether you installed the optional material or not the spdbv root directory will contain the following directories and subdirectories INSTALLING DEEPVIEW 7 Fi spdbv Sure usrstuff dee matrix Deep View directories and subdirectories optional material installed 15e stuff directory This directory contains files used by DeepView internally and cannot be altered 16 download directory Stores all files imported from the server and should be cleared from time to time download directory pdb files PDB and ExPDB files Keyword search results BLAST results PROSITE documentation etc 17 e scripts directory Contains scripting examples and a manual for the use of scripts see Annex 2 Scripting Language 18 e tem
131. mode Move All lt Move Selection Switch from Move All to Move Selection and vice versa by clicking the message Depending on whether the Move Selection mode or Move All mode 1s selected the atom coordinates of a moved layer will be altered 18 DeepViewManual 1CRN 465 x 380 Original structure im C spdbv download 1CRN pd5 Qy n Cn Cn hw X Y Z coordinates of the first seven atoms of the original PDB file to display a PDB file see point 67 move all 1 layer 465 x 380 2 Select File gt Save gt Layer to save the translated structure see Move All mode point 31 E C WINNT Profiles mfh1000o Ccsktsp vicwer downlo Eq 1 Translate the structure using the Translate tool sl 3 Open the translated structure again and display its PDB file the X Y Z atom coordinates did not change Ano hanre ea 2 Select File gt Save gt Layer to save the translated structure see Move Selection mode point 31 bra 1 Select all mE C WINNT Profiles mfh1S0co Desktsp wicwer downlo F residues see point 50 and translate the whole structure using the Translate tool 3 Open the translated structure again and display its PDB file the X Y Z atom coordinates did change AAAI Fp M e n Cn oO hw Move All vs Move Selection modes implications on the atom coordinates 43 e Measuring distances between atoms l Buttons 5 is for measuring distances between atoms Click
132. more charged atoms are present Coulomb approximation Simple Coulomb electrostatic potential computations are very fast but not very accurate as only a uniform dielectric constant is applied both for protein interior and for the solvent space These 134DeepViewManual computations can only give a qualitative picture indicating if it might be interesting to have a closer look using a more accurate method Poisson Boltzmann If we want to account for the different dielectric properties of the protein interior and the solvent we have to numerically solve the Poisson Boltzmann equation Klapper et al 1986 This gives us a much more accurate picture of the electrostatic field around a protein However these computations are quite time consuming and for large molecules you might want to use specialized software like DELPHI Honig and Nicholls 1995 for the computations DeepView will be able to load and display these maps Note The current implementation in DeepView is not able to take the solvent salt concentration into account For more details about electrostatics in macromolecules please see e Honig and Nicholls 1995 Science 268 1144 e Anthony Nicholls Kim Sharp and Barry Honig 1991 Proteins 11 281 e http trantor bioc columbia edu delphi VIL ELECTRON DENSITY MAPS DeepView will read and display electron density maps in the following formats e CCP4 http www dl ac uk CCP CCP4 e dn Alwyn Jones O form
133. mport and then reentering the SWISS PROT accession code and pressing the SwissProt text button in the Import dialog Displaying the SWISS PROT header might be useful to find out if the protein contains target sequences that need to 78 DeepViewManual be removed before performing an alignment or to identify active sites residues to help guide the alignment NOTES e DeepView lets you load only one target sequence at a time except in the special case of multimers where the sequence of the chains must be separated by a semicolon and be In FastA format Since no structural information is available for a target sequence DeepView provisionally models it as an alpha helix P41047 203 x 2 FasL MOUSE STANDARD FET 279 AL P4lo47 O61217 O1 FEB 1995 Bel 31 Created O1 FEB 1995 Bel 31 Last sequence update 15 JUL 1999 Bel 38 Last annotation update Fas ANTIGEN LIGAND THFSF6 DP APT1LC1 OR FASL OF GLE Mus musculus Mouse Eukaryota Metazoa Chordata Craniata Vertebrata Euteleostomi Mammalia Eutheria Rodentia Sciurognathi Muridae Murinae Mus 1 SEQUENCE FROM HW aA MEDLINE 94155175 PubMed 7511063 Takahashi T Tanaka M Brannan C I Jenkins N 4a Copeland N G Suda T Nagata amp Generalized lymwphoproliferative disease in mice caused by a point mutation in the Fas ligand Cell 76 969 976 1994 z SEQUENCE FROM M BJ AND 3SD STRUCTURE MODELING STRAIN CSVBL 6 SwissPr
134. n density maps and electrostatic potential maps This field which cannot be edited provides Electron Density Map Parameters Fa information on the unit cell and on the loaded Infos wate x Y z unit cell size A along a X b Y c Z Unit Cell Size 4 amo fammo sz300 unit cell B y angles CelAnges pooo aoa OO r r sa s Ei fisi E range of sections Min to Max covered by the Min Section 42 i BI map along each axis Max Section a a al Select the display of your EDM Displa From Section to Section limits a volume From Section jz fi 8 4 according to the number of sections that you to Section js 2 enter Around CA limits a volume around the woundca 7500 7500 6 centered aa according to the distances that you enter for each axis around Selected Residues the map 1s I Contour a f O00 sigma with Color P v Dotted displayed around selected amino acids Color f Display only around Selected Residues alow W Contour afso E FOO sigma with W Dotted I You can enable the visualization of two Coarse Contouring Along contours and set their appearance sigma a nf En E Cancel values see point 111 and annex XXX v Draw Unit Cell color and doted vs non doted Check these items for coarse contourings of electron density maps their rendering will be speeded up to the detriment of their appearance the information contained in one section out of two is skipped giving a t
135. nal model for the CD40 ligand predicts that it is a compact trimer similar to the tumor necrosis factors Int Immunol 5 233 238 Peitsch MC 1995 ProMod automated knowledge based protein modelling tool PDB Quarterly Newsletter 72 4 Peitsch MC 1995 Protein modelling by E Mail Bio Technology 13 658 660 Peitsch MC 1996 ProMod and Swiss Model Internet based tools for automated comparative protein modelling Biochem Soc Trans 24 274 279 Peitsch MC and Herzyk P 1996 Molecular modelling of G protein coupled receptors in G Protein coupled Receptors New opportunities for commercial development vol 6 p 6 29 6 37 N Mulford and LM Savage eds IBC Biomedical Library Series Peitsch MC Herzyk P Wells TNC and Hubbard RE 1996 Automated modelling of the transmembrane region of G protein coupled receptor by Swiss Model Receptors and Channels 4 161 164 Peitsch MC Wilkins MR Tonella L Sanchez J C Appel RD and Hochstrasser DF 1997 Large scale protein modelling and integration with the SWISS PROT and SWISS 2DPAGE databases the example of Escherichiacoli Electrophoresis 18 498 501 138Deep ViewManual Peitsch MC 1997 Large scale protein modelling and model repository in Proceedings of the fifth international conference on intelligent systems for molecular biology vol 5 p 234 236 Gaasterland T Karp P Karplus K Ouzounis C Sander C and Valencia A eds AAAI Press Peitsch MC and Guex N 1997 Large scale comparative pro
136. nder the Edit menu select a command to achieve one of the following actions Assign Helix Type to Selected residues are displayed as o helix Selected aa Assign Strand Type to Selected residues are displayed as B strand Selected aa Assign Coil Type to Selected residues are displayed as random coil Selected aa e Click Tools gt Detect Secondary Structure to reset the display to the originally computed secondary structure of the currently active layer b Searching commands 98 e Searching a molecule for a sequence pattern ADVANCED DEEPVIEW COMMANDS 47 Concept Given a molecule its sequence is searched for the occurrence of a specific fragment of amino acids or for a PROSITE pattern that you can enter on the Find Sequence PROSITE pattern dialog Examples of application You can look for specific sites such as active sites glycosylation sites etc This might be useful to compare the conformation of a specific motif in different structures to draw conclusions about its function Procedure Click Edit gt Find Sequence the Find Sequence PROSITE pattern dialog is displayed to let you enter a sequence of amino acids or a PROSITE pattern Enter here one of the following an amino acid sequence in one letter format where a Find Sequence PROSITE pattern x question mark means any residue for example DD T N NIPHSTHPI will look for Asp Asp any aa Thr a PROSITE pattern in this example a N glycosylation site
137. ng or previous amino acid based on distance Backbone bonds are not made if residues are too far apart Add C terminal Adds a carboxy terminus for the C terminal end of the last amino acid residue in the oxygen OXT currently active layer 93 e Altering conformational angles Concept You can alter 0 and conformational angles of selected residues Examples of application Certain combinations of and are forbidden because they result in steric hindrance or clashes between atoms During the last stages of structure determination of proteins crystallographers use Ramachandran plots to check and rebuild unrealistic conformations in their models Procedure e Using the Ramachandran Plot window A Ramachandran plot is a graph of versus For selected residues of the currently active layer the Ramachandran Plot window displays one small square for glycines and one small plus sign for all other residues Symbols are colored according to the current backbone color set on the Control Panel Name of the pointed residue The plot delimits the allowed regions PEERU Cum iq where most of the amino acids of any given protein should plot Select C or N to let ic in yellow regions of sterically move on the Graphic Ti 00 120 b 60 120 Ted an allowed values of and window the C terminal or N terminal parts of the protein when a dot is dragged on the plot in blue regions of maximum tolerable limits of steric st
138. ng the identification of a residue group name and group number will center the view on the carbon alpha of the residue NOTE Text files cannot be edited or printed within Deep View 69 e Obtaining help on the Toolbar Click the small red question mark to obtain help on the Toolbar II USING THE CONTROL PANEL 70 e The Control Panel Currently active layer List of the groups of the currently active layer Groups identification include protein chain A B etc secondary structure h s group name SER GLU etc group number Control Panel i Control Panel x m visible group show side labl nbn col p Control Panel header The first line is for toggling on and off the visualization and movement of the currently active layer and for getting help on the Control Panel The second line provides a series of items to be checked for viewing them on display from left to right the residue show its sidechain side its label labD its molecular surfaces and its ribbon ribn The last column co is for setting the color for each of these objects can move r SER 446 h GLLI447 h ALA448 h GLU449 h PHE450 h amp 5FP451 h SEF452 h TFF453 w AL454 AF405455 PRO4S6 SLU457 sLN456 MET459 eT 49 MLT 411 MET 1 ASN amp THR s VWAL4 amp ARGS 2 BERG LU s L Sa s ASPY SERIO MET11 s GLY12 ST ss SSD s SS S Sa SS ss sss sn sS These two small blac
139. o acid to another It is currently not possible to browse the rotamer library in a script mutate lt selection gt to lt string gt where lt selection gt must contain one valid amino acid first selected 1s taken and lt string gt contains the one letter code of the new residue 119 120Deep ViewManual Related commands none Demonstrated in example script none e name Will get the three letter name of the first selected group found in a selection Returned value is of type lt string gt for ex is ALA or ATP name lt selection gt Alternately you can access directly a specific residue from a specific layer which is faster and handy in loops with name lt layer gt lt int gt Related commands num res chain ss access Demonstrated in example script 11 e normalize Will normalize a vector Returned value is of type lt vector gt normalize lt vector gt Related commands vector operations Demonstrated in example script none e num Will get the number of the first selected group found in a selection Returned value is of type lt int gt num lt selection gt Alternately you can access directly a specific residue from a specific layer which is faster and handy in loops with num lt layer gt lt int gt Related commands name res chain ss acess Demonstrated in example script 11 e omega Will get the omega peptidic bond torsion angle for the first selected amino acid found in a sele
140. o edit the number of flanking amino acids to be considered click Force Field to toggle from this graph to the PP graph The horizontal line is for FF 0 kJ mol points lying above correspond to amino acids in un favored geometries Tools gt Compute Energy Force Field Force Field vs amino acid sequence To display on the Graphic window the resulting force at each atom click Display gt Show Forces These will appear as dotted segments in the direction of the force colored in a gradient 0 Kj mol lt 2500 Kj mol lt 5000 or more Kj mol dark blue gt green gt red 107 e Computing energy minimisation Concept Forces acting on each atom of selected groups are minimized by iterative force field calculations followed by structural adjustments Examples of application Whenever a protein is distorted for example after applying mutations or torsions or after reconstructing loops computing an energy minimisation can repair distorted geometries by moving atoms to release internal constraints Procedure First of all click Preferences gt Energy Minimisation a dialog lets you adjust the minimisation parameters see point 159 108 58 DeepViewManual Enable one two or three cycles of n steps ome of Steepest Descent currently the only Energy Minimisation Preferences xl available energy minimization method wW D 20 steps of Stee est Descent gt x Checkmark the interactions to be oe 20 steps
141. o types of variables script variables that can be used to store values in scripts and program variables internal spdbv variables Assigning a value to a script variable is done with varname value Data types for script variables are attributed implicitly during the assignment Examples X 1 0 will assign the value 1 0 of type lt float gt to X X 1 will assign the value 1 of type lt int gt to X Operations on variables are usually possible only between variables of the same type but you can force a value to be of a different type through typecasting Example X float 1 will assign the value 1 0 of type lt float gt to X Valid typecast are int float string e Arrays Currently only arrays of lt int gt lt float gt and lt vector gt are supported The syntax is the following X lt int gt value The type of array is automatically determined by the kind of value that you put into it the first time Memory is allocated dynamically and will only be released when a thank you statement is reached if you want to get back something memory you better be polite e Operations It is possible to add subtract multiply or divide data types Some operations are of course not possible multiplying two strings or two atom selections Adding two strings will produce a concatenation X Hello World is equivalent to X Hello World In the case of vectors multiplication is scalar i
142. of Steepest Descent considered D 20 steps of Steepest Descent gt Cutoff enter a distance A over which non bonded and electrostatic interactions w ipa INSETS will not be considered Iw Fees Cutott BDI A Show Energy Report check this item to obtain an energy report see point 106 M Torsions Z Show Energy Report F Enter a value to stop minimization when mproper the checked option is verified in addition I Stop when delta E between two steps is below 0 050 kL nel to the default stop after completion of the Stop when Force acting on any atom is below i 0 000 selected number of cycles Select between Lock non selected residues only selected residues will be minimized 50 selected residues Cancel Use an harmonic constraint enter a force ait s s aes KJ mol acting on selected and non oh selected residues to adjust minimizations Check Lock Constraint is for CA only to Energy Minimisation Preferences dialog restrict the lock or constraint to CA w Lock non selected residues T Lock 2 Constrain is for Carbon Alpha only f Use an harmonic constraint On the Control Panel select the residues for which you want to minimize the force field energy and click Tools gt Energy Minimization The force field of the selected atoms is minimized Provided that the Show Energy Report item is checked on the Energy Minimization Preferences dialog an Energy Report is displayed and on the Alignment w
143. og yes no appear for user feedback int_varname ask lt string gt where lt string gt contains the question to be presented to the user Related commands if Demonstrated in example script 08 and 10 e atan Computes the arc tangent of an expression Values are in radians atan lt float gt Related commands sin asin cos acos tan PI Demonstrated in example script none e build ANNEX 2 Adds various objects such as amino acids molecular surface build in lt layer gt molecular surface of quality lt int gt Related commands delete Demonstrated in example script none e center Centers the view on a selection or on visible groups center on lt selection gt center on visible Related commands show hide Demonstrated in example script 05 09 and 13 e chain Will get the chain name of the first selected group found in a selection Returned value is of type lt string gt chain lt selection gt Alternately you can access directly a specific residue from a specific layer which is faster and handy in loops with chain lt layer gt lt int gt Related commands name res ss access Demonstrated in example script 11 e color Colors some parts of the view This is functionally equivalent to the color column of the Control Panel color in lt layer gt lt part gt of lt selection gt by lt vector gt color lt part gt of lt selection_variable gt by lt vector gt color lt part gt of l
144. oints whose value is higher than the given cutoff Similarly a negative cutoff in kT e is used to delimit a red contour lower than the given cutoff e distribution of the electric charge at the molecular surface the molecular surface is colored with a red negative cutoff to white neutral points to blue positive cutoff color gradient Examples of application Comparing the electric field extending into the solvent for different proteins will let you compare their relative ability to attract or repulse other molecules Klapper et al 1986 Displaying the distribution of the electric charge at the molecular surface allows studying protein protein or protein substrate interactions Procedure Tools gt Compute Electrostatic Potential the Electrostatic Potential dialog is displayed where you can set several computing options 54 DeepViewManual Electrostatic Potential x Parameters Check Keep Map to display the Dielectric constant solwent B0 000 Keep Map electric field spreading out into use only charged residues Map Potential to Surface the solvent see below for further use atomic partial charges Red E Emi manipulations white s nha ie a Check Map Potential to Surface to display the electric charge of amp Coulomb the molecular surface Notice that Poiszon Boltamann you must have computed a Dielectric constant protein e5 000 molecular surface first Cancel Enter here the cutoff values of the
145. on the Control Panel van der Waals and Accessible surfaces e Computing it first see point 102 and enabling its display on the Control Panel Molecular surface e Loading it from a file see point 22 any surface Using the Control Panel lets you toggle on and off the display of the van der Waals Accessible and Molecular surfaces assigned to each group individually e select a surface in the pop up menu associated to the surface header fifth header e under the surface header checkmark the groups for which you want to display the selected surface Control Panel surface header Header Surface type Drawing result Van der Waals A dotted sphere surrounding each atom The surface will appear as a solid atom when OpenGL Rendering is enabled or during POV Ray renderings see points 140 141 The density of points can be set in Preferences gt Display see point 167 Accessible Equivalent to plotting the van der Waals surface increased by 1 4 A The density of points can be set in Preferences gt Display see point 167 Molecular Equivalent to applying a shrink wrap to the van der Waals surface model To display a molecular surface this must first be computed by clicking Tools gt Compute Molecular Surface see point 102 The surface quality and its initial appearance can be modified in Preferences gt Surfaces see point 156 u BASIC DEEPVIEW COMMANDS 33 Thel 438 x 337 Thel 438 x 337 Accessible SE Accessible
146. ormation is present in a PDB file as the automatic connection feature is not guaranteed to be able to figure out all connections see note below and Annex 4 Extra connections will be saved with the file Add H Bond This will let you pick two atoms to manually add an H bond in between them Note that these manually added bonds are not saved in the PDB file and will be lost anytime you re compute the H bonds Useful for final polish of a scene when the Tools gt Compute H bonds command has missed the very special H bond you wanted to render see point 101 Add Hydrogens Adds missing polar hydrogen atoms according to GROMOS96 topology X ray derived structures normally do not contain hydrogen positions Warning applying this function currently rebuilds all H atoms of the layer Add H2O A water molecule will be added at 2 6 A of the picked atom in a location where it does not clash too much and where it is able to do H bonds Useful to add water molecules to a structure and to evaluate their position Build menu Remove commands ADVANCED DEEPVIEW COMMANDS 45 Remove Selected Deletes selected residues residues Remove Bond Removes a bond added to a HETA TM You will be prompted for the two bonded atoms the first one must belong to the HETATM see note below Remove H Bond Removes an added H Bond which you will be prompted for by selecting the two bonded atoms Remove Hydrogens Removes all hydrogens from the current
147. os lt int gt residue absolute position in layer start at 0 Pos lt int gt to lt int gt residue range absolute position in layer start at 0 Seq lt string gt a sequence can be a prosite pattern Within lt float gt of lt selection_var gt Example sell select in LATP res Y and chain I It is currently not possible to provide very complex selections in one operation but this is easily overcame as selections can be added or subtracted Example sel sell sel2 sel3 sel4 A special case allows to get the current selection state of a layer into a variable This is useful to capture a selection made directly from the user graphical interface sel get selection of lt layer gt Related commands selcount Demonstrated in example script all 126Deep ViewManual e set Can set DeepView internal variables or atomic coordinates The list of internal variables that can be accessed is given In section B of this annex set lt internal variable gt varname set coord lt string gt of lt selection gt vector_varname where lt string gt contains the 4 characters atom name for ex CA and selection a selection It also allows to toggle the backbone representation for a layer to ca trace set ca_trace ON OFF for lt layer gt Related commands get Demonstrated in example script 07 e show Shows some parts from the view This is functionally equivalent to checking the show column of th
148. ot target sequence and corresponding header 128 e Finding homologous templates DeepView offers two ways to search for and load homologous templates i e proteins whose structure has been experimentally solved and whose sequence is similar to the target sequence which can be PDB or ExPDB files e Select SwissModel gt Find Appropriate ExPDB Templates Automatically your Web browser will open at the BLAST search page of the ExPASY site where your sequence has been already entered in FastA format BLAST will then be used to search the ExPDB database for appropriate templates The ExPDB database is a subset of the PDB database containing all templates available for the SwissModel server in separate entries for every chain A result list will be displayed ADVANCED DEEPVIEW COMMANDS 79 Select an accession code to directly Click Detail to see Link to PDB entry on download the ExPDB file or to save it first the target template the PDB Web site and then opening it from Deep View alignment details dowaload Blast see ExPDB Score TUMOR NECROSIS FACTOR RECEPTOR P55 RACELLULAR DO COMPLEXED r HTNRA 62 14 etal X RAY 285 85 me Ena MADY z E IDOGD 313 Detail e 13 Detail 1 z 40 me 1D0G CRYSTA RYSTAL STRUCTURE OF DEATH RECEPTOR 5 DRS BOUND TO APO2L TRAIL r 1D0GBE 3e 13 13 Detail XRAY aE Ea 40 SERER CRYSTAL STRUCTURE OF DEATH RECEPTOR 5 DR5 BOUND TO APO2L TRAIL BLAST score Experimental details P
149. ow By convention the first loaded layer is the reference layer whereas the currently active layer which is the layer currently governed by the Control Panel see point 70 can be manually selected on the Control Panel on the Layers Infos window and on the Alignment window see points 113 114 112 e Classification Advanced commands that can be applied to a project can be grouped into three categories Merging Edit gt Create Merged Layer Builds a new layer by from selected 115 commands from Selection residues in all other layers 116 Fit gt Magic Fit Automatically superpose two structures Fit gt Iterative Magic Fit Fit gt Explore Alternate Fits FA Superpose two molecules based on inn selected residues Fit gt Fit molecules from selection Superposing commands Fit gt Improve Fit Improves a superposition Fit gt Calculate RMS Calculate the root mean square Fit gt Set Layer Sdt Dev into deviation of two superposed structures B factors e Fit gt Reset Orientation current Reset the orientation prior to a layer only superposition Fit gt Reset Orientation every layer follows e Fit gt Generate Structural Generates the structural alignment of 121 Alignment Alignment superposed molecules commands Fit gt Compress Gaps Compresses non sense aligned gaps in the Alignment window gaps present In all layers for a specific column e Fit gt Reset Alignment Resets an al
150. p directory Stores all files generated by DeepView such as energy reports see point 106 PROSITE search results see point 99 alignments see point 121 Although its content is usually cleared when DeepView is closed it might be necessary to clear it from time to time 19 e tutorial directory This supplementary directory contains the tutorial and all files needed to run the examples given in the tutorial DeepViewManual 20 e usrstuff directory This is the User s stuff directory which stores the settings and the default preferences usrstuff directory recfile ini Contains the five last loaded files prosite dat Contains all PROSITE patterns The user has to install this file by retrieving it from the ExPASy site http www expasy org prosite Default prf Contains the default preferences see point 146 matrix Contains all matrices that can be used for sequence alignments PAM 200 being the default matrix see annex 162 Starting a DeepView Session Initiating a DeepView session means e displaying molecules by loading molecular coordinate files e displaying optional objects by loading molecular surfaces electrostatic potential maps and electron density maps molecular surfaces and electrostatic potential maps can also be computed see points 102 and 103 e displaying the required windows All these actions can be achieved by using the File and Window menus of the Toolbar as explained in
151. play a lot of text instead of prompting you where to save the program click on the link during about 2 seconds until a pop up menu appears Then choose the option Save link as and check that Source is displayed in the pop up not Text Then drag the downloaded archive file onto Stuffit Expander 13 e Installing DeepView on Linux DeepView can be downloaded from http www expasy org spdbv or any of the mirror sites mentioned there a Download Swiss Pdb Viewer 6 DeepViewManual b tar xzf spdbv35 Linux tar gz c cdSPDBV DISTRIBUTION d install sh The Linux version is a port of the Macintosh version done using a preliminary release of Latitude for Linux kindly made available by Metrowerks Inc We wish to thank Kevin Buetner for his support and Greg Galanos for allowing us to release a version of DeepView that makes use of Latitude NOTE An error might occur in loading shared libraries JibMesaGL so 3 because the newer Mesa now uses different names for the libraries than those with which DeepView has been linked with Libraries are now called JibGL so and libGLU so instead of libMesaGL so and libMesaGLU so However since the new Mesa is completely backward compatible it should not harm DeepView from working properly Therefore there is no need to install an old Mesa version and just a little adjustment is needed If you can get root access to your Linux box make the following symbolic links from the new libraries to the old na
152. pt 06 08 e sub This command is nothing else than a goto that remembers where it was before It will resume execution where it was before entering the subroutine as soon as a return statement is reached sub lt label gt lt note that this must be the only command on a line Execution will continue immediately after lt label gt which must end with a colon Note that subroutines must be located at the end of the script after the thank you statement All variables beeing global be very careful when you use them especially loops variables Example please do sub elsewhere thank you elsewhere print Is grass really greener here return Related commands goto do while return Demonstrated in example script 08 and 10 e substring Allows accessing substrings within a string by position Substrings are separated by spaces and numbering start from 0 string _varname substring lt int gt of lt string gt Examples X substring 0 of Hello World will put Hello into X X substring 1 of Hello World will put World into X Demonstrated in example script 04 superpose This command is equivalent to the Fit gt Magic Fit of spdbv lt int gt superpose lt layer gt onto lt layer gt using lt string gt where lt string gt contains the method to be used CA backbone all ss This returns the number of solutions as an int 128Deep ViewManual When ss is used and more
153. r the target Sequence alignment between the target and the templates Amino acid pairs linked by a stick are identical those linked by two dots are very similar PAM exchange matrix score 1 those linked by one dot are weakly similar PAM exchange a N n H a RSI P s E EDT YGT LI s R VKYKKGG matrix score 1 GOP SKONSLLWRANTORAFLOOGFSLSNNSLLYVPTSG ANP OAEGOLOWLNRRANALLANGVELRONOLYVPSEGL Y Fit gt Fit Raw Sequence NOTES e The Fit Raw Sequence command is only available if at least one structure and a target sequence are loaded e If more than one structure is loaded the target sequence is aligned to the first loaded reference layer Applying Fit Raw Sequence automatically computes the threading energy for the target The corresponding threading energy plot can be displayed by e selecting the target as the currently active layer e clicking the small white arrow on the Alignment window 131 e Viewing the threading energy The SwissModel menu offers three commands to let you visualize the threading energy of the sequence alignment between the target and the templates SwissModel menu Update Threading Enabling this option updates the threading energy plot for the target sequence Display Automatically whenever the sequence alignment is edited see point 105 Update Threading If the former option is not enabled select this option to update the threading energy Display Now plot for the target sequen
154. rain To alter the backbone conformational angles of one residue click and drag its symbol on the Ramachandran 120 Plot To modify only hold down 180 L 1 180 the 9 key while dragging the symbol 160 120 60 0 bD 120 180 to modify only hold down 0 zero Name of the currently active layer Ramachandran Plot window e Using the Tools menu For selected residues on the Control Panel window the Set Omega Phi Psi command under the Tools menu offers a submenu that allows altering the values of backbone conformational angles Tools gt Set Omega Phi Psi command 44 DeepViewManual Alpha Helix Rebuilds selected amino acids as one long alpha helix 60 p 40 The helix is not perfectly straight since only and angles are modified whereas bond lengths and angles of the backbone are not altered Beta Sheet Rebuilds selected residues in beta conformation 120 120 Only 9 and angles are modified bond lengths and angles of the backbone are not altered Other A dialog allows setting numerical 0 p and values for selected amino acids 1 e for one or many residues at once Setting 0 and to 180 degrees shows the backbone in its most extended form By default the N terminal part of the protein will stay static while the C terminal part will move according to the applied change in the backbone angles However you can choose to let move the N terminal part of the protein by removing t
155. ranslating zooming and rotating the molecule The currently active button is mapped onto the left mouse button On the Graphic window the cursor changes to show which button is selected Pressing tab repeatedly cycles through the three commands from left to right Holding down the Shift key while pressing tab repeatedly cycles through the three commands from right to left Linux Irix in addition to buttons 2 to 4 the left mid and right mouse buttons provide rotation zoom and translation respectively provided that the rotate button is selected mapped on the left mouse button It is therefore suggested to leave the rotate button selected permanently so that it is possible to fully control the molecule motion with the three mouse buttons Windows use the left mouse button to rotate a molecule the right button to translate it and both buttons to zoom it provided that the rotate button is selected mapped on the left mouse button It is therefore suggested to leave the rotate button selected permanently so that it is possible to fully control the molecule motion with the two mouse buttons When either the translate or the rotate tools are active the selected movement can be constrained about or along the X Y or Z axes by using the following key modifiers Ma Rotation and translation can also be applied to selected groups by clicking on the message space below the tools to switch from Move All mode to Move Selection
156. rgy computed by a Sippl like mean Annex 4 Energy force potential see Dark blue means that the threading energy is low the residue is happy with its environment red means that the threading energy is high the residue is not happy with its environment By Force Field Colors each residue according to its force field energy computed with a partial Energy implementation of the GROMOS 96 A dialog lets you choose what kind of interaction you want to compute bond angles improper electrostatic and ask for a text report where detailed energy of each residue is given Especially useful during refinement of a model as you can color by bond and angle deviations only and this will identify distorted parts of the protein By Protein The backbone of those residues whose 0 angles do not plot in the allowed area of the Problems Ramachandran Plot is colored in yellow The backbone of proline residues whose 9 angle deviates more than 25 from the ideal 65 value is colored in red Buried sidechains of residues that could make H bonds but do not are colored in orange Clashes are computed and will appear as pink dotted lines 66 Color menu fourth block Color menu Command Coloring action By Other Color Prompts you for a single color to be applied to the entire layer It is functionally equivalent to a shift click on any color box of the Control Panel window see point 81 By Backbone These last five commands
157. ring gt where lt string gt contains the method to be used CA backbone all Related commands rms superpose Demonstrated in example script none e generate structural alignment Generates a structural alignment It is functionally equivalent to the Generate Structural Alignment command under the Fit menu fit lt layer gt onto lt layer gt using lt string gt generate structural alignment Related commands rms superpose fit Demonstrated in example script none e get Can access internal DeepView variables or atomic coordinates retrieve amino acid sequences or capture the current selection status of a specific layer when modified directly from the graphical user interface sel get selection of lt layer gt Svarname get lt internal variable gt Svector_varname get coord lt string gt of lt selection gt string varname get seq of lt selection gt where lt string gt contains the 4 characters atom name for ex CA and selection a selection The list of internal variables that can be accessed is given in section B of this annex Related commands set Demonstrated in example script 07 08 09 and 10 e goto One of the most useful and controversial commands that allows to continue the execution from a different point of the script goto lt label gt Execution will continue immediately after lt label gt which must end with a colon Example 118Deep ViewManual goto else
158. rotein description method and resolution SwissModel gt Find Appropriate ExPDB Templates result list e Select all residues on the Control Panel and click Edit gt Blast Selection vs ExPDB DeepView will connect to the DeepView server to run a BLAST search vs ExPDB database for homologous templates see point 100 E C spdbv download blast tct gt BLASTP 0 10 Aug 6 19499 lt BHeference Altschul Stephen F Thomas L Madden Alejandro X Schaffer Jinghui zhang zheng zhang Webb Miller and David J Lipman 13371 Gapped BLAST and PSI BLAST a new generation af protein database search programs Nucleic Acids Res 5 33589 3402 Query query For explanations 279 letters on this result list Database ExNRL see point 100 22 969 sequences amp 176 101 total letters Searching Sequences producing significant alignments hits v4 Click one accession code to download the file 71 7O TO Edit gt BLAST Selection vs ExPDB result list NOTE A template can also be manually loaded by clicking File gt Import and on the Import dialog that is displayed entering its accession code before pressing the PDB file or ExPDB file buttons depending on the template file type II GENERATING A MODELING PROJECT Generating a modeling project means adjusting a sequence alignment between the target and the templates This is the alignment that will be submitted to and used by Swiss Model to construct the
159. rs its visualization e Some advanced commands output result text files that can be opened with a text editor and printed a Modifying commands 88 e Mutating amino acids i Concept Given a molecule you can mutate an amino acid by first replacing its sidechain and then browsing a rotamer library Rotolib aa which provides the most commonly observed orientations for the new sidechain Examples of application Studying mutations by using DeepView can be very useful to quickly evaluate their putative effects before actually performing them in the lab Procedure To initiate a mutation click the Mutate tool 12 button of the Toolbar and following the instructions that appear in the message space below pick the amino acid to be mutated by clicking any of its atoms on the Graphic window A list with the 20 protein amino acids is displayed Chose a new amino acid in the list the original sidechain of the selected group will be replaced by the best rotamer of the new amino acid Clicking outside the list or pressing return or enter will highlight the original amino acid in the list For a definition of the best rotamer see Annex 4 Mutations Once a mutation is done the number and the score of the displayed rotamer are shown in the message space below the tools For example rotamer 4 16 score 1 means that rotamer 4 out of 16 available rotamers is currently on display and scores 1 see Annex 4 On the Graphic window H bon
160. s might be useful to properly place side chains 1 e making a maximum number of H bonds and a minimum number of clashes Procedure Click Tools gt Compute H Bonds These will be automatically drawn on the Graphic window according to the distance and angles constraints given above NOTE Certain atoms can behave as H Donors or as H Acceptors depending on certain conditions Therefore when hydrogen atoms are not explicitly present it might be possible to find erroneous predictions of H bonds computed between two H Donors or between two H Acceptors These erroneous H bonds can be removed by clicking Build gt Remove H bond e Computing molecular surfaces Concept For a given a protein DeepView can compute and display its molecular surface which is defined as the area that can be reached with the surface of a solvent molecule radius 1 4 A that is rolled over the protein see point 80 The drawing result is equivalent to applying a shrink wrap to the van der Waals surface Examples of application Building molecular surfaces allows visualizing the shape of a protein and its surface properties Procedure Tools gt Compute Molecular Surface will compute a molecular surface using a numerical grid algorithm Surfaces can also be loaded in three different file formats e saved from a previous DeepView session sfc e written by the program MSMS Sanner amp Olson 1996 e written by the program GRASP Honig et al 1991 Molecular
161. select Fit gt Improve Fit NOTE The process is aborted if DeepView cannot find similar atoms close to each other This will happen if you try to improve the fit for two proteins that have not been superposed first e Evaluating a superposition Concept DeepView lets you evaluate the quality of a superposition between two molecules by calculating the RMS between 2 layers or the standard deviation between more than two layers at each residue Procedure On the Control Panel select for each concerned layer the same number of corresponding residues and then select Fit menu Calculate RMS Evaluates the quality of a fit by calculating the RMS Root Mean Squared deviation see Annex 4 between two superposed molecules The RMS amp Auto Fit options dialog is displayed to let you specify which are the two molecules static and superposed to be considered as well as which atoms are to be used in the RMS calculations see point 116 Only selected groups on the Control Panel are taken into account HETATM should not be included unless you are sure that their atoms appear in the same order in the two PDB files On the Toolbar the message space will display the number of atoms that were involved in the calculation and their RMS computed value On the Alignment window pointing a residue belonging to the superposed molecule second layer will calculate the backbone RMS deviation to the aligned residue in the static molecule first layer The R
162. sure your graphic card is running with the correct vertical refresh rate e g 60Hz before switching your emitter e g EPC2 to stereo Provided that OpenGL stereo is supported by your graphic card DeepView automatically uses it as the default hardware stereo format You should see both left and right eye views superposed in one window We have tested this mode successfully on an HP visualize fx4 video card with an HP1100 monitor SGI The only hardware stereo mode supported for now is Above Below STR RECT In principle SGIs are ready for stereo display but you might need additional adaptators on certain machines and an emitter in all cases We have tested this successfully on an Indy with a SGI 20 monitor Linux The only hardware stereo mode supported is Above Below DeepView will determine different video modes supported by your hardware from the configuration file etc X11 XF amp 6Config While switching to stereo view the program will install a video mode with a lower vertical refresh rate to stay within monitor limits when you activate your emitter On switching back to mono view it will reinstall your previous settings Example In the following it is assumed that you are using a resolution of 1280 times 1024 with an appropriate vertical refresh rate We want to add a new video mode at 1600 times 1200 which the program will use to display the stereo view You have to adjust your configuration file for the X server et
163. surfaces can be colored in a similar manner as all other graphical objects e First select act on Surface in the Color menu see point 62 or in the Control Panel header see point 81 e Then select any of the coloring functions in the color menu or use the control panel to assign specific colors The default appearance of a molecular surface is defined in the Surface preferences dialog see point 156 which offers three different surface colors by Cavity Atom Type or Electrostatic Potential 52 DeepViewManual Surface Preferences F iS Control Panel General Appearence General Appearence Real Time Dotted Lines Not drawn Z visible gt can hove Jw C Plain Lines Dotted Lines Filled Triangles only in 3D mode Plain Lines Filled Triangles Quality 1 6 fi Transparency will show only on SGI or when Transparency D the scene is rendered with POY Default surface Color C Cavity Ignore Selected Residues Atom Type for example cofactor C Electrostatic Potential Cancel Red White Blue Cancel 1 400 0 000 1 400 OOO a a v v v v v v v v v v v Y v v v v v v v v v lt lt lt lt lt lt lt lt lt lt lt lt lt lt lt lt lt lt lt lt lt lt lt lt lt lt lt lt lt lt lt lt lt lt lt lt lt lt lt lt lt The Surface Preferences dialog offers three default surface colors Use the Control Panel to assign Cavity the mol
164. t commands Access to additional variables will be added in the future as needed nbLayer returns the position of the last layer as it starts at 0 when one layer is loaded its value is 0 Its value is 1 for two layers etc active layer returns the position of the currently active layer the one shown in the Control Panel gDotDensity changes the density of dots on van der Waals surfaces in normal display mode eCurrentOS contains MAC SGI LINUX or WINDOWS The following variables affect the behaviour of alerts presented during the load of a protein It might be useful to disable them set to 0 when a batch of files is to be treated geReconstructSidechain 0 or 1 reconstructs missing sidechains gShowConnectAlert 0 or 1 reports missing or bad CONECT records gShowHETATMAlert 0 or 1 reports ATOM treated as HETATM gLoadWater 0 or 1 loads solvent molecules gPartialOccupancyWarning 0 or 1 issues a warning when atoms have a partial occupancy as defined in the PDB file Demonstrated in example script 08 and 10 NOTE Access to other internal variables will be added in the future III LIST OF COMMANDS access Will get the relative accessibility of a residue X compared to a 100 ref value being computed in an extended conformation in the pentapeptide GGXGG The returned value is of type lt float gt access lt selection gt Alternately you can access directly a specific residue from a specific layer whic
165. t selection_variable gt in lt color gt when in lt layer gt is omitted the currently active layer is assumed lt part gt can be any combination of res side label surface ribbon vdw lt vector gt is a RGB color with intensity of each component are between 0 0 and 1 0 lt color gt is any of the predefined keywords red green blue yellow white black grey cyan orange purple example color In 1crn ribbon of res F N by lt 1 0 0 0 0 0 gt Related commands hide show Demonstrated in example script 05 and 13 e compute Performs various computations on a protein compute in lt layer gt electrostatic potiential using coulomb pb with partial full charges compute in lt layer gt hbond lt floatvar gt compute in lt layer gt energy Related commands discard minimize Demonstrated in example script 07 and 09 115 116Deep ViewManual e clear Clears a file on disk USEFUL but DANGEROUS clear file lt string gt where lt string gt is a variable that contains a filename Related commands open close readin Demonstrated in example script none e close Closes a layer or a file close lt layer gt close file lt file gt where lt file gt is a variable that contains a file previously open Related commands open clear readin Demonstrated in example script 02 03 and 04 cos Computes the cosine of an expression This returns the value in radians cos lt float gt cos lt int gt
166. table as possible I would recommend separating the file name from the path which will let you or other users change just the path one line to make a generic script run on their machine Consider this example open System pdb 1crn pdb open System pdb latp pdb it is better rewrote like this path System pdb change this line to point to your pdb files directory open path Icrn pdb open path latp pdb The open command also allows to create files or open arbitrary text files for further processing or allows to open a file as read only file_varname open file lt string gt file varname open file lt string gt for reading or allows to open a file as write CAUTION when USING THIS file varname open file lt string gt for writing or allows to append to a file CAUTION when USING THIS file_ varname open file lt string gt for appending In fact using the full path of your file directories filename is potentially dangerous if for some reason the filename get screwed up Besides it is not cross platform and you likely wish to have your scripts running everywhere I suggest that you and work with files store the files in your usrstuff directory using the following equivalent commands file _varname open file lt string gt in usrstuff file varname open file lt string gt in usrstuff for reading Sfile_varname open file lt string gt in usrstuff for writing
167. te Structural Alignment e Compressing gaps Concept On the Alignment window gaps aligned with gaps are removed These non sense alignments may occur if you have edited the alignment deleted some residues or removed a layer from the alignment Procedure Select Fit gt Compress Gaps e Resetting alignments Concept Un aligns the currently active layer by resetting its sequence on the Alignment window the sequence will start at the left of the Alignment window and will show no gaps Procedure Select Fit gt Reset Alignment HOMOLOGY MODELING 124 125 e Overview DeepView offers a series of commands that let you model new structures by submitting modeling requests to Swiss Model a server for automated homology modeling The Glossary given in Annex 5 includes some homology modeling terminology To facilitate understanding of the following points the most essential terms are here introduced This chapter can not provide an introduction to homology modeling for further details please refer to the references provided at the end of this manual page 137 ff Homology modeling also called comparative protein modeling or knowledge based modeling is the process by which a 3D model of a target sequence is built based on an homologue experimentally solved structure experimental processes include X ray crystallography and solution nuclear magnetic resonance A target sequence is the primary sequence of a protein whose struct
168. tein modelling in Proteome research new frontiers in functional genomics p 177 186 Wilkins MR Williams KL Appel RO Hochstrasser DF eds Springer Guex N and Peitsch MC 1997 SWISS MODEL and the Swiss PdbViewer An environment for comparative protein modelling Electrophoresis 18 2714 2723 Guex N and Peitsch MC 1999 Molecular modelling of proteins Immunology News 6 132 134 Guex N Diemand A and Peitsch MC 1999 Protein modelling for all TIBS 24 364 367 Nicolas Guex Torsten Schwede and Manuel C Peitsch 2000 Protein Tertiary Structure Modeling Current Protocols in Protein Science 2 8 1 2 8 17 SC Lovell JM Word JS Richardson and DC Richardson 2000 The Penultimate Rotamer Library Proteins Structure Function and Genetics 40 389 408 Energy Minimisation Force Fields GROMOS96 W F van Gunsteren et al 1996 in Biomolecular simulation the GROMOS96 manual and user guide Vdf Hochschulverlag ETHZ Sippl J M 1990 Calculation of Conformational Ensembles from Potentials of Mean Force an approach to the knowledge based prediction of local structures in globular proteins J Mol Biol 213 859 883 Glossary 1 Norah Rudin 1997 Dictionary of Modern Biology Barron s Educational Series Inc 504 pp 2 ISO AFNOR 1997 Dictionary of Computer Science The Standardized Vocabulary 3 Nicolas Guex Torsten Schwede and Manuel C Peitsch 2000 Protein Tertiary Structure Modeling Current Protocols in
169. tes etc you need to have downloaded the latest version of prosite dat from http www expasy org prosite and placed it into your usrstuff directory 48 DeepViewManual PROSITE accession codes click an AC to im C spdbvitemp proslist tt import a text file HPROSITE FSOOOOS Protein Einase C phosphorylation site FSOOOOS W myristoylation site PSOOS42 Microhbodies C terminal targeting sinal pattern PSOOLZSy Alpha lactalbumin lysozyme C sinatur containing detailed information on the Pattern description click a pattern to highlight it on the structure according to the settings entered in the Find Edit gt Search for PROSITE pattern result list Sequence PROSITE pattern dialog see point 98 100 e Searching SWISS PROT and ExPDB databases Concept You can use the DeepView server to search SWISS PROT and ExPDB databases for amino acid sequences similar to a previously selected fragment of amino acids in the currently active layer Examples of application Given a molecule you can find other proteins with a similar sequence for modeling purposes Procedure Under the Edit menu select one of the following commands Edit menu You first need to select a fragment of at least 10 amino acids BLAST selection The Deep View server uses BLAST Altschul 1990 to search SwissProt and TrEMBL for vs SwissProt proteins containing a fragment of amino acids similar to your selection A result text file n
170. than one solution is possible a temp file match txt is written and a window will be opened with one solution per line Related commands rms fit Demonstrated in example script 05 e system Executes a shell system command USEFUL but DANGEROUS system lt string gt This command is supported only for SGI and Linux versions It is mainly useful to execute a script that will put results into a file that can then be open as read only with the open file command and read line by line with readIn Demonstrated in example script none e tan Computes the tangent of an expression Returns the value in radians tan lt float gt tan lt int gt Related commands sin asin cos acos atan PI Demonstrated in example script none e torsion Computes the torsion angle ABCD between four atoms vectors In other words the angle between planes ABC and BCD lt floatvar gt torsion A B C D where A B C and D are lt vector gt values Result is returned in degrees Related commands dist get Demonstrated in example script none e thank you Polite way of ending a script which will also free any memory assigned for arrays Related commands please do Demonstrated in example script all e zoom This command changes the camera position to zoom In or out zoom lt float gt where lt float gt is the percent change 100 0 means no change 110 0 will do a close up enlarge the image by 10 90 0 will zoom out d
171. the button and follow the instructions that appear in the message space below the toolbar 1 Pick 1 atom 2 Pick 2 atom After you have picked two atoms on the molecule the distance is shown as a label along with a dotted line Distance measured between two atoms picked on the Graphic window BASIC DEEPVIEW COMMANDS 19 60 1 44 e Measuring bond angles Button 6 is for measuring bond angles Click the button and follow the instructions that appear in the message space below the toolbar 1 Pick center atom 2 Pick 2 atom 3 Pick 3 atom After you have picked three atoms on the model the angle is shown as a label along with a dotted line Angle measured between three atoms picked on the Graphic window we 45 e Measuring dihedral angles Button 7 is for measuring dihedral angles e Click the button and following the instructions that appear in the message space below the toolbar pick one atom The values for 6 and of the amino acid containing the selected atom are displayed on the message space ELEn Px gt HUTATE T Fsten Selected oo OE S S P gt T w 179 367 phi 96 55 psi 13487 Values for 0 and of a selected amino acid are given on the message space e Click the button while holding Ctrl and following the instructions that appear in the message space below the toolbar pick 4 atoms The torsion angle of the four atoms is displayed on the message space u PT F
172. the menus and tools of the program 39 e The tools Tools for basic Tools for advanced functions functions 4 3 6 7 8 9 10 11 12 13 7 5A 60 1 ee Wy Wy i HUTATE TORSIOH PARA Re Belles ica A active tool appears in Deep View tools inverse video A tool is selected by clicking its icons To deselect tools 2 to 10 either select another tool or press Esc to activate the rotation tool For explanations on tools 11 12 and 13 which are for achieving advanced function see points 117 88 and 89 respectively Tools 5 to 8 add labels on the Graphic window To remove those labels see point 61 40 e The menus Menus containing commands for basic functions Edit Select Build Tools Fit Display Color Preferences SwissModel vvindow Help Y Y Y Menu for initiating Menus containing commands Menu for setting Menu for Menus for getting ending a session for advanced functions preferences homology help and displaying modeling windows BASIC DEEPVIEW COMMANDS 17 a Using the tools 41 e Centering a molecule Button 1 is for centering the molecule this will be automatically adjusted so that visible residues fit the Graphic window All platforms can also center a molecule by using the Home key oblique arrow on Mac or the key 42 e Translating zooming and rotating a molecule i For all platforms buttons 2 3 and 4 control movement of the molecule From left to right these buttons allow t
173. the region around the rebuild loop e For details about clash scores PP and FF calculations see Annex 4 91 e Matching sequence fragments in poly Alanin models Concept This function tries to match fragments of sequence into a poly Alanin model according to the fit with a given electron density map Examples of application X ray derived protein models are built in Electron Density Maps in several steps Usually the first step is to identify the secondary structure elements and build them as a generic poly Ala chain without sidechains This provides the initial framework of fragments of the peptide chain As loops initially are not always visible these secondary structure elements are often not connected It is therefore necessary to identify which part of the protein primary sequence might fit in a specific secondary element in order to achieve the construction of the whole peptide chain Procedure To construct a fragment of the peptide chain of a protein you first need to load the following files e apoly Alanin model of the protein chain molecular coordinate PBD file e an Electron Density Map of the protein this might be a dn6 ccp4 or x plor formatted map e the amino acid sequence of the protein this is a text file to be loaded from the SwissModel menu SwissModel gt Load Raw Sequence to Model or to be imported from the SwissProt database under the File menu see point 21 On the Control Panel display the Poly Alanin
174. this chapter I LOADING FILES 21 e Loading molecular coordinate files The File menu offers the following commands to load a molecular coordinate file This can be a PDB mmCIF or MOL file Open MOL File Displays a dialog box that allows loading a Molecular Design Limited MolFile MDL MolFile Import Displays a dialog box that allows doing one of the following l Retrieving PDB files from a local directory by typing the molecule accession code and selecting Grab from disk PDB File NOTE The path of the local directory which is the directory in your computer that contains your own collection of PDB files needs to be specified see point 164 2 Retrieving PDB SwissProt sequence and SwissProt text files via a special Deep View network server You achieve this by typing the molecule accession code or its SwissProt identification and selecting the appropriate button under Grab from server NOTE The network server must be configured see point 163 3 Keyword Search for PDB ExPDB files available on the server using the AND and NOT connectors A list of the PDB entries is displayed To load a file from the given list just click its name appearing in red Ifa PDB entry contains more than one chain several ExPDB file names are available Click the right name to load the whole PDB entry e g 1a00 and click the left name to load just one chain e g 1a00c loads only chain C The bottom of the File menu also provides a
175. toms and eventually without sidechains However the previous options should be progressively disabled when the total number of lines to display is greater thar In order to reduce even more the CPU load you can allow the program to draw only one group out of n Besides if the total number of lines still exceeds the previous settings draw only one group out of NOTE the maximum number of lines that can be drawn during real time operations is deliberately limited to 65000 152 e Rock and Roll By pressing gt DeepView animates molecules with a rolling motion around the vertical screen axis This lets you perceive their 3D geometry under normal display no stereoscopic view no 3Drendering The following dialog lets you set some parameters for the rolling motion Rock and Roll x Max Rotation Angle 30 000 j In this example molecules will rock between Angle Step 5 000 i 30 and 30 along the y screen axis being on display during 100 ms every 5 Frame Delay ma 100 m Z Reverse rotation when mas angle has been reached Unchecking this option will annul the Max Rotation Angle set above and the molecule will roll around 360 Use the gt key to Start Stop the n rocking Leite SETTING PREFERENCES 153 e Labels settings Set the appearance of the labels that are displayed on the Graphic window by e using the Control Panel for naming amino acids e using the Toolbar tools for
176. toms of lt selection gt by lt float gt deg rad around bond lt string gt lt string gt Related commands zoo move Demonstrated in example script 05 06 and 09 e return Will resume execution where it was before entering the subroutine See sub for more explanations Related commands goto do while sub Demonstrated in example script 08 and 10 e rms This command is equivalent to the Calculate RMS command under the Fit menu rms of lt layer gt and lt layer gt using lt string gt lt floatvar gt rms of lt layer gt and lt layer gt using lt string gt where lt string gt contains the method to be used CA backbone all Related commands fit superpose Demonstrated in example script 05 ave Saves all or part of pdb files from some layers save lt layer gt as lt string gt save selection of lt layer gt as lt string gt where lt string gt contains the full filename see discussion in open An alternative set of commands that will save files in predefined directories located under the spdbv main directory is available Directories can be usrstuff temp or download save lt layer gt as lt string gt in usrstuff temp download save selection of lt layer gt as lt string gt in usrstuff temp download in this case lt string gt must contain ONLY the filename as the directory is implicit This is very useful to make scripts portable among the various OS supported Windows Mac Irix an
177. transformation matrices in their MTRIX lines These are matrices that describe specific transformations for example 4mdh pdb contains the transformation matrix needed to superpose chain B onto chain A Examples of application The asymmetric unit of a crystallographic unit cell may contain only part of oligomeric protein structures Often the information to construct the biologically active form from the initial coordinates is provided as a transformation matrix in REMARK 350 lines of PDB files See for example files lout pdb trout hemoglobin Procedure e General procedure Once a molecule has been loaded select on the Control Panel the groups to be transformed and click Tools gt Apply transformation on current layer This will display the Transformation dialog box to let you enter a transformation matrix ADVANCED DEEPVIEW COMMANDS 61 Transformation x This will act on the curent coordinates not those present in the file You might hawe to reset the orientation first Rotation To apply a matrix contained in a PDB file fi o00 JENI fac z Open the PDB file scroll it down until the coordinates and click a MTRX line the o oo fiom z matrix values will be copied into the Transformation dialog To apply a matrix of your own choice Enter here the matrix values ie M Y ce ee MTRIX lines just before the atom Zs Jo 000 gt Appl Reverse Transformation entered is valid you can undo a trans
178. translation along a and b TRANSLATION ALONG ONE AXIS along a and c along b anc along a b and c Click one translation to translate the molecule Here only translations TRANSLATION ALONG a and b along one axis and along a Control click one and b are shown translation to translate a copy of the molecule Tools gt Translate Layer along Unit Cell NOTE The unit cell must be displayed on the Graphic window this can be achieved by checking the Draw Unit Cell option In the Electron Density Map Parameters dialog see point 158 e Applying crystallographic symmetries Concept Applying a crystallographic symmetry means generating layers of symmetrical molecules by applying crystallographic symmetry operators Examples of application This function is used to generate the symmetry related molecules in a crystallographic unit cell e g to examine crystal contacts identify protein protein contact surfaces or identify the biological active arrangement of an oligomeric protein Procedure Tools gt Build Crystallographic Symmetry this will display a list of space groups with their corresponding symmetry operators If the current PDB contains a properly formatted CRYST1 card the correct space group should be shown on top of the list You can apply the provided operators individually or all together by clicking on the space group symbol 60 DeepViewManual me CAWINNT Profiles mfh10000 Desktop viewer download hel t
179. ture elements in Control Panel window Even non amino acid groups are selected non TRANS aa Residues with cis or distorted peptide bonds aa with Phi Psi out Residues outside of the common o B and a core regions see point 93 Ramachandran of Core Regions Plot aa with Phi Psi out Residues with unusual and or values Few residues should be here except for Gly see of Allowed Regions point 93 Ramachandran Plot NOTE 24 DeepViewManual You can select an individual secondary structure by clicking on a h s or in the second column under the group header of the Control Panel see point 74 54 e Selecting groups with respect to a reference The following commands presuppose that a structural alignment has been computed see point 121 aa identical to Selects residues that are strictly conserved between the currently active layer and the ref reference layer first loaded aa similar to ref Selects similar residues between the currently active layer and the reference layer first loaded By default the PAM 200 matrix will be used and the minimum score needed to be considered similar can be modified in Preferences gt Alignment see point 162 aa matching ref Selects residues of the currently active layer whose backbone has a RMS deviation to the structure reference layer inferior or equal to a certain threshold 55 e Selecting groups by distance The three following commands prompt t
180. u can open many Text windows for viewing text files such as PDB files energy reports BLAST results help texts etc Text files cannot be edited or printed directly in DeepView Please use any text editor for this purpose INSTALLING DEEPVIEW I REQUIREMENTS AND INSTALLATION 10 e Requirements Required Hardware Required Operating System Pentium or 486DX Win 95 98 2000 NT4 Open GL Power Mac Mac68K are no longer supported Open GL 256 colors monitor QuickDraw3D no longer supported Extended Keyboard highly recommended Linux US Keyboard Linux for PC with glibc 2 0 or higher 3 button mouse Preferably RedHat X11R6 with at least 1 6bits MESA libraries Irix 02 Octane IRIX 6 x preferably 6 5 IRIX 5 3 no longer supported NOTE See ANNEX 3 HARDWARE REQUIREMENTS for hardware stereo support 11 e Installing DeepView on PC DeepView can be downloaded from http www expasy org spdbv or any of the mirror sites mentioned there a Download amp install Swiss PdbViewer DeepView is distributed either as a self extractable archive exe or as a zip archive zip e exe Double click the file By default a directory called spdbv will be created in your C drive You can move this directory where you want on your hard drive Be sure to maintain the directory content see points 15 20 To launch DeepView double click the application icon E e zip The file can be expanded using WinZip In this case
181. ubmitted alignments are sent here for modeling structures server set by default Template Server If you want to align a raw sequence to a http ww expasv ch svissmodcarbiriyblaste pclb cgl pro tein Sins coh adel seanchacdhis Serer for the appropriate templates server set by default Tour Name Your E Mail your ametayours erer country Enter here your name and your e mail to allow Swiss Model sending you back its modeling results Z Alert user when some 44 are auto excluded from the modelling This option has currently no effect 164 e Deep View file server settings For using BLAST and importing PDB files you must define the Web server Server Settings x Enter the computer IP Number and Port to use BLAST for retrieving Name IP Humber Port proteins from SwissProt and Ele Caney Jin gwer ch 27000 ExPDB databases Pah aloca PL B Biles CAWINAT SProfiles oofh OO00 Desktop view Enter the directory where you Cancel store your PDB files this will let you use the Import command under the File menu SETTING PREFERENCES 101 165 e 3D rendering parameters Use this dialog to enter several parameters setting 3D renderings 3D rendering parameters General settings Render image C Left eve e Standard C Bight eye Left Standard and Right Z Use Meshes nicer But slower Stay solid during motion eye have currently no effects Bonds enable Use Meshes to Edit these DEPE 0
182. ups that you want to see in the new merged layer Then click Edit gt Create Merged Layer from Selection the merged molecule will appear in a new layer named merge You can rename it by using the Rename Current Layer command under the Edit menu see point 49 NOTES e Edit gt Create Merged Layer from Selection can be used as a copy paste function e Groups will be saved in the order of their original layers 1 e all selected residues of the first layer then second etc When creating chimerical proteins make sure the order of layers corresponds to the N gt C order of the selected residues b Superposing commands 116 Superposing two structures Concept Two given structure can be superposed on the Graphic window Examples of application Superposing two molecules lets you compare their structures for various purposes See for example next chapter on homology modeling Procedure The Fit menu offers three commands Magic Fit Iterative Magic Fit and Explore Alternate Fits to superpose a molecule onto another Invoking these commands displays the RMS amp Auto Fit Options dialog in which you can specify RMS amp Auto Fit options x Select the type of atom to C Backbone atoms only be considered to r Sidechain atoms only superimpose the Select here All atoms superposed molecule onto reference layer by defaul ianed Cancel Note that Sidechain atoms efault Ahes d molecule B ma mi only and All atoms c
183. ure has to be modeled When first loaded in the workspace it Is provisionally drawn as a long helix A template structure or simply a template is an experimentally solved structure used as a scaffold to model the structure of the target sequence Template sequence is the primary sequence of a template e Swiss Model Swiss Model is a server for automated comparative protein modeling It is available free of charge at the ExPASY Expert Protein Analysis System site http www expasy org swissmod where extensive documentation on the architecture and use of Swiss Model can be found The ExPASY Expert Protein Analysis System site is the proteomics server of the Swiss Institute of Bioinformatics SIB The server is dedicated to the analysis of protein sequences and structures Amongst other documentation it curates several protein databases such as SWISS PROT TrEMBL and PROSITE and provides links to many other molecular biology databases such as PDB SWISS PROT is a protein sequence database that provides high quality annotations such as description of the function of proteins of the structure of protein domains of post translational modifications of variants etc TTEMBL is a computer annotated supplement of SWISS PROT that contains all the translations of EMBL nucleotide sequence entries not yet integrated in SWISS PROT PROSITE is a database of protein families and domains It consists of biologically significant sites patterns and pro
184. ut tab Cycle through mouse actions translate zoom rotate ru E SEEE EEE 104 DeepViewManual option click group PC left mouse Center group and map Ramachandran Plot 9 nine click and drag symbol Change group phi only 0 zero click and drag symbol Change group psi only Action shift Act on all layers control Select Add to current selection II LIST OF MENUS sosueyy ISd lud Suunp Ped utj91 O IAOW TPO PS Lpg XIT9H eyqd y Isd Iud eS tuO 19S SdNOID Dp9159 9S zruwopuey omjon ng AIepuoo s PARA oujIn 19870 PAMA suIeuUog Pq 20 Yun Suore 1 t T IJSULIL Am uru s o1ydessojeysAlg prng IALT JUIN uo uonguroJsug1 A ddy SUI eOUUY p e nuurs yoreasg Ansneuxq Ay q pue 3omo sureuoopiS P9159 9S XIA NH0 uonestwru y AsIouq platy 23104 Assougq 1nduioo Surpe iu L Asiouq nduroo dey g nSuer enu loq Sng1sono H nduioo oujin IMN Ndw spuoq H nduroo nusuli sI00 SUOISIY P AoJ V JO MO ISq lud YM ve SUOISOY 2100 JO INO ISd lUd YUM pb spioe our SN V 2LL uou SIO spuens S H spioe ourtue Iejodq uou 199 9S spioe ourtue Iejod 199 9S SPIO OUTIL SIPIOY 199 9S sprog OUTUUR SISeg 159J9S puog S S JUSATOS WLV LAH sprHosponu o Jo s1 ee OZ JO ISI Sploe oure p 1on1isuoo 2 spuog H Jodolg SUYO sureysapt s DUJE YUM Soyse D FUEN ve SoYyse D Supo ve ISALT 199 0 UB 0 DSOTD SdnoIH urpguO 19410 ug 0 s SdnoIH BB P9
185. where print Never done elsewhere print welcome Related commands sub do while return Demonstrated in example script none e groupcount Will return the number of groups in a layer This is functionally equivalent to a select all followed by a selcount although it is quicker int_varname groupcount of lt layer gt Related commands selcount Demonstrated in example script 02 03 and 04 e hide Hides some parts from the view This is functionally equivalent to unchecking the show column on the Control Panel hide lt part gt of lt selection gt hide in lt layer gt lt part gt of lt selection gt where lt part gt can be any combination of res side label s urface ribbon vdw Related commands show color Demonstrated in example script 06 e inline gt text lt inline This is used in conjunction with the open command to load PDB files directly embedded in the script which is useful mostly for web servers that need to return a scriptt pdb file in a single file open pdb INLINE gt ATOM 1 N THR 1 17 047 14 099 3 625 1 00 13 79 ATOM 2 CA THR 1 16 967 12 784 4 338 1 00 10 80 ATOM 3 C THR 1 15 685 12 755 5 133 1 00 9 19 ATOM 4 O THR 1 15 268 13 825 5 594 1 00 9 85 ATOM 5 CB THR 1 18 170 12 703 5 337 1 00 13 02 ATOM 6 OG1 THR 1 19 334 12 829 4 463 1 00 15 06 ATOM 7 CG2 THR 1 18 150 11 546 6 304 1 00 14 23 lt INLINE Related commands open Demonstrated in example script none is selected Che
186. wo fold speed up per coarse contouring enabled This allows navigating in real time and interactively changing the sigma value with the up and down arrow keys for very large maps 98 DeepViewManual 159 e E minimization preferences Define here the energy minimization process Energy Minimisation Preferences x Enable one two or three cycles of n steps of Steepest Descent currently the IY D 20 steps of Steepest Descer only available energy minimization De 20 steps of Steepest Descent method D 20 steps of Steepest Descent Checkmark the interactions to be considered see point 107 gt HES 7 Nenbended Q I Cutoff enter a distance A over which l uta i 0 000 non bonded and electrostatic interactions M Angles H a will not be considered Z Torsions Z Show Energy Report I Improper Enter a value to stop minimization when checked option is verified Stop when delta E between two steps is below 0 050 k zrol P Stop when Force acting on any atom is below i 0 000 Select between Lock non selected residues only Lock nor selected residues T Lock 2 Constrain is selected residues on the Control Panel for Carbon Alpha only will be minimized Use an harmonic constraint enter a 50 care cue Lance force acting on selected and non 5000 non selected residues OK selected residues to adjust minimizations Option restrict selected Lock or Constraint to CA only f Use an harmonic constr
187. y pjoysoy uono l op spuoq H uongziuuuIrjA AsIOUq dew Ajisusq uono lH enu loqd 9e S01109 q soovjins suOgqral SIO OD sjoqe OH pue 35021 Aejds q uun evy ugod SUIPeOT erauay SE SOOUDIIJOIg BAS s oocu oJoJ91d uodo SORIA SPd ISET AJIDOIW nud S 32 9 I9Jo9 14 u0n29S 99S SMOT OJ JaAR AIDAD uonp uorO PSIA A UO JOAB JUDLIND uongluouoO JOSIA 10 JUSWIUSITY 19S2 sdey ssoiduiod JUSWUSITY eIn nys IIUI SIOJOVJ G OUI AIG p1S JaAP T 19S d I1nO SING SPMI Wy Ao 1dul uogos woy s no outu Wy IN 1nO JJiuS W 190 SILT eUu191 V o10 dxq Ly AZEN ALIY HA IBEN ou nb S mey NA puvului0 nuou ri U01 99S 99S ejod UON SUdSOIPAPY SAOWIDY ITV SUdsOIPAH Aoulo puog H AouI qI puog dAouDY SONPISIY paS DAOUIDY OCH PPV sudsOIPAH PppV Puod H PPV puod PPY onpisoy PPV LXO u sS xO PUIUIO ppV quoqyorg 231 quoqyoeg yeoig s pyd q SUMA soq put4 aseqeyeq doo T usos dooT prng nusu pring u0Dno29S 99S ouel dutoO YTA J099 syur pouyoq 9SN enuen jeooT JenuUeN MMM MOPULM 1O d UeIpueyoewey MOpUIM JuoulusSI v AOPUIAN Waa soJu SI2 LT pued 10u00 Ieq oo L T A IAqpd SSIAS IpdNA IY JOMOI A GPd SSIMS Inoqy nuu dpH m em aa CIV pued Ionuoo Ee ro IV 1eq oo L u0n29S 99S puvurtuo nusu A0DUIAA pum orudei5 pue 1eqloo L 3urT LHVO JYS s oeJjunS pue sonrard I I3O JHUS HNO 199 T 19
188. y structure by default Helix red Strand yellow Other gray 96 DeepViewManual 155 e Ribbon preferences Set the appearance of ribbons on the Graphic window Fast display non solid edit the nb of strands to represent the ribbons for static and moving molecules 3D display check here to enable the solid display of ribbons for static and moving molecules and set the display quality 2 better than 1 Ribbons Preferences Fi nb Strands 3 During Real Time Rotations 3 M Render as Solid ribbon also in real time Quality 1 2 fi For helices sheets and Helices Sheets Coils coils width 2 000 width 2 000 Width o a00 Edit their width and Height IED Height PEN Height n ann height in Angstroms For 3D display only F Use this Top Ea Use this Top Coto F Use this Top Loto check these items to use Z Use this Side Color I Use this Side Color M Use this Side Color top side and bottom Use this Bottom Color Use this Bottom Color Use this Bottom Color colors which can be Arrow at C terminus Z Arrow at C terminus Shape selected by clicking width 165 000 width X 175 000 cm cece aa poe For Isplay only Height gt 100 000 Height gt DDD a s ie select a section shape For helices and sheets Check these items to enable representation of an arrow at C terminus and enter its width and height as a perc
189. y type Select gt Group Kind command All residues of the choosen type All nucleotides of the choosen type Non standard nucleotides cannot be recognised instead they can be selected as hetero groups HETATM All groups defined as a hetero group Solvent All water molecules i e groups named WAT SOL HOH or H20 NOTE Water molecules are not loaded by default To load them disable Ignore Solvent in the Loading Molecule Preferences dialog box see point 150 SS bonds Identified Cys Cys disulfide bonds 52 e Selecting groups by property Click Select gt Group Property A submenu lets you select amino acids according to four property categories It is currently not possible to change which residue belongs to which category but scripting commands can be used to add a menu that define your own selections seeAnnex 2 Scripting Language Select gt Group Property command Ala Cys Gly Ile Leu Met Phe Pro Trp Val 53 e Selecting groups by secondary structure Click Select gt Secondary Structure A submenu lets you select all residues that belong to a standard secondary structure type or all amino acids that verify a specific main chain property Select gt Secondary Structure command Subcommand Groups selected Helices All residues of any helix h in Control Panel window Strands All residues of any strand s in Control Panel window Coils All residues of any coil between two specific secondary struc

DeepView – The Swiss-PdbViewer User Guide v. 3.7

Contents

Download Pdf Manuals

Related Search

Related Contents

DeepView &ndash; The Swiss-PdbViewer User Guide v. 3.7

Contents

Download Pdf Manuals

Related Search

Related Contents

DeepView – The Swiss-PdbViewer User Guide v. 3.7