ACD/3D Viewer User's Guide (ver. 8.0)
Contents
1. 2 Click ChemSketch hem ak on the Window Switching bar This will switch you to the ChemSketch window 3 Click Dictionary in the upper right part of the window Note The free ChemSketch version does not include the Dictionary module This module is a commercial one so if you are using a free ChemSketch program draw any desired structure using the ChemSketch interface tools For details on drawing structures refer to the ACD ChemSketch Tutorial 4 In the Quick Search box of the ACD Dictionary dialog box that appears type a few keystrokes for the name cinchonidine Cinchonidine is an anti malarial agent that is extracted from the bark of various species of Cinchona 5 As soon as the required name is selected in the list and the corresponding structure Is displayed click OK Note that the shadow of the selected structure hangs over the cursor Click the workspace to place the structure in the ChemSketch window ACD 3D Viewer User s Guide 6 Operating with Molecules View 6 Click Copy to 3D Hop to sD on the Window Switching bar to transfer the molecule into the ACD 3D Viewer interface You will see a simple stick figure appear in the 3D window 7 To create a 3D model of a 2D chemical structure click 3D Optimization 43 Note that the hydrogens are added 3 3 Customizing Molecule View 3 3 1 Rotating Moving and Zooming 1 Click 3D Rotate and drag over the workspace to rotate the2. ACD 3D Viewer Version 8 0 for Microsoft Windows User s Guide Viewing 3D Structures and Calculating their Structural Parameters Advanced Chemistry Development Inc Copyright 1997 2004 Advanced Chemistry Development Inc All rights reserved ACD Labs is a trademark of Advanced Chemistry Development Inc Microsoft and Windows are registered trademarks of Microsoft Corporation in the United States and or other countries Copyright 2004 Microsoft Corporation All rights reserved IBM is a registered trademark of International Business Machines Corporation Copyright IBM Corporation 1994 2004 All rights reserved Adobe Acrobat PDF Portable Document Formats and associated data structures and operators are either registered trademarks or trademarks of Adobe Systems Incorporated in the United States and or other countries Copyright 2004 Adobe Systems Incorporated All rights reserved All the other trademarks mentioned within this guide are the property of their respective owners All trademarks are acknowledged Information in this document is subject to change without notice and is provided as is with no warranty Advanced Chemistry Development Inc makes no warranty of any kind with regard to this material including but not limited to the implied warranties of merchantability and fitness for a particular purpose Advanced Chemistry Development Inc shall not be liable for errors contained herein or for any di
3. butane gif 000 butane gif O00 butane gif 000 butanel9 gif O00 butane 0 gif O00 butane 1 gif O00 Click Play to step through the animation frame by frame Click Loop fa to make the movement repeat endlessly Add or remove GIFs as needed to complete the motion smoothly You may wish to explore other options such as setting color scales time dwells dirty rectangles etc in order to enhance the animation or make a smaller GIF file Ba From the File menu choose Save Optimized As and then enter BUTANE GIF 8 Open this file in your Web browser to view it You can open it by drag and drop or by entering the file path as an URL ACD 3D Viewer User s Guide 19
4. If you have not selected all formats the default file association can be viewed or changed at any time from the File menu choose File Associations If you have selected all formats then you receive a message all supported file types are already associated with the current application In this case you can change the file associations through Windows Explorer 1 Open Windows Explorer and select a file with the extension for which you want to create the association 2 Hold down SHIFT and right click on the file From the pop up menu choose Open With 3 Set the application that should be used to open the file and select the Always use this program check box 4 Click OK and close Windows Explorer 2 4 Changing Default Directories If you are running a single user stand alone copy of ACD 3D Viewer the default directory settings are likely fine If you have a network copy it is advisable to change the default directory settings in the ACD Labs software so that the default drive for saving work in progress is the user s local hard drive not the remote server After creating local access for either limited or unlimited numbers of seats then at each local installation 1 In the ChemSketch window from the Options menu choose Preferences 2 Click on the General tab In the Default box specify the directory that will be opened every time you open the Import Open Save or Export dialog boxes in the ChemSketch window D
5. Bond Angle Initial bond Angle C 4 0 5 C 1 100 530 Deg New Value f 00 53 Deg M Instant Preview Also the calculated angle value appears on the status bar for example Bond Angle C 4 C 5 C1 100 530 Deg 4 To change the angle in the Bond Angle dialog box type the desired value in the New Value box If the Instant Preview check box is selected the changes are immediately applied The initial angle is always present in the dialog box so if you decide not to change the angle you can easily return to the initial settings 5 Click OK to apply changes if any and close the dialog box 6 To cancel the selection and start a new measurement click somewhere in the empty workspace To stop using this tool click on its button to deselect it ACD 3D Viewer User s Guide 13 Operating with Molecules View 3 5 3 Calculating and Changing a Torsion Angle 1 Click Torsion Angle 2 Click two atoms participating in a common bond The corresponding bond becomes selected 3 In the same manner click two more atoms adjacent to a previously selected bond The final result will be three adjacent bonds participating in a torsion angle which will be selected The Torsion Angle dialog box appears Ka Torsion Angle Initial torsion Angle C 6 C 3 C 2 C 1 152 090 Deg New Value f 52 09 Deg M Instant Preview Note Without selecting the third bond it is possible to look through the values of
6. MM parametrization The modifications involve some simplification and were intended to increase the stability and soeed of computation Note that 3D optimizer is NOT a full scale molecular mechanics engine Its design aims to reliably reproduce reasonable conformations from possibly very unreasonable 2D drawings rather than to precisely optimize 3D structures Refer to B R Brooks R E Bruccoleri B D Olafson D J States S Swaminathan and M Karplus CHARMM A program for macromolecular energy minimization and dynamics calculations J Comput Chem 4 187 217 1983 ACD 3D Viewer User s Guide 1 Introduction Occasionally the 3D optimization produces a molecular conformation different from what you have expected It is the very essence of the conformational analysis that molecules typically have many possible conformations The optimizer finds only one and it is not necessarily the one you have expected For example you probably expect a cyclohexane fragment to be a chair but the optimizer may generate a twist boat which is also one of its suitable conformations indeed in many structures this fragment exists in a twisted form To obtain another conformation move some atoms in the resultant 3D structure to make the initial structure closer to the final conformation and then optimize the structure once again If you try to obtain a specific enantiomer for a structure with chiral centers in the process of optimization the con
7. all possible torsion angles neighboring the last selected atom by moving the mouse pointer over adjacent atoms 4 Try changing the value in the New Value box Ifthe Instant Preview check box is selected the changes are immediately applied The initial torsion angle is always present in the dialog box so if you decide not to change the angle you can easily return to the initial settings 5 Click OK to apply changes if any and close the dialog box 6 To cancel the selection and to start a new measurement click somewhere in the empty workspace To stop using this tool click on its button to deselect it ACD 3D Viewer User s Guide 14 4 Creating an Animated GIF With help of ACD 3D Viewer you can create animated GIF files for your site with minimum effort minimum cost and maximum impact The GIF file format may not be as sophisticated as Java Flash ActiveX or more chemistry oriented formats such as RasMol and Chime but these newer applications are not as accessible to casual Web visitors who may not have the appropriate plug ins or a connection that is fast enough For true accessibility a GIF file is still the cornerstone of Web design Animated GIFs are a nice touch for many Web pages whether to emphasize something on the page e g the New revolving spheres on the ACD Labs download page or to show pictorially something which is better sketched while explaining it to someone e g electron density movement in the c
8. ccccccccccnseesesecccesessneeeessecesssaeeessesees 14 4 Creating an Animated GIPF ccccccssseeseseeeeseeeeseeeeseseeseeeeseeeeseeoenenones 15 4 1 Obtaining the Animation Software cccccccccccssccecesececeeseeeeeeececseeeeseeeeesaeeeeas 15 4 2 Step Wise Motion in ACD SD VICWEL cccccesscecceeeececseeseeeesseseeeesseseesssaeeess 16 4 3 FINE TUNING the Picture Sars a E Yaa haw anee iad Rodelaselwes 17 44 ObtaininG a SerieS Of GUE S ricseescec hecvneesne eccdnedctac se svewiedeeinaddessxddecsusiaucdossaeeese doves 18 49 Final Stage ANman secrets cette tad acta i i a a ditevcneeust ueseuetaaes 18 ACD 3D User s Guide i Before You Begin Thank you for purchasing ACD 3D Viewer We have endeavored to produce the easiest to use 3D chemical display program available today About This Guide Completion of this guide should give you the tools needed to get started with ACD 3D Viewer it is designed for either online use or to be printed and used as a hard copy version The screen shots shown throughout this reference manual have been taken with a relatively small window size The colors and other properties of the window elements described throughout this manual correspond with the default Windows Display Properties This guide is provided in electronic form readable with Adobe Acrobat software If you cannot locate an index topic you need please do a text string search for the relevant word o
9. e Balls and Sticks view mode bx for a better view of the atoms 2 Click Distance P 3 3 Click any atom to select it and then move the mouse pointer over another atom to highlight them with the selection color The Internuclear Distance dialog box appears 2 Internuclear Distance Initial distance C 5 C 3 2 5184 Hew Value 2518 Pa M Instant Preview ACD 3D Viewer User s Guide 12 Operating with Molecules View Also on the status bar you can see the distance between the selected atoms Distance C5 C3 25180 4 4 To change the distance in the Internuclear Distance dialog box type the desired value in the New Value box If the Instant Preview check box is selected the changes are immediately applied If the check box is not selected after each change you need to click Preview The initial distance is always present in the dialog box so if you decide not to change the distance you can easily return to the initial settings 5 Click OK to apply changes if any and close the dialog box 6 To cancel the selection and to start a new measurement click somewhere in the empty workspace To stop using this tool click on its button to deselect it 3 5 2 Calculating and Changing the Angle Between Two Bonds 1 Click Angle 4 2 Click two neighboring atoms which form a bond 3 Move the mouse pointer to the third atom which makes a bond with the last selected one The Bond Angle dialog box appears
10. e Sections 3 3 6 and 3 3 7 ACD 3D Viewer User s Guide 11 Operating with Molecules View 3 Click OK and in the dialog box that appears specify the name of the file and location drive and directory Note that the file should be saved with a 3DS extension 4 Click Save to save the file 3 4 2 Loading View Settings If you have previously saved the view settings you can load them for the current session 1 From the Options menu choose Load Settings to open the Load Settings dialog box 2 Find the 3DS file you want to load 3 Click Open The settings contained in this file will be loaded for the current working session 3 4 3 Setting Default View Settings If you want to use specific settings each time you work with ACD 3D Viewer you should set them as default ones 1 Specify the required view settings refer to Section 3 3 2 To save them to a file from the Options menu choose Save Settings 3 From the Options menu choose Set Default Settings to open the Set Default Settings dialog box 4 Find the file with the setting you want to set as the default 5 Click Open From this point on each time you open ACD 3D Viewer these settings will be loaded until you specify other ones Tip To return to the system default settings from the Options menu choose Restore Default Settings 3 5 Calculating and Modifying Structural Parameters 3 5 1 Calculating and Changing Distance Between Two Atoms 1 Switch to th
11. e ee eee eee 6 3 2 Inserting a Molecule and 3D Optimizing cccceceeeeeceeeeeeeeeceeeeeeeseeeeeeeseeeeeeeeas 6 3 3 CUSTOMIZING Mol cule VIEW sesi e a S 7 3 3 1 Rotating MOVING ANC ZOOMING seci a e aea R a aiii 7 3 3 2 Changing Structure REPreSe ntatiOn ccccccccssseeeeeeeceeecssseeeseecccessseseeeeeecesssssaaesseeees 8 39 3 SONGRGING COl S 5 3222 ca sae Sos Bet ais ce 3 has alas aces dels Ea ie ac dentaln apse aaiee 9 3 3 4 Obtaining the Mirror ViGW ccccccccssssssssseeccccnsccesssesesccssacnssesesccsssaaanuseesscesssaaaaassseees 10 335 Jnverting Structure CONIC rions incer e a A eines ccleaner 10 3 3 6 Changing Atom Radius of a Specific Element cccccccssseeeeeecceeeenanessseecessesaesseeees 10 3 3 7 Changing the Display of Atom Radius ccccccsseeeeseeceeecnnaeeeseeeeeeeseaaneneeeessssaaannsensees 11 3 4 Saving and Loading View SettingS cccccccsseecccceseeeeeseeeeeeeseeeeeeesseeseeessaeeeees 11 3AA GAVN VIEW SCHINOS aae a a el ee eee 11 O42 Loading VieW SCHINGS era ei eee a a ee ee ee 12 94 3 Setting Default View Seting Sepen a e ee 12 3 5 Calculating and Modifying Structural Parameters ccccccececeeeeeeeeseeeeeeeeeees 12 3 5 1 Calculating and Changing Distance Between TWO Atom s ccccccssseeeeesseseeseeeseaees 12 3 5 2 Calculating and Changing the Angle Between Two Bonds 1ssccccssssseeeeeeeeaeeees 13 3 5 3 Calculating ANd Changing a Torsion ANGIE
12. ecule is visible 3 Press CTRL A to select both objects click Center Horizontally and then Center Vertically to align the objects relative each other 4 If you do not want the border of the rectangle to be visible select the rectangle only and then right click the left most crossed section on the Color Palette above the status bar to set the border s color to None Left clicking any color will change the fill color of the rectangle this can be useful if you have used any special background color when copying molecules in the 3D window Note If there is no Color Palette displayed refer to the View section of the General tab in the Preferences dialog box Options menu The Palette check box should be selected 5 As soon as the rectangle is of the desired color and size select it alone and copy it to the clipboard so that you can then simply paste it for other snapshots 6 Switch to the next page press CTRL V and click the molecule to paste the rectangle over it Then click Send to Back th press CTRL A to select both objects and align them by clicking Center Horizontally in and Center Vertically Hel 7 Repeat step 6 for each page ACD 3D Viewer User s Guide 17 Creating an Animated GIF 4 4 Obtaining a Series of GIFs 1 From the ChemSketch page list scroll to the first 3D image likely page 1 or 2 Important When exporting to a GIF file ChemSketch exports the whole page with no regard to whether the objects are se
13. figuration input may occasionally change to an opposite one To solve the problem it is usually enough to draw all four substituents of the chiral carbon atom and use both Up and Down Stereo Bond tools to define the required direction of bonds in the initial 2D structure If it doesn t work you can move the atoms manually in the resulted 3D structure and optimize the structure once again In any case we recommend answering No when you are asked whether to remove hydrogens before starting optimization in the unfolding 3D Structure Optimization dialog box 1 2 1 Limitations of ACD 3D Optimizer ACD 3D Viewer can only optimize structures containing atoms from Hydrogen to Xenon with standard valence and bonding states Also it does not take into account hydrogen bonding The maximum allowed number of atoms in the structure to be optimized is 250 including implicit hydrogen atoms ACD 3D Viewer User s Guide 2 2 Basics of ACD 3D Viewer 2 1 Objectives This chapter will familiarize you with e Starting the program e Setting and changing file associations e Changing default directories for opening and saving files and e Exiting the program Instructions for system requirements and for installing and uninstalling the software are provided on a separate sheet of paper shipped with the software itself 2 2 Starting ACD 3D Viewer Once ACD 3D Viewer has been installed on your computer follow these basic steps to start it 1 Start M
14. ge Radius box that appears Change Radius Radius ena Cancel 4 Click OK to save changes Note The atomic radius is expressed in relative units 5 As soon as the changes are made in the Atomic Radii dialog box click OK Next time you start ACD 3D Viewer the default values will be reset to their previous values For more details on how to save and load default settings refer to Section 3 4 3 3 7 Changing the Display of Atom Radius 1 Click Increase Atoms Radii by 5 Fil Each additional click on this button increases the radii of all displayed atoms by 5 2 Click Decrease Atoms Radii by 5 to decrease the radii of all displayed atoms by 5 Important These tools do not affect the actual radii of atoms those specified in the Atomic Radii dialog box but only change the display 3 4 Saving and Loading View Settings You can save settings that you have specified during the current work session as a 3DS file load them from a previously saved file and set them as the new default 3 4 1 Saving View Settings 1 From the Options menu choose Save Settings to display the following dialog box Save Settings Include Style Attributes W Colors mM Radi x Cancel 7 Help 2 Select the check boxes of the attributes that you want to be saved Note that selecting the Radii check box will allow you to save settings specified in the Atomic Radii dialog box but not the current radius display options se
15. icrosoft Windows 2 Double click the 3D Viewer icon OR On the Start Run menu in the Windows 98 2000 NT or XP taskbar point to ACD Labs and then choose the 3D Viewer icon OR Double click the program file SHOW3D EXE in the folder where you have installed all ACD Labs software By default this is ACD8 OR If you have other ACD Labs programs running from the ACD Labs menu choose 3D Viewer You should see an opening splash screen If this is the freeware version you will see a 15 second list of ACD Labs products scroll by Be patient and click Cancel when it becomes active ACD 3D Viewer User s Guide 3 Basics of ACD 3D Viewer 2 3 Setting File Associations If this is the first time you have started the program the File Associations dialog box will appear Note If you open the File Associations dialog box from the File menu choose File Associations under Windows NT but have no rights to change file associations a warning message appears Contact your system administrator to resolve this matter This contains a selectable list of file extensions and file types which you may want to open automatically with ACD Labs software from now on If so click the check boxes of the file formats you want to add and then click Yes If you do not want to have 3D Viewer automatically open files with the listed extension or are not sure leave the check boxes blank and click No 2 3 1 Changing File Associations
16. ing color display With ACD 3D Viewer you can e Manipulate 3D models move 2D and 3D rotate resize change styles and colors e Display a 3 D structure as stick ball and stick spheres or disks e Add an overlay of small dots at approximately the van der Waals radius level to the solid 3 D structure e Measure and change bond lengths plane bond angles and torsion angles e Optimize the structure using a 3 D CHARMM type of force field e Switch from 3D to 2D display in the ChemSketch window at the click of a button e Set the 3D molecule to Auto rotate with or without changing the style of structure display e View 3D structure in perspective e Display multiple bonds in the Wireframe view mode and e Export 3D models to other geometry optimization programs and use them as good starting configurations 1 2 3D Optimization Algorithm The 3D optimization algorithm rapidly transforms the planar 2D structure from ChemSketch into a realistic 3 dimensional structure It is based on modified molecular mechanics which take into account bond stretching angle bending internal rotation and Van der Waals non bonded interactions Modifications include minor simplification of potential functions and enforcement of the minimization scheme by additional heuristic algorithms for dealing with bad starting conformations The 3D optimization algorithm is a proprietary version of molecular mechanics with the force field initially based on CHAR
17. irectories Private C AMy Documents ee Default E T mg F ACD 3D Viewer User s Guide 4 Basics of ACD 3D Viewer Note In the Private box you can set the directory for recording the configuration of the ChemSketch program e g TEMPLATE CFG and GRSTYLES STL files 3 Click OK 4 Switch to the 3D window from the Options menu choose Set Default Folder and specify the required folder for opening and saving files Click OK 2 5 Exiting ACD 3D Viewer You can exit from the program in any of the following ways e Click in the upper right hand corner of the title bar of any window OR e From the ACD Labs menu choose Close All This will attempt to close all ACD Labs programs that are currently open one right after the next OR e From the File menu choose Exit This will close only the currently open ACD Labs program You will be prompted to save your work in the appropriate file formats depending on the window that you are exiting ACD 3D Viewer User s Guide 5 3 Operating with Molecules View 3 1 Objectives In this chapter you will learn how to e Insert molecule into the 3D window and 3D optimize it e Customize the view of molecules position size color atom radii e Save and load view settings and e Measure and change the distance between atoms and calculate and change the angle between bonds 3 2 Inserting a Molecule and 3D Optimizing 1 Start ACD 3D Viewer as described above
18. lected or not so make sure that the page contains only those objects that you want to appear in a GIF file 2 From the File menu choose Export and select GIF Bitmaps GIF as the format to be saved in Specify the name for the file e g BUTANE0O1 GIF 3 Click OK and the image on that page will be saved 4 Move to the next page by clicking Next Page on the status bar or PAGE DOWN on your keyboard 5 Repeat steps above saving the files under a slightly different name each time in the sequence BUTANE02 GIF BUTANE03 GIF BUTANE04 GIF etc 4 5 Final Stage Animating Depending on the animation software the interface for input of GIF files differs The following is described with respect to the Animagic software package from RTL Software 1 Open the animation software Animagic GIF Untitled File Edit Animation Frames Options View Effects Help BAI HS AZAR A ee Frame List mm E y No transparent color This is not intended as a product endorsement ACD 3D Viewer User s Guide 18 Creating an Animated GIF 2 Insert the series of BUTANEO GIF files as frames into the frame list For example in Animagic it can be done with a drag and drop operation Make a multiple selection of the file icons from their folder or from Windows Explorer and drag them until they are in the Frame List panel oo Ss 6S Frame List butane gif 000 butane gif 000 butanel4 git 000 butaneO5 gif 000
19. o contact us is via electronic mail Questions on pricing sales availability and general issues should be directed to info acdlabs com Technical and scientific support issues should be addressed by visiting http support acdlabs com Please tell us the name of the software purchaser the product name version number build number and license ID of the product you are contacting us about from the Help menu choose About to find this information as well as a description of the problem you are having If applicable please tell us the name of the distributor from whom you purchased the software Online Updates Version 5 0 and later of all PC based ACD Labs software contains the capability to have software updates delivered online You will need the registration numbers of the software and an Internet connection from the same computer on which the software is installed The updates are small fixes for example bringing the actual version number of a program from 8 00 to 8 01 For more information refer to the Online Updates document included with the rest of the product documentation in your Documents folder or e mail our technical support department ACD 3D Viewer User s Guide iv 1 Introduction 1 1 What is ACD 3D Viewer ACD 8D Viewer is a fast yet accurate 3D modeling and visualization program It is fully integrated with ACD ChemSketch allowing you to draw 2D structures and quickly obtain their 3D representations in a strik
20. on To see the latest in ACD Labs software and services please visit our Web site at http Avww acdlabs com Our Web site is being accessed at the rate of tens of thousands of hits per day There s a reason for this much is offered through our Web site As of Spring 2004 we offer free ChemSketch 5 0 a free ISIS 3D Add in free ChemDraw extensions and a free 2 week demo key for Interactive Laboratory sessions where you can run test calculations using Java applets without purchasing software There are TechSmith Camtasia based movies which show the operation of many of our software packages especially ChemSketch available for download We are constantly updating the information on our Web site The Web site will tell you at which scientific conferences you can visit the ACD Labs booth You can browse the Frequently Asked Questions page or drop in and chat on our newsgroup which can also be reached via our web page If you would like to stay informed of the latest developments in chemical software at ACD Labs please be sure to sign up for e mail broadcasts at our Web site page http www acdlabs com feedback mailing html If you would like to partake of the ChemSketch newsgroup please access news news acdlabs com acd public chemsketch ACD 3D Viewer User s Guide iii Before You Begin How to Contact Us We are accessible through our Web site phone fax and regular mail but by far the most popular way t
21. ourse of a Diels Alder reaction 4 1 Obtaining the Animation Software Animated GIFs can be created with commonly available software such as packages listed through the Tucows site Such software is often freeware evaluation ware or shareware Disclaimer ACD Labs makes no recommendation or claim for one animation product over another For the present example we used Animagic shareware from RTL Software Inc An evaluation or shareware copy can be downloaded from the Web page http www rtlsoft com animagic and installed on your PC An animated GIF file can be created by linking in succession one still or snapshot GIF image after another Each still GIF contains nearly the same image as the previous GIF but is changed just enough to give the human eye the illusion of movement when one GIF is shown after the other Good animation software will optimize the linkage so that the size of the overall animated GIF will be as small as possible The export of a ChemSketch or 3D file to GIF format is straightforward A set of these GIFs is used as input to a special GIF animator program which will output the moving image after some editing and optimization to the animated GIF format We go through these steps in detail below TUCOWS is an acronym for The Ultimate Collection of Windows Software See www tucows com ACD 3D Viewer User s Guide 15 Creating an Animated GIF 4 2 Step Wise Motion in ACD 3D Viewer We will start
22. r phrase or related words Advanced Understanding This guide is intended to be a part of the technical documentation for ACD Labs software To study ACD Labs products gradually we recommend the following order of working through the technical documentation Documents for ACD ChemSketch and ACD Dictionary familiarize you with features of drawing and looking up structures ACD Forms Manager is required to learn how to create input dialog boxes for user data and an interface for consistent database input ACD 3D User s Guide li Before You Begin Mouse Conventions You may perform several actions during your work with this software the following specific words are used to describe them e Point tomeans move the mouse pointer be to an item e Click or left click means point to an item and press the left mouse button e Right click means point to an item and press the right mouse button e Double click means point to an item and quickly press the left mouse button twice e Drag means point to an item press and hold down the left mouse button while you move the item e Select means highlight or make an interface element active by either clicking it or dragging over it other actions are possible if specified in documentation If used in select the check box it means that the check box should be marked with a tick as opposed to clear the check box when the check box should be cleared without a mark For More Informati
23. rag the cursor strictly horizontally and to the same destination each time ACD 3D Viewer User s Guide 16 Creating an Animated GIF 13 Switch to the ChemSketch window As a result of repeated pastes to new pages you should have a document with a series of pages each containing a snapshot of the rotating molecule You may check the number of pages and switch between them by clicking Page on the status bar Page 13 14 Page 14 15 Page 15 Page 16 Page 17 15 Page 16 Fage 19 20 Page 20 21 Page 21 OFEA 22 Page 22 INAMEOO SK2 Modified Ag Page 19 22 EH 4 3 Fine tuning the Pictures If you look through all the pictures you will notice that the size of each picture is different This will affect the final animation and will make it uneven If your animation software allows you to change the size of the used gifs and modify their contents you can skip this section and do the necessary changes in your animation software If you are using animation software that does not include these capabilities you can use the Draw mode in ACD ChemSketch to help standardize the image of each snapshot 1 Display the page with the biggest picture on tt 2 In the Draw mode choose the Rectangle tool O and drag over the picture of the molecule so that the rectangle fully includes the molecule Release the mouse button to fix the rectangle and click Send to Back to send the rectangle to the background so that the mol
24. rame dots or spacefilled click the corresponding buttons on the toolbar eet B mal or aa respectively You can also right click in the window workspace to switch among the view mode buttons Note that if any of the measure tools Pl rl or Ph are active right clicking will toggle between them only 3 3 3 Changing Colors 1 From the Options menu choose Colors or click Set Colors to display the Colors dialog box Background Selection P Greer Elements Hydrogen C White Alphabetical Order 2 To change the color of the background of the display select the desired color in the Background list Tip lf you are printing a lot it is best to change the background to white to save toner 3 When measurements are being made the set of atoms whose distance or angles are being measured are given a special highlight color The default is bright green To change the color of the atoms that are selected from the Selection list choose the desired color and click OK Note Selection works only with the Distance e a Angle Lo and Torsion Angle Ei tools 4 To change the color of a chemical element click the name of the element in the list and then choose the desired color to the right Note Selecting the Alphabetical Order check box sorts the names of the elements in the list otherwise the elements are listed in the order they appear in the Periodic Table of Elements ACD 3D Viewer User
25. rect indirect special incidental or consequential damages in connection with the use of this material Table of Contents Berore VOU BEGIN cis csnesevece renee cevencvecevenetedewescvegewaseececescweteiesesedaiedssetedveessdonsvesssecs il ABOU TAIS 10 0 gt serpent erent mn re REECE recent Bren emt SENT Rr er CEES Tren i stn i Prenat en terre er li Advanced CGETSIQNOING ai soevdiiet sche Saves R Sel iiaarinavediwbai deste ite rosa A EE ii MOUSE GC OM VENTION S ssor N E ar iii FOF WIOGE IMOnmmMa lOr E lil FOW TOC ON ACING Sets tastes sepa ctaa ta E tease eape aia tanner oe eae iv ONM EUPA E S r r ENTE T asesausateca uated E T iv l aiige s U ci ela peepeerer cere cere trr Me nerr rr E ane ene eee ee ence ee errr 1 LE NVilatis AGD SD Views nonien e a a a 1 t2 3D ODUMIZaTION AJON ciena a a a a 1 t21 Limitations ol ACGD 3D OPUMIZEN arice sl E E ea hae 2 2 Basics of ACD 3D VieWe fe naa aa aa Aaaa aia AERE 3 20k OD OCIVO S cia a ieee pidec enue ea tohetdas 3 22 otaning ACD SD VIEWS s aoi a E E 3 2 9 OCW FIS ASSOCIAUOMNS crcr aor aaa ii a a ia a Ee 4 2 3 1 Changho FIC ASSOCIQUONS seori ainar EE aves teroguale tiie EA 4 2 4 Changing Default Directories cccccccccssececseeeecseeeecceeeeeseusecseneeesaeeesseeeesaaees 4 25 JEXMNG AGD 3D VIEW El c caacsencs a on aE N 5 3 Operating with Molecules View ccccsscccsssescsssesssssescesseseesseseneesseneees 6 2 ODECE aRe ane renee ne ene cre ene ene ee ee ee eee ee
26. s Guide 9 Operating with Molecules View 3 3 4 Obtaining the Mirror View 1 Click Mirror to obtain a mirror image of the currently displayed structure All the stereo centers present in the initial structure will be inverted in this case 2 To return back to the initial view click this button again 3 3 5 Inverting Structure Center 1 Click Invert Center el and then click the atom to invert This tool inverts the configuration of chiral center by changing the spatial position of one or several substituents of the selected atom Note After the current operation it may be necessary to optimize the chemical structure once more To perform this click 3D Optimization hal on the Top toolbar 2 To return back to the initial structure view click Invert Center again 3 3 6 Changing Atom Radius of a Specific Element 1 From the Options menu choose Radii to open the Atomic Radii dialog box containing the default settings for atom radii of various elements Atomic Radii Beryllium Boron Carbon Nitroger Osuger Fluorine Meon Sodium N atrium Magnesium Aluminium Silicon Phosphorus F Alphabetical Order 2 To view the currently set radius of any element click it in the list In the right column the corresponding value is highlighted ACD 3D Viewer User s Guide 10 Operating with Molecules View 3 To change the atom radius for an element double click it in the list and type the new value e g 0 5 in the Chan
27. structure in the tree dimensional space 2 Now switch to the Z rotate mode by clicking Rotate If you drag in the workspace now the structure will be rotated in the two dimensional plane only 3 Click Move to enter the Drag mode where you can move the structure up down left or right in the workspace 4 Toresize the structure display click Resize and drag Dragging from the center of the structure to the border of the screen makes the structure larger and dragging to the center of the structure makes it smaller 5 Click 3D Rotate to switch back to the 3D Rotate mode ACD 3D Viewer User s Guide 7 Operating with Molecules View 3 3 2 Changing Structure Representation 2 To add a dots halo to the current molecule view click With Dots something like this wer nonameD s3d Uptiong ACD Labs Help MOMAMEO2 S30 ChemSk CopytoChemsk 3D g 3 To display multiple bonds switch to the Wireframe mode by clicking on the Top toolbar and then from the View menu choose Show Multiple Bonds ACD 3D Viewer User s Guide 8 Operating with Molecules View 4 To rotate a molecule automatically as it is without changing its view type click Auto Rotate To rotate a molecule automatically changing its view type click Auto Rotate and Change Style Note To represent the structure as disks wiref
28. with a very simple structure obutane that is easy to draw and process 1 In the ChemSketch window Structure mode draw butane CH3 CH3 2 Click Copy to 3D Hapy to sD lon the Window Switching bar 3 In the 3D window click 3D Optimization hal to optimize the structure 4 Switch to the Balls and Sticks view ES and click Increase Atom s Radii several times to make the atoms more prominent 5 From the Options menu choose Colors and in the Element section of the dialog box set the green color for hydrogen and blue color for carbon In the Background section choose White You should obtain something like the following 6 Now copy the molecule to the Clipboard from the Edit menu choose Copy 7 Switch to the ChemSketch window by clicking ChemSketch hemsk lon the Window Switching bar 8 If there is anything drawn in the current page create a new page by clicking E 9 Press CTRL V to make a fast paste of the image from the Clipboard Click in the workspace to place the image 10 Switch back to the 3D window by clicking 3D 3D make sure that the 3D Rotate mode is on Pe and slightly rotate the structure by dragging over it 11 Again copy the structure to the clipboard switch to the ChemSketch window create a new page and paste the structure 12 Repeat the steps above until your structure appears in the same position as it was at the first step Tip To make structure rotate strictly horizontally and evenly d
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