User's Guide

Viewing 3D Structures and
Calculating their Structural Parameters

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Advanced Chemistry Development Inc.

 

Copyright © 1994-2001 Advanced Chemistry Development Inc.  All rights reserved.

 

ACD/Labs is a trademark of Advanced Chemistry Development Inc.

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All the other trademarks mentioned within this Manual 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 direct, indirect, special, incidental or consequential damages in connection with the use of this material.

Part number:  G11_0208

Table of Contents

1. Introduction.................................................................................................................

1.1 What is ACD/3D Viewer?...........................................................................................

1.2 3D Optimization Algorithm.........................................................................................

1.2.1 Limitations of ACD/3D Optimizer...............................................................................

1.3 What’s New in 5.0?....................................................................................................

1.3.1 General ACD/Labs Functions....................................................................................

1.3.2 ACD/3D Viewer-Specific Functions............................................................................

1.4 Useful Definitions........................................................................................................

1.5 About this Guide.........................................................................................................

1.6 For More Information…...............................................................................................

1.6.1 Web Site.................................................................................................................

1.6.2 How to Contact Us...................................................................................................

1.6.3 Online Updates—New to 5.0!.....................................................................................

2. Basics of ACD/3D Viewer.........................................................................................

2.1 Objectives...................................................................................................................

2.2 Starting ACD/3D Viewer.............................................................................................

2.3 Setting File Associations—New to 5.0!......................................................................

2.3.1 Changing File Associations.......................................................................................

2.4 Changing Default Directories.....................................................................................

2.5 Exiting ACD/3D Viewer...............................................................................................

3. Operating with Molecules View..............................................................................

3.1 Objectives...................................................................................................................

3.2 Inserting a Molecule into the 3D Window...................................................................

3.3 Customizing Molecules View...................................................................................

3.3.1 Changing Colors.....................................................................................................

3.3.2 Changing Atom Radius of a Specific Element............................................................

3.3.3 Changing Display of Atom Radius............................................................................

3.4 Saving and Loading View Settings...........................................................................

3.4.1 Saving View Settings..............................................................................................

3.4.2 Loading View Settings............................................................................................

3.4.3 Setting Default View Settings..................................................................................

3.5 Calculating Structural Parameters...........................................................................

3.5.1 Calculating Distance Between Two Atoms................................................................

3.5.2 Calculating Angle Between Two Bonds.....................................................................

3.5.3 Calculating a Torsion Angle.....................................................................................

4. Creating an Animated GIF......................................................................................

4.1 Obtaining the Animation Software............................................................................

4.2 Step-Wise Motion in ACD/3D Viewer.......................................................................

4.3 Fine-tuning the Pictures...........................................................................................

4.4 Obtaining a Series of GIFs.......................................................................................

4.5 Final Stage:  Animating.............................................................................................

5. Conclusion................................................................................................................

 

1.1     What is ACD/3D Viewer?

ACD/3D Viewer is a program that converts two-dimensional structures from ACD/ChemSketch into their three-dimensional counterparts and calculates bond angles and atom-to-atom distances.  ACD/3D Viewer is fully integrated with the ChemSketch structure drawing program.    It provides a wide range of features:

·         Import:  Read in structures in the MDL molfile format, which is highly compatible with other computational chemistry software.

·         Export:  ACD/3D Viewer provides additional file-saving options—from the 3D interface as 3D OLE server files, or from the ChemSketch interface as sketch, bitmap or MDL molfiles.

·         Display:  Specify the representation of the structure displayed: molecule’s color and “view–type” .  Structural display options range from using sticks, balls-and-sticks, to the more sophisticated opaque space-filling technique or transparent dots-on-a-sphere.

·         Move:  The position of the molecule can be changed through mouse control.  Or, a structure can be set to auto-rotate, with or without changing the display styles.

·         Measure:  Perform atom-to-atom measurements, and 3- and 4-vertex (torsion) angle measurement.

·         Customize:  You can modify individual atomic radii and colors, as well as background color.

·         Integration:  Copy the contents from the workspace to the Clipboard and paste it into other OLE-supported Microsoft Windows applications, such as word processors or graphics applications.

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 CHARMM parametrization.[1] The modifications involve some simplification and were intended to increase the stability and speed 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.

Occasionally an R-conformation input will change to an S-conformation in the process of optimization.  This is because the algorithm does not restrict conformations.  If ACD/3D Viewer produces a molecular conformation different from what you have expected, do not be surprised.  It is the very essence of conformational analysis that molecules typically have many conformations.  The optimizer finds only one, and it is not necessarily the one you expected.  For example, you probably expect a cyclohexane fragment to be a chair, but the optimizer may generate twist-boat, which is also one of its suitable conformations (indeed, in many structures this fragment exists in a twisted form).  In some cases, for example, if you want to obtain desired enantiomers for structures with a chiral center, you can use the Up and Down Stereo Bonds tools in the ChemSketch Window to define the required direction of bonds.

1.2.1     Limitations of ACD/3D Optimizer

ACD/3D Viewer can only optimize structures containing C (IV), H (I), F (I), Cl (I), Br (I), I (I), N (III, IV), O (II) and S (II, IV, VI).  It cannot optimize organometallic compounds or structures with charged atoms (except azide and nitro groups).  Also, it does not take into account hydrogen bonding.

1.3     What’s New in 5.0?

1.3.1     General ACD/Labs Functions

·       All ACD software programs run as 32-bit applications on PCs with Windows 95/98/NT/ME/2000 operating systems, except for ACD/I-Lab for Intranets, Batch for the SGI and Batch for Sun Solaris products.

·       All ACD software programs running on PCs are controlled by ACD/Host which allows you to set loading, timeout and auto-reload parameters.

·       All PC versions of ACD software (except for PhysChem Batch, LC Simulator and GC Simulator) include a new feature that automatically detects the default file association for certain file extensions that are special to ACD software (e.g.  .sk2, .esp, .lud).  As of release 5.0, most ACD windows now contain the File Associations...  command (File menu).

·       All PC versions of ACD software have a new command listed under the Help menu: Bug Report / Feature Request.  If you have an Internet-enabled PC, selecting this command will bring you automatically to the ACD web page for bug reports and new feature requests.

·       A convenient new feature for all input/output dialogs in all windows of release 5.0 is that the standard Select File dialog boxes can be resized (lower right-hand corner of dialog).  As well, file and folder manipulations such as new folder creation, clearing the desktop, and display of file details can be done without once leaving the dialog box.

·       PC versions of most ACD software include a new feature that simplifies frequent operation.  Message box preferences can be set up so that you can control the level of system prompts for the actions you do.  The Help menu contains the Message Box Preferences command.  Depending on your choice of settings, you can be constantly prompted, or never be prompted for certain actions.

·       All ACD PC-based software can be updated through the Internet, using the Online Update facility.  Please see Section 1.6.3 below.

1.3.2     ACD/3D Viewer-Specific Functions

·       The new Colors dialog box includes instant color display and the ability to sort element names alphabetically.  See Section 3.3.1.

·       Similarly, the list of elements displayed in the Atomic Radii dialog box can also be ordered alphabetically.  See Section 3.3.2.

1.4     Useful Definitions

In this tutorial the following terms are used to describe various actions:

Þ   Point means move the mouse pointer  to an item.

Þ   Click or left-click means move the mouse pointer to an item, and press the left mouse button.

Þ   Right-click means move the mouse pointer to an item, and press the right mouse button.

Þ   Double-click means move the mouse pointer to an item, and quickly press the left mouse button twice.

Þ   Drag means press and hold down the left mouse button while you move the mouse.

1.5     About this Guide

To start using ACD/3D Viewer in its full power you don’t have to read a manual, it is so intuitive and simple to use.  That’s why this guide doesn’t provide comprehensive descriptions of all the options available in the program; rather, it just gets you started.  After reviewing these exercises, you will be able to use ACD/3D Viewer yourself, without any further assistance and with maximum speed and efficiency.

Þ   This User’s Guide is provided in electronic form, readable with a commonly available word processing program.  If you cannot locate an index topic you need, please do a text string-search in the word processing program for the relevant word or phrase, or related words.

Þ   The screen-shots shown throughout this guide have been taken with a relatively small window size.  The default display is a window that fills the screen.  Click once on the Minimize button  (upper right-hand corner of window display) to get a smaller working area; click on the Maximize button  to return to full-screen display.

Þ   The screen-shots have been taken with the next-to-last version of the software.  We have made every effort to match what you will see in ACD/3D Viewer with what the guide shows, but there may be slight discrepancies.

Þ   This Guide assumes you have basic familiarity with mouse and file manipulation in Microsoft Windows.

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Once you have used this Guide, we would like your feedback.  How can we improve the documentation for this product?  We have a short questionnaire we would like you to complete.  All eligible respondents will be entered in a draw for a prize of ACD/ChemFolder (or equivalent discount toward the purchase of any ACD software).  Please use MS Word 6.0 or later to open the file “survey.doc” or use Adobe Acrobat Reader to open “survey.pdf” on the documentation CD you have received with this software, or visit the “Feedback” page at our Web site, http://www.acdlabs.com/feedback/guides.html.  The winner of the draw is announced at the end of each calendar year.

 

1.6     For More Information…

1.6.1     Web Site

To see the latest in ACD software and services, please visit our Web site at

http://www.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 2001, we offer free ChemSketch 4.5, a free ISIS 3D Add-in, free ChemDraw extensions and a free 2-week demo key for  “Interactive Lab” sessions where you can run test calculations using Java applets without purchasing software.  There are Lotus Cam-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 booth.  You can browse the Frequently Asked Questions page or drop in and “chat” on our freeware newsgroup, which can also be reached at:

news://news.acdlabs.com/acd.public.chemsketch

If you would like to stay informed of the latest developments in chemical naming software products at ACD, please be sure to sign up for e-mail broadcasts at our Web site page:

http://www.acdlabs.com/feedback/mailing.html

1.6.2     How to Contact Us

We are accessible through our Web site, phone, fax and regular mail, but by far the most popular way to 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 to

support@acdlabs.com.

Please tell us the name of the software owner, the version number and release date of the product you are contacting us about.  (This information is available by selecting Help/About.)  If applicable, please tell us the name of the distributor from whom you purchased the software.

1.6.3     Online Updates—New to 5.0!

Version 5.0 of all PC-based ACD 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 5.00 to 5.01.  Please refer to the document, "Online Updates," included with the rest of the product documentation in your Documents folder for more information on this, or e-mail our technical support department.

 

2.1     Objectives

This chapter will familiarize you with

·       how to start the program;

·       how to set and change file associations;

·       how to set default directories; and

·       how to exit ACD/3D Viewer.

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 Microsoft Windows.

2.    Double-click the 3D Viewer icon.
–OR–
From the Start/Run menu in the Windows 95/98/2000 or NT taskbar, choose ACD/Labs and then choose the 3D icon.
–OR–
Double-click the program file “show3d.exe” in the folder where you have installed all ACD software.  By default this is ACD50.
–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 products scroll by.  Be patient and click Cancel when it becomes active.

2.3     Setting File Associations—New to 5.0!

1.    If this is the first time you have started the program, the File Association dialog box will appear.

2.    This contains a selectable list of file extensions and file types which you may want to open automatically with ACD software from now on.  If so, click the check boxes of the file formats you want to add, and then click the Yes button.

3.    If you do not want to have 3D automatically open files with the listed extension, or are not sure, leave the check boxes blank and click the No button.

2.3.1     Changing File Associations

If you have not selected all formats, the default file association can be viewed or changed at any time by going to the File menu and selecting File Association.  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, to change the file associations, you can do it 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 the SHIFT key and right-click on the file.  From the pop-up menu, select 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 3D, 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 the Preferences command.

2.    Click on the General tab.  And in the Default box at the bottom of the tab specify the directory that will be opened every time you open the Import, Open, Save, Export dialog boxes in the ChemSketch window:

3.    Click OK.

4.    Switch to 3D Window and from the Options menu choose the Set Default Folder… command and find the required folder.  Click OK.

2.5     Exiting ACD/3D Viewer

You can exit from the program in any of the following ways:

·       click  in the upper right-hand corner of the title bar of any window;

- OR -

·       from the ACD/Labs menu choose the Close All command.  This will attempt to close all ACD programs that are currently open, one right after the next.

- OR -

·       select the Exit command from the File menu.  This will close only the currently open ACD program.

You will be prompted to save your work in the appropriate file formats, depending on the window that you are exiting.

3.1     Objectives

In this chapter you will learn how to:

·       insert molecule into the 3D Window;

·       customize the view of molecules (color, atoms’ radii);

·       save and load view settings; and

·       measure distance between atoms and calculate angle between bonds.

3.2     Inserting a Molecule into the 3D Window

1.    Start up ACD/3D Viewer as described above.

2.    Click the ChemSketch button  on the Window Switching bar at the bottom of the window.

3.    This will switch you into the ChemSketch window.  Click the Dictionary button  in the upper right part of the ChemSketch window (circled in blue below):

4.    This will display the ACD/Dictionary dialog box.  In the Quick Search box type in a few key-strokes 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 corresponding structure is displayed, click OK.  Note that the shadow of the selected structure hangs over the cursor.  Click in the workspace to place the structure in the ChemSketch window:

6.    Click the Copy to 3D button  at the bottom of the ChemSketch window to transfer the molecule into the ACD/3D Viewer interface.  You will see a simple stick figure appear in the 3D window:

3.3     Customizing Molecules View

 

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