ACD/3D Viewer. User's Guide

Transcription

1 ACD/3D Viewer for Microsoft Windows User's Guide Operating with Molecules View and Physical Parameters

2 Advanced Chemistry Development Inc. Copyright Advanced Chemistry Development Inc. All rights reserved. ACD/Labs is a trademark of Advanced Chemistry Development Inc. Microsoft is a registered trademark and Windows is a trademark of Microsoft Corporation. IBM is a registered trademark of International Business Machines Corporation. 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.

3 TABLE OF CONTENTS 1. INTRODUCTION WHAT IS ACD/3D USEFUL DEFINITIONS FOR MORE INFORMATION How to Contact Us BASICS OF ACD/3D OBJECTIVES SYSTEM REQUIREMENTS STARTING ACD/3D EXITING ACD/3D OPERATING WITH MOLECULES VIEW INSERTING A MOLECULE INTO THE 3D WINDOW CUSTOMIZING MOLECULES VIEW Setting Desired Colors Editing Atoms Radii OPERATING WITH VIEW SETTINGS Saving View Settings Setting Default View Settings Loading View Settings CALCULATING MOLECULES PHYSICAL PARAMETERS Calculating Distance Between Two Atoms Calculating Angle Between Two Bonds Calculating a Torsion Angle...16 ACD/3D User s Guide 3

4 1. Introduction 1.1. What is ACD/3D ACD/3D is a program, converting the normally two-dimensional structures from ACD/ChemSketch into the three dimensional counterparts. ACD/3D is fully interfaced with the ChemSketch program. One or many input molecules from the latter can be imported into the 3D window by clicking on the Window Switching Bar. ACD/3D provides additional file-saving options - from the 3D interface as 3D OLE server files, or from the ChemSketch interface as sketch, bitmap or MOL files. It provides a wide range of features. You can: Specify the representation of the structure displayed: color and view type of molecules. Structural display options range from using sticks, balls-and-sticks to the more sophisticated opaque space-filling technique or transparent dots-on-a-sphere. Copy the contents of the workspace onto the Clipboard using the Copy command (Edit menu). Once the object has been copied, you can paste it into other Microsoft Windows applications, such as word processors or graphics applications. Customize fully and individually the atomic radii. Perform atom-to-atom measurement, and 3- and 4-vertex (torsion) angle measurement. Import structures into a MOL-format file, which is highly compatible with other computational chemistry software. Set a structure to auto-rotate, with or without changing the display styles. To switch to the 3D window from the ChemSketch window, click OR draw a structure and click the button on the Window Switching Bar. In this tutorial the following terms are used to describe various actions: Point means move the mouse pointer to an item Useful Definitions Click or left-click means move the mouse pointer to an item, and press the left mouse button. Right-click means move the mouse pointer to an item, and press the right mouse button. Double click means move the mouse pointer to an item, and quickly press the left mouse button twice. ACD/3D User s Guide 4

5 Introduction Drag means press and hold down the left mouse button while you move the mouse. In Windows the default mouse button side is on the left. You can change the default side to the right by summoning the Mouse dialog box from the Windows Control Panel. (This also permits you to change the speed and motion attributes of the mouse.) 1.3. For More Information To see the latest in ACD software and services, please visit our web-site at 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 1999, we offer free ChemSketch 4.0, a free ISIS 3D Add-in, free ChemDraw extensions and economical 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 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 newsgroup, which can also be reached via our web page. 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 broadcasts at our web site page: 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. ACD/3D User s Guide 5

6 2. Basics of ACD/3D 2.1. Objectives This chapter will familiarize you with the computer requirements for running ACD/3D; installation of the software; and how to start the program System Requirements To install and use ACD/3D, you need the following: a licensed full-featured version of ACD/3D, or a demonstration version of ACD/Labs; an based IBM PC or compatible (Pentium recommended); a VGA color monitor; 12.5 Mb disk space for installation of the licensed full-featured version of the ACD/ChemSketch (estimate includes Dictionary; about 5 Mb disk space without Dictionary); and 1 Mb disk space for the ACD/3D program. a Microsoft mouse or fully compatible pointing device; an operating system: Microsoft Windows 95/98, Windows NT 3.51 OR Windows NT 4.0; 8 Mb or more of random-access memory (RAM) (16 RAM recommended) Starting ACD/3D Once ACD/3D has been installed on your computer, follow these basic steps to start it: 1. Start Windows. 2. Double click the ACD/3D icon to start ACD/3D. OR choose the ACD/3D icon from the Start/Run menu in the Windows 95 or NT Taskbar. ACD/3D User s Guide 6

7 Basics of ACD/3D OR double click the program file show3d.exe in the ACD folder. You will see the splash screen appear, followed by the ACD/3D window: 3. 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. 4. Then you will see a Tip of the Day box, which you can close after reading Exiting ACD/3D Once the ACD/3D window appears, you can exit from the program any time by selecting the Exit command (File menu). Do not forget to save your work before exiting, as ACD/3D does not prompt you to do that. ACD/3D User s Guide 7

8 3. Operating with Molecules View To insert a molecule into the 3D window: 3.1. Inserting a Molecule into the 3D Window 1. Click the ChemSketch button at the bottom of the window: 2. This will switch you into the ChemSketch window. Click once the Dictionary button in the upper right part of the ChemSketch window: ACD/3D User s Guide 8

9 Operating with Molecules View The free ChemSketch version doesn t include the Dictionary module. This module is a commercial one, so if you have a free ChemSketch in use, draw any desired structure by using the ChemSketch interface tools. (For details upon drawing structures refer to the ACD/ChemSketch User s Guide.) 3. This will display the ACD/Dictionary dialog box - a 47,000-entry look-up table. 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. 4. Click OK to accept the drawn molecule. It will appear in the ChemSketch window: H 2 C H HO H N H N ACD/3D User s Guide 9

10 Operating with Molecules View 5. Click the Copy to 3D button at the bottom of the ChemSketch window to transfer the molecule into the ACD/3D interface. You will see a simple stick figure appear in the 3D window Customizing Molecules View 1. To create a 3D model of a 2D chemical structure, click the 3D optimize button. 2. To represent the current structure as balls and sticks, click the Ball and Sticks button. 3. To add dots halo to the current molecule view, click the with Dots button. 4. The structure will look something like this: 5. To rotate a molecule automatically as it is, without changing its view type, click the Autorotate button ; ACD/3D User s Guide 10

11 Operating with Molecules View To rotate a molecule, automatically changing its view type, click the Auto-rotate and Change style button. To represent structure as disks, wireframe, dots or spacefilled, click the corresponding buttons on the toolbar (,,, ). Or right-click in the window workspace. Note that if any of the Measure menu shortcut buttons are pressed: (,, ), rightclicking will switch you between them only. You may rotate structure obtained for better view by dragging the mouse pointer over the window workspace Setting Colors To set screen colors you consider to be the best: 1. Click the Set colors button. This will display the Colors dialog box: 2. To make the atom being selected, of the desired color, in the Selection list choose the desired color and click OK. 3. To change the Background color, select the desired color in the corresponding list. 4. To change the color of a chemical Element, click the name of the element in the list and then click the desired color. ACD/3D User s Guide 11

12 Operating with Molecules View Editing Atoms Radii There are several ways of changing default radii values: To look through and edit atoms' radii corresponding to different chemical elements: 1. Click the Radii command (Options menu). This will cause the Atoms' Radii dialog box to appear: 2. Click Hydrogen in the Element list. This will display its atom s radius (101) in the text input box and will highlight it in the list. 3. Enter in the box the new value (e.g. 200) and click OK. 4. For better performance depress the with Dots button and press the Spacefill button (the last becomes active only when changed something like this: is depressed). The structure view will be ACD/3D User s Guide 12

13 Operating with Molecules View To increase the atom s radius by 5%: Click the corresponding button on the toolbar: atom's radius increases by 5%. To decrease the atom s radius by 5%: Click the corresponding button on the toolbar: atom's radius decreases by 5%.. Every time you click this command, the. Every time you click this command, the The last two described buttons are active only when the Balls and Sticks button is depressed Operating with 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 default. This chapter describes all these options in work Saving View Settings To save the settings specified above: 1. Click the Save Settings command (Options menu). Clicking this command opens the Save Settings dialog box. This dialog box includes the View type, Background and Selection Colors, Elements Colors and atoms' Radii check-boxes: 2. Make sure all these check-boxes are selected to include current view settings, background colors, elements colors and radii values into the file being saved. 3. Click OK. This will cause another Save Settings dialog box to appear where you can choose the needed drive, directory and specify the *.3ds file name (e.g. test.3ds). 4. Click OK. ACD/3D User s Guide 13

14 Operating with Molecules View Default View Settings 1. To set current settings, saved before, click the Set Default Settings command (Options menu). This will display the Set Default Settings dialog box. 2. Choose the needed file path and select the test.3ds file. 3. Click OK. The test.3ds file will be loaded during the next work session. To test the default settings: 1. Click the Exit command (File menu). Note that you must save your file previously by clicking the Save command (File menu) because the program won t prompt you to do this. 2. Run the ACD/3D Window. 3. Into the 3D window, transfer a structure from the ChemSketch window (see description above). The settings specified before, will be set as default. ACD/3D User s Guide 14

15 Operating with Molecules View Loading View Settings 1. To load settings saved previously, click the Load Settings command. This will open the Load Settings dialog box. 2. Select the right file path for the test.3ds file: 3. Click OK. The settings from the file loaded will be applied to the structure on the screen Calculating Molecules Physical Parameters Calculating Distance Between Two Atoms To calculate distance between two atoms of the structure displayed: 1. Press the Calculate distance between two atoms button. 2. Click any atom. It will become selected. 3. Move the mouse pointer to the second atom and click it. The current calculated data and selection will be reflected on the Status Bar, something like this: Without selecting the second atom, you can look through the distances between the atoms by moving the mouse pointer over them. To switch this feature off, depress the Distance button OR right-click the window workspace. The last will make the Bond Angle command (Measure menu) selected. Sequential multiple right-clicking will make the Distance command selected again. ACD/3D User s Guide 15

16 Operating with Molecules View Calculating Angle Between Two Bonds To calculate the angle between two bonds: 1. Press the Calculate angle between two bonds button. 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 calculated angle value appears on the Status Bar, e.g.: 4. To fix the calculated value, click this atom. Without selecting the second bond, it is possible to look through the angles between the selected bond and all the bonds neighboring the last selected atom by moving the mouse pointer over them. To switch this feature off, depress the Bond Angle button OR right-click the window workspace. The last will make the Torsion Angle command (Measure menu) selected. Sequential multiple right-clicking will make the Bond Angle command selected again Calculating a Torsion Angle To calculate a torsion angle: 1. Click the Calculate torsion angle button. 2. Click two neighboring atoms, which form a bond. The corresponding bond becomes selected. 3. In the same manner, select two more bonds by clicking the atoms neighboring to the bond last selected. The current calculated data and selection are reflected on the Status Bar, e.g.: Without selecting the third bond, it is possible to look through the values of all possible torsion angles neighboring the last selected atom by moving the mouse pointer over them. To switch this feature off, depress the Calculate torsion angle button OR right-click the window workspace. The last will make the Distance command (Measure menu) selected. Sequential multiple right-clicking will make the Torsion Angle command selected again. ACD/3D User s Guide 16