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   ISIS/draw introduction

The Silicon Graphics Teaching Laboratory
has been replaced by the
Chemical Information Laboratory
and this information is for historical interest only

ISIS/Draw Introduction

ISIS/Draw is a chemical drawing program somewhat similar to ChemDraw. It works in a slightly different way, so it will take a while to get used to using it.

ISIS/Draw may be downloaded from the MDL web site


  • Indigo only Start ISIS/Draw by typing isisdraw. The first time you run the program in any directory, it will copy two configuration files tpl.cfg and isisdraw.cfg into that directory.

Documentation and a tutorial is available at the Daresbury Laboratory

When ISIS/Draw is started, a window appears with a list of tools down the left hand side of the window, and a list of templates along the top. There are two buttons towards the top left of the window: Molecule and Sketch. To draw chemical structures, make sure that Molecule is selected. If you choose Sketch, you get the opportunity to draw other shapes which may be useful to annotate and beautify diagrams.

ISIS/Draw tools do not behave in the same way as ChemDraw tools. For example, consider the benzene drawing tool . Click on this tool, then click anywhere in the drawing window. A benzene ring will be drawn, at a standard size, from a single mouse click. Click once on any atom of the benzene ring, and a new ring will appear, connected by a single bond. Click on any bond of the benzene ring, and a new ring will appear, fused to that bond.

The bond drawing tool works in much the same way. Click on to select this tool, then click anywhere on the screen. A bond will be drawn by this single click. If you click on an atom, you will extend the chain. Click on an atom in a benzene ring to make toluene. Click on a double bond in a benzene ring to reduce it to cyclohexadiene.

The main difference between ISIS/Draw and ChemDraw is that the former draws most substructures with a single click. This may be confusing, at first, particularly as ISIS/Draw will also let you draw bonds by clicking and dragging, as with ChemDraw. This is unlikely to look as neat.

  • Help

    The program includes a comprehensive help system. The Table of Contents page (ToC) is a good place to begin. The Quick Reference section of the table of contents page is particularly helpful.

  • Lasso Tool
    This is used for selecting things. Once some atoms are selected, they can be dragged around, deleted, etc.

  • Rotate Tool
    Selecting this tool makes a cross appear in the middle of the screen. The cross is the centre of rotation, and can be moved around by clicking and dragging. The tool now behaves like the lasso, except that if you select anything then drag it, it will rotate around the central cross.

  • 3D-Rotate Tool
    Select 3D Rotate from the 3-D sub-menu of the Chem menu to change the rotate tool into a 3D rotate tool. If your drawing has three-dimensional data, then it can be manipulated with this tool.

    You can Import MacroModel structures into ISIS/Draw. Write a MacroModel structure to a file, such as taxol.dat Convert the file format using Babel (Type babel -ik taxol.dat -omdl taxol.mol). Choose Import from the File menu of ISIS/Draw, and select Molfile. You will be presented with a list of files ending .mol. Choose taxol.mol, or whatever your filename was, and it will be imported into ISIS/Draw.

  • Component Tool
    This is used to select molecules. It has a different purpose to the lasso, but the uses can be confused. After a whole molecule has been selected with this tool, it can be stretched or enlarged by dragging one of the handles around the molecule. When a molecule is selected, it can be 'cleaned up' by choosing Clean from the Chem menu.

    This tool is also used to select molecules for substructure searching in ISIS/Base.

  • Label Tool
    This tool allows you to change atoms from carbon into other elements. Select one or more atoms with this tool, then choose Atom... from the Style menu. You can then change to any element or group of elements. The latter is useful if you are setting up a search query for ISIS/Base.

  • Template Tool
    This tool is not active until you choose a template page from the Templates menu. Once you have done this, selecting this tool will summon the selected template menu.

  • Previous Template
    This tool also is activated by choosing a template page. It restores the tool to the last template you chose from a template page.


Consystant and Chemeleon

Two additional programs have been supplied with ISIS/Draw. These allow you to open ChemDraw files using ISIS/Draw and to cut and paste between ChemDraw and ISIS/Draw. Unfortunately, it is not easy to open ISIS/Draw files using ChemDraw.



© Goodman Group, 2005-2017; privacy; last updated December 7, 2017

department of chemistry University of Cambridge