ISIS/Draw - An Introductory Guide

   Original version of this Guide by Greg Pearce

There is a new program, called Symyx Draw, version 3.1 -- offered as a successor to Isis/Draw 2.5. (In fact, it seems to have changed name again, to Accelrys Draw, and is up to version 4, as of March 2011.) As before, the program is available free to academics and personal users. The old version of Isis/Draw for the Mac is no longer available, and has no successor.

The web address for Symyx Draw (Accelrys Draw) is: http://accelrys.com/products/informatics/cheminformatics/draw/.

I started a guide to Symyx Draw v 3.1, modeling that guide after this one for ISIS/Draw. Symyx Draw - An Introductory Guide. I have not kept it up, and don't really plan to, at least for now. If anyone would like to take over the project of completing the Symyx page, please drop me a note. (I'll link to your improved guide -- and avoid unnecessarily competing with your effort. Please include a statement acknowledging the source.)


I will leave this ISIS/Draw page here, since many will already have this program.

A. Introduction
B. Getting and installing ISIS/Draw
C. Drawing a simple molecule: Propane
D. Drawing a more complex molecule: Glycine
     Multiple bonds, Heteroatoms, Displaying hydrogen atoms
E. Using templates: 2-phenylnaphthalene

F. Additional useful features in ISIS/Draw
   1. Lasso Select
   2. Eraser
   3. Chain Tool and Multi-bond Tool
   4. Clean Molecule
   5. Naming structures: The AutoNom add-in
   6. Cyclohexane: chair conformations
   7. Stereo bonds (including wedge bonds)
   8. Unusual atoms labels (X for halogen, Me, etc)
Bottom of page; return links and contact information
  Folic acid Folic acid, drawn with ISIS/Draw.

The time needed to draw this complex structure, using the features described below, was less than two minutes.

A. Introduction

This is an introduction to ISIS/Draw, a program from MDL that is free for non-commercial use. You can use it to draw chemical structures, and export them for viewing as 3D models. Instructions for exporting structures for 3D viewing are given on the RasMol page; see "Method 2" there. (Isis/Draw has a menu item called "View molecule in RasMol". It seems to not work properly, and we ignore it here.)

  Folic acid, 3D A 3D view of folic acid, made from the ISIS/Draw structure shown above.

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B. Getting and installing ISIS/Draw

The ISIS/Draw program is no longer available. It has been succeeded by the program Symyx Draw (Accelrys Draw), available only for Windows. (There is no Mac successor program.) Thus this page no longer contains information about how to obtain ISIS/Draw. The page is maintained for those who may already have it.

For information on Symyx Draw, see my page Symyx Draw - An Introductory Guide. That page includes information on how to obtain the program.

Requirements. ISIS/Draw 2.5 is distributed as a version for Windows 98, 2000, NT 4.0, or XP. (I think it runs fine on newer versions of Windows.) A version of ISIS/Draw for the Macintosh is also available.

Obtaining ISIS/Draw. As noted at the top of this section, the program is no longer available.

Optional. If you do obtain the program, you may also get the following two optional files:
* The AutoNom Standard add-in. This add-in allows you to name structures you draw, and is discussed below under F. Additional useful features in ISIS/Draw. (If the AutoNom installer detects an old version, it will ask you if you want to proceed. You probably want to continue, and install the new version in the correct folder.)
* The help file. The basic installation does not include a help file. For basic use the instructions given here should be sufficient.

Installation. To install the program, run the exe file, draw25.exe. If you have either of the optional items discussed above, install them by running their exe files.

You can add the optional items later. If not sure about them when you start, it is fine to ignore them.

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C. Drawing a simple molecule: Propane

The following instructions show how to draw a simple molecule, propane.

propane

Load ISIS/Draw. You should be presented with a blank page, with two toolbars: One toolbar, on the left, contains buttons for drawing and viewing molecules. The toolbar at the top opens templates to insert pre-drawn molecules such as cyclohexane and aromatic rings.

The buttons at the top of the left-hand toolbar, the most commonly used, are shown below, with their names:

Left toolbar, top part

Click the Single Bond button, and then click on the blank space. A single bond (shown as a line) will appear. At each end of the line is a carbon atom. ISIS/Draw omits the letter, as is common practice in drawing chemical structures. Similarly, hydrogen atoms are not shown, but the correct number of hydrogens has been added to each carbon automatically.

Now hold the pointer over one end of the line. A faint box will appear. Single click. A structure identical to the one shown above (but not necessarily in the same orientation) should be visible; this is the shorthand notation for propane.

Any structure can be extended by using the Single Bond tool. Click on the atom where you wish a new bond to begin, and a single bond to a new carbon atom will be added.

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D. Drawing a more complex molecule: Glycine

The following instructions show how to draw a more complex molecule, the amino acid glycine. To do this, creating the structure shown below, you will learn to create multiple bonds and heteroatoms and to display hydrogen atoms.

glycine

Use the Single Bond tool to draw a chain of four single-bonded carbon atoms (you need three clicks to do this). Click on the second atom from the right to add a branched carbon atom. We will now change some of the carbon atoms to other atoms.

Click the Atom button. Position the pointer over the terminal carbon on the right (a faint box should appear). Click, and a drop-down box will appear. Click the arrow, and choose "O" to change to an oxygen atom. Repeat this for the branched carbon to make that oxygen, too (this time, the "O" will already be selected; just hit your Enter key). Now click on the terminal atom on the left, and change it to nitrogen (N).

The branched oxygen needs to be double-bonded to the carbon atom. There are two ways to insert a double bond in ISIS/Draw. One way is to draw a single bond (as you have done) and then click on the bond again with the Single bond tool. This increases the bond order to 2.

Further clicks cycle the bond order between 1, 2 and 3 (although in this case a bond order of 3 is not possible). This can be used to insert multiple bonds in structures, or convert a multiple bond back to a single bond.

Alternatively, a double bond can be drawn from the start by clicking and holding the Single bond tool and then selecting Double bond from the menu that appears. A double bond can then be drawn in the same way as a single bond.

You may now want to display the hydrogens -- at least those on heteroatoms. The glycine structure shown above shows the hydrogens on the heteroatoms (as is the usual convention). To show the hydrogen atoms in a structure, go to the Options menu and choose Settings. Find the Chemical Drawing tab. At the top of the tab, on the left, there is a drop-down box called Show hydrogen labels. By default, this is set to "Off". To show hydrogens on heteroatoms, choose "On Hetero". To show hydrogens on heteroatoms and terminal atoms (those on the ends of a molecule), choose "On Hetero or Terminal". To show hydrogens on all atoms, choose "On All". Click "OK". If you have already drawn structures, ISIS/Draw will ask whether to apply the settings to the sketch. Click "Yes".

If you are drawing structures to be converted to 3D, using ViewerLite, there is no need to display hydrogens here.


Notes about heteroatoms:

If you want an atom of an element that is not listed in the drop down box when you select the atom... Choose More. That leads to the Edit Atom dialog box. Look at the symbol part, and open that drop down box. If your element is listed, choose it. If it is not listed, choose periodic table (at bottom), and then click on the element in the periodic table.

Alternative procedure. Instead of using the Atom tool... Select the atom(s) you want to change. Then, either right-click or go to the Object menu; in either case, choose Edit Atom. This gives you the Edit Atom dialog box referred to above. For simple cases, this alternative procedure probably has no advantage. However, it does allow you to edit multiple selected atoms at once, and also to change other properties.

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E. Using templates: 2-phenylnaphthalene

ISIS/Draw contains many templates that can be used to speed up drawing large molecules. This example shows how to make an aromatic compound using a template.

2-phenylnaphthalene

The template icons (on the toolbar across the top of the page) make it easy to draw commonly-used structures such as rings.

template icons shown on main screen

Click on the benzene ring. Click again on the page to place the ring. Now hold the pointer over one of the bonds of the ring, so that it is highlighted by a faint box. Click again to fuse another ring to that bond. Now hold the pointer over a specific atom, at the right side, and click. The ring added will be bonded to the atom you clicked, and the structure of 2-phenylnaphthalene is complete. (If you add this last ring at an atom next to the ring fusion, you get 1-phenylnaphthalene.)

ISIS/Draw has a large number of templates in addition to the basic structures on the toolbar. Choosing a template set from the Template menu will bring up a window containing many pre-drawn structures. Click on a structure and then on the page to insert it. Template structures can be added on their own, or fused to existing bonds or atoms like the benzene ring.

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F. Additional useful features in ISIS/Draw

Although not necessary when drawing simple structures, there are several features in ISIS/Draw that may be helpful.

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1. Lasso Select

The Lasso Select tool allows any part of a structure to be selected. Choose the Lasso Select tool, click and drag around the structure so that the items to be selected are enclosed in the "lasso", then release the button.

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2. Eraser

Choose the Eraser tool and hold the pointer over a part of the structure (an atom or a bond). A grey box will be shown; click to delete the contents of the grey box. Alternatively, click and drag the Eraser tool to delete a larger selection.

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3. Chain Tool and Multi-bond Tool

The Chain tool makes it easy to draw chains of carbon atoms (for instance, those found in fatty acids).

Chain tool, from left toolbar

Choose the Chain tool, then click and drag to create a chain of atoms. This saves time if you need to draw more than 2 atoms in a chain.

Click and hold the Chain tool icon and choose Multi-bond tool from the pop-out menu to access the Multi-bond tool. This is a more versatile tool; click and drag to create structures such as cyclohexane easily.

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4. Clean Molecule

Use the Lasso Select tool to select the entire structure, or go to the Edit menu and choose Select All. Now go to the Object menu and select Clean Molecule. This "tidies" the structure that has been drawn, which may make it easier to show more complex molecules. ISIS/Draw uses nominal bond angles and bond lengths to do this. Note that it is not necessary to do this before exporting to ViewerLite; this feature of ISIS/Draw is simply a convenience when drawing molecules.

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5. Naming structures: The AutoNom add-in

The AutoNom add-in allows ISIS/Draw to apply the IUPAC system of naming to a molecule. (Note that it does not know common names; using it on our examples of glycine or folic acid will give the IUPAC names for these molecules.) It is accessed by the Generate Name with AutoNom button (bottom of left hand toolbar).

Naming button

The AutoNom add-in was first made available to users to Isis/Draw with version 2.4. At that point, its installation was an optional step within the basic package. For version 2.5, the AutoNom add-in is a separate download and installation. If you do not see the Generate Name with AutoNom button, shown above, you need to go back and download/install the add-in. See B. Getting and installing ISIS/Draw.

Use the Lasso Select tool to select the entire structure, or go to the Edit menu and choose Select All. Take care to select exactly what you want to be named -- if you leave the most recently-added bond selected, for example, only that will be named.

Click the Generate Name with AutoNom button. ISIS/Draw will name the compound, providing it is not too complicated, and place the name below. You can move it around by selecting it and then dragging, or erase it with the Eraser tool.

Naming programs -- especially free ones -- always have limitations. For example, the naming feature of ISIS/Draw does not assign cis/trans (or E/Z) at double bonds when needed. (The naming feature of the successor program Symyx Draw does assign E/Z. The program ChemSketch also assigns E/Z.)

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6. Cyclohexane: chair conformations
7. Stereo bonds (including wedge bonds)

Both of these features (#6 & #7) are discussed in the separate page on Rings: Showing cis/trans and axial/equatorial relationships.

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8. Unusual atoms labels (X for halogen, Me, etc)

Sometimes you want to label an "atom" (a particular position on a structure) with something other than an ordinary element symbol. Examples include: D for deuterium, X for a general halogen, Me for methyl.

The idea of changing an atom from one element to another was introduced above in the section Drawing a more complex molecule: Glycine, including the "Notes about heteroatoms" at the end of that section. The immediate task there was to change a C to the heteroatom O or N. That same basic procedure can be extended to provide symbols beyond those of the elements.

Recall that the basic procedure there was to draw the desired structural backbone, using C atoms. Then, go to the Edit Atom dialog box, by any of the procedures described earlier. (One procedure involves using the Atom tool. Alternatively, you select the atom(s) to be changed, and either right-click or go to the Object menu to get Edit Atom.) Look at the Symbol section of that box. There is a drop down menu, which includes some element symbols. But it includes more -- just look around. One thing it includes is a Periodic Table. The Periodic Table lets you choose any element. Further, if you click on "Extended" on the Periodic Table, you will get some additional symbols, such as D for deuterium, X for a general halogen, and amino acid symbols (3 letter). And if you don't find what you want, just type it in -- in the Symbol box. You can create any atom label you want.


All feedback encouraged. Please e-mail me any comments/corrections/suggestions. See Contact information, below.

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Last update: December 14, 2013