Symyx Draw - An Introductory Guide

April 2009. This is a new page, and is still "in progress". I think the information is substantively ok, but I am still checking it. Not all the links to other pages may be right. Please let me know if you find any problems.

June 2011. My project to complete this page is on hold. The program has changed hands again, and new versions continue to appear. The program is now Accelrys Draw, from Accelrys, and is up to version 4, as of March 2011. The current source address is: http://accelrys.com/products/informatics/cheminformatics/draw/. Scroll down to "For Academic and Non-Commercial use -- No-fee Accelrys Draw". I hope that the information below, for an earlier version, is a useful start.

February 2013. The program is now Accelrys Draw version 4.1.

If anyone would like to take over the project of completing this 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.)

A. Introduction; Symyx Draw and ISIS/Draw
B. Getting and installing Symyx 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 Symyx Draw
   1. Lasso
   2. Eraser
   3. Chain Tool and Multibond Tool
   4. Clean Molecule
   5. Naming structures
   6. SMILES and InChI
   7. Cyclohexane: chair conformations
   8. Stereo bonds (including wedge bonds)
   9. Unusual atoms labels (X for halogen, Me, etc)
Bottom of page; return links and contact information
Folic acid Folic acid, drawn with the (substantially equivalent) predecessor program, 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 Symyx Draw, a program from Symyx 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.

Symyx Draw and ISIS/Draw. The program discussed here, Symyx Draw, is related to another program called ISIS/Draw. It is probably a useful simplification that Symyx Draw 3.1 is a successor to ISIS/Draw 2.5. The basics seem quite similar. The Windows version of ISIS/Draw is apparently no longer available -- having been superseded by Symyx Draw. (The Mac version of ISIS/Draw is also no longer available, with no successor. Mac users should check my page Writing, drawing and viewing chemical formulas for some suggestions.) For those who may have ISIS/Draw, I still maintain ISIS/Draw - An Introductory Guide.

Some of the figures used on this page are from ISIS/Draw. In writing this page starting from the ISIS/Draw page, I replaced only figures where Symyx seemed substantially different.

  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 Symyx Draw

See note at top of page for newer information.

Requirements. Symyx Draw runs under Windows XP or Vista (32 bit only).

Obtaining Symyx Draw. Go to the Symyx Draw page at [SEE TOP OF PAGE].

You can also get add-ins, which provide additional features. From the page listed above choose "Add-ins". On the resulting page, scroll down to Resources, near bottom. That leads you to a page that lists the add-ins. You can download a complete set, or individual add-ins as you wish. At this point, I have no experience with the add-ins, and there is no discussion of them below. However, they include some aids for simpler 3D viewing; I will follow this up.

The current version of Symyx Draw is 3.1 (actually 3.1.2), distributed as SymyxDraw-3_1_2_AE.exe. If you find a more recent version, please let me know, and I will update this guide as needed. (Version 3.2 will be available soon.)

Installation. To install the program, run the exe file that you have downloaded.

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C. Drawing a simple molecule: Propane

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

propane

Load Symyx 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 has templates to insert pre-drawn molecules such as cyclohexane and aromatic rings.

Left toolbar, top part The buttons at the top of the left-hand toolbar, including some of those most commonly used, are shown at the left. The names of some are also shown.

The top button, for the Lasso tool, looks slightly different: it seems to be in a lighter box. That means that this button has been chosen. Any button you choose will take on this appearance.

Some of the buttons have a small black triangle at the right. If you click on the triangle, you will get a pop-out menu showing alternatives for this choice. For example, the single bond tool button can be expanded to allow double or triple bonds. The appearance of the button will change to correspond to your choice. Thus, buttons and their names may not look like what is shown in the figure here; they can vary depending on user choice.

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. Symyx 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 little 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 Change Atom Type button. (For simplicity, we will sometimes call this simply 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 Symyx 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 -- even if the program allows it). 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 using the Double bond tool. To get this tool, click on the little arrowhead on the Single bond tool, then select Double bond from the pop-out 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. In the top block of items, called Atoms, there is an item called Show hydrogen labels. Click on it, and an arrow will appear at the right. That arrow is for a drop down menu -- with choices for how hydrogens are shown. 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 "Apply".

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 a periodic table; click on the element in the periodic table.

Alternative procedure. Instead of using the Atom tool... Select the atom(s) you want to change; right click. This gives you a menu of Atom Properties. Choose Atom symbol. This gives you the periodic table 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

Symyx 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 toolbar Template toolbar

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, 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.)

Symyx Draw has a large number of templates in addition to the basic structures on the default templates toolbar. These are accessible with the two buttons shown at the left end of the templates toolbar. The left-most button, looking something like a folder, lights up as "Template directory". Click on that button, and you have access to all available template sets. The other button, rather non-descript, lights up as "Change to different template toolbar", and has a little down-arrowhead that opens up a menu; this menu allows you to change to show another template set on the toolbar. In all cases... 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 Symyx Draw

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

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1. Lasso

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

A variation of the Lasso tool allows you to use a rectangular frame as the selection border. This tool is available by clicking on the little down-arrowhead to expand the Lasso tool button, and is labeled Select tool.

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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 blue box will be shown; click to delete the contents of the blue box. Alternatively, click and drag the Eraser tool to delete a larger selection.

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3. Chain Tool and Multibond 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 The button for the Chain tool, as it normally appears on the left toolbar.
Expanded Chain tool, from left toolbar The button for the Chain tool, expanded to reveal the Multibond tool at the right.

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.

Expand the Chain tool choices by clicking on the right hand part of it -- where the arrowhead is. From the resulting pop-out menu, choose the right hand tool, the Multibond tool. This is a more versatile tool; click and drag to create structures such as cyclohexane easily.

The difference between the Chain tool and the Multibond tool... The Chain tool draws only "straight" chains. You can change the direction of the chain as you wish, but it will be one simple zig-zag in that direction. The Multibond tool lets you change direction.

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4. Clean Molecule

Use the Lasso tool to select the entire structure, or go to the Edit menu and choose Select All. Now go to the Chemistry menu and choose Clean. This "tidies" the structure that has been drawn, which may make it easier to show more complex molecules. Symyx 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 Symyx Draw is simply a convenience when drawing molecules.

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5. Naming structures

From the Chemistry menu, choose Generate Text from Structure. From the resulting pop-out menu, choose IUPAC name. Symyx Draw will name the compound, providing it is not too complicated. You need to click the mouse button to drop the name where you want it on the screen. After that, you can move it around by selecting it and then dragging, or erase it with the Eraser tool.

If there is more than one structure on the screen, you will probably want to "select" one for naming, by using the lasso. Otherwise, Symyx Draw will name all structures on the screen. This might be useful in some cases, but it makes labeling difficult: it creates a single text box with all the names in it; there is no way to position individual names with individual structures.

Naming programs -- especially free ones -- always have limitations. At this point, I do not know what the limitations are here. The Help file has no useful information on this. I have found that Symyx Draw will assign E or Z at double bonds; this is a feature that was missing in ISIS/Draw.

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6. SMILES and InChI

SMILES and InChI are both ways to describe a chemical structure in simple text characters.

SMILES = Simplified Molecular Input Line Entry Specification.
InChI = (IUPAC) International Chemical Identifier.

This is not the place to try to explain them, but if you want to try them, they are available. Both are available from the Chemistry menu. To generate the code, expand the Generate Text from Structure item, and you will see SMILES and InChI options (along with IUPAC name, discussed above). To generate the structure from the code, expand the Generate Structure from Text item, and you will see SMILES and InChI .

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

Both of these features (#7 & #8) are discussed in the separate page on Rings: Showing cis/trans and axial/equatorial relationships.

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9. 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.

A few extra symbols are available from the "Extended periodic table". Go to the periodic table as described earlier, and check the box for "Show Extended Table". This leads to an extra row of symbols at the bottom. These include symbols such as D for deuterium or X for a general halogen.

Beyond that, you can create your own symbols or abbreviations. To do that you need to get to the "Create chemical template/abbreviation" box. You get there using the same approaches as before. If you use the Atom tool, the last choice on the drop down menu is "Create abbreviation". If you right click on a selected atom, a choice near the bottom is "create template/abbreviation". Once you get the "Create chemical template/abbreviation" box, type the desired symbol in the box.


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

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Last update: February 17, 2013