From ghart at videotron.ca  Wed Jun 21 07:34:45 2006
From: ghart at videotron.ca (Geoff Hart)
Date: Wed, 21 Jun 2006 09:34:45 -0400
Subject: Tools: Software for drawing chemical structures?
Message-ID: <70e4a94e23605eb96238018fd5476e47@videotron.ca>

For an article I'm writing, I need to be able to generate an image of 
the 3D structure of a moderately complex chemical such as a simple 
protein. In fact, a sequence of half a dozen amino acids would more 
than suffice. I don't need to draw any specific molecule(s); I'm just 
trying to illustrate a few different levels of abstraction, starting 
with "realistic" (the 3D molecule) and working my way up the chain of 
abstraction to the base triplets that encode the amino acids. Clip art 
could work, but I'd rather generate the image myself to avoid any 
potential copyright entanglements.

Lots of stuff turns up in Google, but before I spend a few hours 
spelunking and testing, I thought I'd look for personal recommendations 
from people who have actually used the software.

Criteria: I'm looking for something free (I almost certainly won't use 
it again), free of copyright entanglements, easy to use, and able to 
produce a crisp image that would ideally also work in black and white 
or greyscale. System requirements: I'm on a Mac using OS X (Panther, 
not Tiger). A browser-based tool would be fine.

Thanks in advance!

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Geoff Hart   ghart at videotron.ca
(try geoffhart at mac.com if you don't get a reply)
www.geoff-hart.com
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From auswoman at princomm.com  Wed Jun 21 08:42:04 2006
From: auswoman at princomm.com (Deborah Ausman)
Date: Wed, 21 Jun 2006 09:42:04 -0500
Subject: Tools: Software for drawing chemical structures?
In-Reply-To: <LYRIS-52707-2901157-2006.06.21-07.55.13--auswoman#princomm.com@lists.stc.org>
Message-ID: <000001c69540$e2880b50$6401a8c0@princomm>

Geoff wrote: 

> For an article I'm writing, I need to be able to generate an 
> image of the 3D structure of a moderately complex chemical 
> such as a simple protein.

I say: It's been awhile since I've used any of this, but I used to work for
MDL, which offers a free drawing package called ISIS/Draw. To download it,
you need to register at their Web site. It used to be a good program, but
that was about 8 years ago.

Good luck!

Deborah




From ghart at videotron.ca  Thu Jun 22 12:32:03 2006
From: ghart at videotron.ca (Geoff Hart)
Date: Thu, 22 Jun 2006 14:32:03 -0400
Subject: Tools: Summary of responses to "Software for drawing chemical structures?"
Message-ID: <bacbd2824b9d25858401e5632e292fb1@videotron.ca>

Yesterday, I asked for suggestions on tools to help me draw a 
moderately complex chemical structure. Since the respondents proposed a 
range of tools, each of which will meet different needs, I haven't 
explored each tool and presented a recommendation. I'll do that myself 
later for my own specific needs, with the proviso that YMMV. That being 
said, here's my summary based on a quick glance at the recommended 
resources:

There are many professional-tools available for scientists, not all of 
which are accessible to those who only play one on the Internet. <g> 
For non-professionals (as opposed to unprofessionals <g>), there are 
several alternatives.

Electric Rain provides a range of tools for 3D illustration 
(http://www.erain.com/downloads/trials/), also available in trial 
versions. These don't seem to be directly dedicated to chemistry, but 
may be useful if you want full control and are comfortable with a "roll 
your own" solution. Similarly, the VTK (Visualisation Toolkit, 
http://vtk.org/) also appears powerful, but not a dedicated application 
for chemistry.

Adept Scientific's ChemDraw 
(http://www.adeptscience.co.uk/download/dldcat/22/0/All/ChemDraw.html) 
looks promising, and will run on Mac and Windows.

ADC's Chem Sketch (http://www.acdlabs.com/download/) also looks cool, 
and is free for home/educational use, but a quick look suggests it's 
Windows only. That won't fly on my Mac.

MDL's ISIS/Draw (http://www.mdli.com/downloads/): Didn't take the time 
to register and check whether it'll run on my Mac, but Google suggests 
that it will.

Rasmol and OpenRasmol (http://www.rasmol.org) also appear promising, 
and are open source software that should run on Mac, Windows, and Unix. 
Ditto for PyMol (http://pymol.sourceforge.net/pmimag/screen.html).

The University of Illinois' Visual Molecular Dynamics software 
(http://www.ks.uiuc.edu/research/vmd) seems to be a power tool for real 
molecule geeks, and runs under Mac, Windows, and Unix. ETH Zurich's 
MOLMOL software (http://hugin.ethz.ch/wuthrich/software/molmol/) falls 
into the same category, but seems to be Windows/Unix-only. The 
aforementioned geeks may also appreciate the links at the Protein Data 
Bank site <http://www-iphicles.rcsb.org/pdb/software-list.html>.

Clip art may also be an option, but I'll use it as my last resort to 
avoid any copyright issues. If I draw the molecule myself, then barring 
any software licensing agreements to the contrary, copyright won't be 
an issue.

Thanks to Heidi Arnold, Cathy Arthur, Deborah Ausman, Debra Bissantz, 
Sandy Harris, Rob Hodgins, Joe Malin, and Iwan Thomas. If I missed your 
name or didn't include the information you provided in my summary, 
sorry 'bout that... possibly the message never arrived, or I just 
missed it. Feel free to re-post your message for the benefit of others.

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Geoff Hart   ghart at videotron.ca
(try geoffhart at mac.com if you don't get a reply)
www.geoff-hart.com
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