From owner-chemistry@ccl.net Wed Jan 11 16:14:01 2006
From: "Warren DeLano warren#delsci.com" <owner-chemistry#server.ccl.net>
To: CCL
Subject: CCL: Simple molecular graphics
Message-Id: <-30458-060111153556-26700-QGHIdpNUSNZDeeFZtSXcUw#server.ccl.net>
X-Original-From: "Warren DeLano" <warren---delsci.com>
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Date: Wed, 11 Jan 2006 11:50:40 -0800
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Sent to CCL by: "Warren DeLano" [warren(a)delsci.com]
Leif,

PyMOL can now do black & white nicely, as well as photorealistic color
on black, white, or transparent backgrounds.  It can be used for
everything from electron density, ball & stick, and cartoon, all the way
way up to megadalton EM tomography surface representations.

Some examples at:

http://www.pymolwiki.org/index.php/Ray

Latest builds d/l at

http://delsci.com/beta

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                     
Principal Scientist

. DeLano Scientific LLC  
. 400 Oyster Point Blvd., Suite 213           
. South San Francisco, CA 94080 USA   
. Biz:(650)-872-0942  Tech:(650)-872-0834     
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:warren|a|delsci.com      
 

> -----Original Message-----
> From: owner-chemistry|a|ccl.net [mailto:owner-chemistry|a|ccl.net] 
> Sent: Wednesday, January 11, 2006 10:46 AM
> To: Warren DeLano
> Subject: CCL: Simple molecular graphics
> 
> Sent to CCL by: "Leif  Olson" [leif.olson,,kodak.com] Hi CCL people,
> 
> I know this is similar to previous questions that have been 
> sent to the list in the past.  But I am going to ask it 
> anyway...I keep searching for a program that will make simple 
> publication quality molecular graphics pictures (usually 
> black-and-white), but with a couple of added features, and 
> runs on Windows or Linux.  
> 
> Vast numbers of molecular graphics programs are advertised 
> for their capability to make "publication quality" images.  
> But what this always seems to refer to is the ability to 
> create stunning color pictures complete with shadows, fog 
> effects, dramatic backgrounds, etc., perhaps rendered with 
> the help of POV-Ray.  Nice, but not what I usually need for 
> figures to put into journal articles or technical reports.  I 
> usually just want ball-and-stick, black-and-white (or a 
> simple color scheme to highlight heteroatoms), maybe some 
> cross-hatching to suggest depth, and some labeling 
> capability, with the end result a high-resolution image or 
> vector output.
> 
> An example of a program that comes pretty close to what I 
> would like is XChemEdit, where I can read in a structure, and 
> quickly rotate/translate it to a desired orientation.  Then, 
> with a few mouse clicks I can remove undesired bonds, make 
> dashed bonds (e.g. for hydrogen bonds or transition states), 
> label bond distances/angles/dihedrals, resize and move 
> labels, etc.  This only takes a minute or two, unfortunately 
> the resulting images are not, in my opinion, good enough for 
> external publication.  They are nicely labeled and clear, but 
> low-resolution.
>     
> As an alternative, I have tried Schakal99, which can make 
> excellent publication-quality b/w molecular graphics, and it 
> seems that one has extensive control over the final image.  
> But I find it difficult to use even after studying the manual 
> and going through quite a few examples, and I am not sure 
> that certain things like labeling bond angles can even be done.
> 
> I have also looked at XBS, Molden, ORTEP, and WebLab Viewer, 
> but they aren't quite what I am looking for either.  We don't 
> own Cache, Chem3D, or Gaussview, so I haven't tried 
> them...what about those or other software?  Is it best to 
> just put in the time to really learn Schakal usage?  Would 
> you agree that fancy photorealistic "publication quality" 
> graphics are often discouraged by journal editors anyway?
> 
> Thanks!
> 
> Leif Olson
> Eastman Kodak Research Laboratories
> 
> 
> 
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