From owner-chemistry@ccl.net Wed Jan 11 19:21:00 2006
From: "forli_-_unisi.it" <owner-chemistry(!)server.ccl.net>
To: CCL
Subject: CCL: Simple molecular graphics
Message-Id: <-30463-060111185528-7109-MnBHrtrGKrx3ioJ2o5B+3Q(!)server.ccl.net>
X-Original-From: forli]=[unisi.it
Date: Wed, 11 Jan 2006 20:13:25 +0200 (MET-DST)


Sent to CCL by: forli]|[unisi.it
Dear Leif
Try Pymol! It's powerful, well supported around the web, support
raytrace of nice pics (internally), is easy enough to play with, and
it's free.
Linux, Mac and Win are supported.

http://pymol.sourceforge.net/

Hope this helps,

Stefano


>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>
>
>


---

***********************************
 Stefano Forli
 Dip. Farmaco Chimico Tecnologico  
 Universita' degli Studi di Siena  
 Via Aldo Moro                    
 I-53100 Siena, Italy              
 Phone: ++39 0577 234307      
 Fax: ++39 0577 234333   
 e-mail: forli * unisi.it
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