[Molvis-list] polygons

Inbal Tuvi-Arad inbaltu at openu.ac.il
Fri Feb 11 02:30:34 EST 2005

Dear Sinasi,
  A possible solution will be to change the connectivity in the coordinate
file such that a polygon is drawn and not the real chemical bonds.  If you
work with a pdb format, you could have 2 models in your file - one with the
chemical connectivity and the other with the polygon connectivity.  I can
send you a sample file if needed.  If I'm not mistaken, the default
presentation will be of both models, so you'll be able to see both the
molecule and the polygon around it.  However, this change should be done
manually - I'm not familiar with software that can change the connectivity
in this way.

Good luck,


Dr. Inbal Tuvi-Arad
Department of Natural Sciences
The Open University of Israel
108 Ravutski St., POB 808, 
Raanana, 43107, Israel
Tel: 972-9-778-1773 
Fax: 972-9-778-0661
Email: inbaltu at openu.ac.il

-----Original Message-----
From: molvis-list-bounces+inbaltu=openu.ac.il at bioinformatics.org
[mailto:molvis-list-bounces+inbaltu=openu.ac.il at bioinformatics.org] On
Behalf Of Sinasi Ellialtioglu
Sent: Thursday, February 10, 2005 7:59 PM
To: molvis-list at bioinformatics.org
Subject: [Molvis-list] polygons

Hi everybody,

I am a Rasmol user, and since this list is now bringing together a 
multi-software society
I would like to ask if drawing polygons around oxygen octahedra or 
tetrahedra in various
crystal structures (like in YBCO) is possible in any of Rasmol, Jmol, 
Chime, Protein Explorer, or else.
I am aware that it is possible to have such a functionality in ATOMS and 
it would be more convenient for me if I can solve my problem within the 
domain of my reach.
For instance, is it possible to add such a property to, say, "cartoon" 
comment in Rasmol?

Your comments and suggestions will be appreciated very much.
Sinasi Ellialtioglu

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