presets criteria
Hello,
I have upgraded to Chimera 12417 with the new presets for visualization. What are the criteria within "Interactive 1:setup ribbons" preset for determining which residue side chains are depicted as sticks in the binding pocket?
This is a useful shortcut, but I would like to understand the specific criteria.
Thank you very much,
Roberta
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Roberta S. King, Ph.D.
Associate Professor
Department of Biomedical and Pharmaceutical Sciences
College of Pharmacy
University of Rhode Island
Hi Roberta, That preset will depict residues with non-backbone atoms within 3.5 angstroms of: a metal-ion-only residue; a residue classified as ligand (that classification explained here: http://www.cgl.ucsf.edu/ chimera/docs/UsersGuide/midas/surface.html#surfcats). Also, residues involved in a metal-coordination complex will be depicted, though usually that is also covered by the first criteria above. Nucleic acid side chains are always depicted. The idea was to quickly get to a view that would be relatively easy to understand yet still useful for analysis. This was my best first approximation. I'm open to suggestions for improvements.
--Eric Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu
On Jul 17, 2007, at 6:26 AM, Roberta King wrote:
Hello,
I have upgraded to Chimera 12417 with the new presets for visualization. What are the criteria within “Interactive 1:setup ribbons” preset for determining which residue side chains are depicted as sticks in the binding pocket?
This is a useful shortcut, but I would like to understand the specific criteria.
Thank you very much,
Roberta
Roberta S. King, Ph.D.
Associate Professor
Department of Biomedical and Pharmaceutical Sciences
College of Pharmacy
University of Rhode Island
http://www.uri.edu/pharmacy/faculty/king
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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Eric Pettersen
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Roberta King