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

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