[Chimera-users] presets criteria

[Eric Pettersen]

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 at 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 at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20070717/86fec5e4/attachment.html>