[Chimera-users] Suggestion for Metal Geometry Feature

Elaine Meng meng at cgl.ucsf.edu
Mon May 7 10:21:57 PDT 2007

Hi Walt,
Thanks for your suggestion.  What was that reference?

I should mention that Chimera does not create bonds automatically -  
it just takes the bonds and links specified in the input, and makes  
those to metal ions into "pseudobonds" (those purple dashed lines).   
We were thinking that such a tool should probably look in the  
vicinity of the metal for additional ligands regardless of whether  
they were explicitly bonded according to the input file.  Other  
issues include  geometric tolerances and how to deal with missing  
ligands (potential water sites).

Your suggestion will be added to the list; just be forewarned that  
the list is very long!

p.s. happily I'm not the only "answerer" on this list, but you're  
right, I do answer many of the general usage questions!
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On May 4, 2007, at 9:53 AM, Walter Fast wrote:

> Hi Elaine (I think!),
> I know there is a measure angle feature in Chimera.  I have been  
> using this
> to define metal ligand geometries in our protein structures (for  
> example,
> distinguishing between square pyramidal and trigonal bypramidal  
> geometries).
> Maybe if there is enough interest, this could be an automated  
> feature in the
> future where a metal ion is selected and then all of the ligands  
> and angles
> are automatically displayed along with an assigned geometry.
> We've been using the following reference for assigning them.
> Just a suggestion!
> Many thanks,
> Walt
> -- 
> Walter Fast, Ph.D.
> Assistant Professor
> The University of Texas at Austin
> College of Pharmacy
> The Division of Medicinal Chemistry
> Phone:  (512) 232-4000
> Fax:    (512) 232-2606
> Lab:    (512) 471-5839
> Email:  WaltFast at mail.utexas.edu
> http://www.utexas.edu/pharmacy/divisions/medicinalchem/faculty/ 
> fast.html
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