Suggestion for Metal Geometry Feature
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@mail.utexas.edu http://www.utexas.edu/pharmacy/divisions/medicinalchem/faculty/fast.html
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! Best, Elaine 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@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html 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@mail.utexas.edu http://www.utexas.edu/pharmacy/divisions/medicinalchem/faculty/ fast.html
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participants (2)
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Elaine Meng -
Walter Fast