VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Mar 26 2008 - 06:15:42 CDT

On Wed, 26 Mar 2008, Ben Chern wrote:

BC> Hello,

ben,

BC> given a PDB file, can we get the secondary structure, tertiary
BC> structure and quaternary structure?

BC> What I mean is not the picture displayed by the VMD, but the
BC> primitives(perhaps triangles) generated to display.

it is not quite clear to me, what you mean by "primitives".
could you elaborate a little more?

VMD uses the bundled "stride" program to get secondary structure
assignments (used for cartoon representations and "structure"
colorization). the result of those assignment can also be
retrieved via "selection" on the script level.

cheers,
   axel.

BC>
BC> Thank you.
BC> 

-- 
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Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
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If you make something idiot-proof, the universe creates a better idiot.