From: Ben Chern (futuredream.1_at_gmail.com)
Date: Wed Mar 26 2008 - 20:44:00 CDT

Tahnk you very much.

"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."

That's what I want to get. The 'primitives' are the elements the VMD
renderred to display for us. It also includes the atoms which compose the
secondary structure.
I think the output of the bundled "stride'" program is the "primitives" I
want.
As to the quaternary structure, it's the atoms who are at the same chain.
How about the tertiary structure? Which atoms are at the same tertiary
structure?

On Wed, Mar 26, 2008 at 7:15 PM, Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu>
wrote:

> 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>
>
> --
> =======================================================================
> 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
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
>

-- 
Ben