VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Mar 26 2008 - 21:26:46 CDT

Ben,
  STRIDE doesn't output any geometric data, it just assigns a
secondary structure "type" to each atom/residue. All of the
geometry that is displayed on the screen is computed internally
inside VMD. VMD interprets the secondary structure assignments
that STRIDE has made for each atom/residue and uses that information
when it builds the graphics/geometry for the display. The actual
triangles that compose the displayed structure can be exported
from VMD in various formats using the File->Render menu. If you
want the secondary structureh codes assigned to the atoms/residues
by STRIDE, you can get those using the atomselect command in VMD,
or you can run STRIDE for yourself and use your own software
to interpret its output.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Mar 27, 2008 at 09:44:00AM +0800, Ben Chern wrote:
> 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 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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