VMD-L Mailing List

From: Ben Chern (futuredream.1_at_gmail.com)
Date: Wed Mar 26 2008 - 22:12:12 CDT

Thank you very much.

On Thu, Mar 27, 2008 at 10:26 AM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> 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
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> 

-- 
Ben