VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Apr 08 2004 - 16:57:13 CDT

Hi,
  VMD uses the program Stride to calculate the secondary structure
for all of the files it loads. If you want to use the secondary structure
provided in a PDB file, you can use the vmd_read_pdb_ss script in the
VMD script library:
  http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/vmd_use_pdb_ss/

You can also use the atomselect commands to query/alter secondary structure,
some of which is exemplified in the sscache script, also in the
VMD script library:
  http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/sscache/

I suspect that the issue in your case is just that Stride yields a different
secondary structure than what the PDB came with.
Let us know if you have more questions about this.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu
  

On Mon, Apr 05, 2004 at 08:44:44PM -0400, weiz wrote:
> Dear John:
>
> I have a small protein, whose structure looks a little bit different in
> vmd and in rasmol. which is, some fragments are defined as random coil in
> vmd but as sheet or helix in rasmol.
>
> can you tell me what is the definitions of secondary motiffs in vmd for
> the use of graphics?
>
> Wei 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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