[Chimera-users] on beta strand assignmet by chimera

Elaine Meng meng at cgl.ucsf.edu
Thu Jul 2 09:55:55 PDT 2015


Dear Smith,
If the PDB files came from the Protein Data Bank repository, generally the proteins already have secondary structure assigned in HELIX and SHEET records.  If so, Chimera just uses those assignments.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#secondary>

If the PDB file of a peptide/protein doesn’t have HELIX and SHEET records in it, then it runs a method “ksdssp” described here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html>

If you don’t like the results for some reason, you could try re-running the “ksdssp” command (or the “compute SS” function in the Model Panel) with different (nondefault) parameters, or just manually assign residues as helix or strand however you like with the “setattr” command, as shown in the lower part of this previous post:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-January/009574.html>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jul 2, 2015, at 6:09 AM, Smith Liu <smith_liu123 at 163.com> wrote:
> 
> Dear All,
> 
> I have a protein, which contains fragment aa 239-251. The protein has been fitted its map with 2 different (minor difference) resolution, and thus I have 2 PDB. For PDB 1 (the first resolution), the H-bonds inside aa 239-251 include:
> #2 Gly 245.A N-Asn 242.A O 2.708A
> #2 Asn 242.A N-Tyr 246.A O 3.120 A
> #2 Val 248.A N-Val 240.A O 3.120 A
> #2 GLN 251.A N-Ser 238.A 0 3.033 A
> 
> For PDB 2 (the second resolution), the H-bonds inside aa 239-251 include:
> #0 Gly 245.A N-Asn 242.A O 2.715A
> #0 Asn 242.A N-Tyr 246.A O 3.1206 A
> #o Val 248.A N-Val 240.A O 2.858 A
> #0 GLN 251.A N-Ser 238.A 0 3.074 A
> 
> Naked eye check found the H-bonds in PDB 1 were almost the same H-bonds in PDB 2.
> 
> However for PDB 2, aa23-242 and aa 247-251 form 2 strands, but for PDB 1, it was a un-disconnected loop for aa 239-251.
> 
> Will you please explain how chimer assign beta strand?
> 
> Best regards.
> 
> Smith
> 



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