[Chimera-users] [chimera-dev] some questions

[Elaine Meng]

On Oct 4, 2010, at 7:44 AM, Gentile, Maria Antonietta wrote:
> Hi,
> I would have some information about CHIMERA. Is it possible to obtain the topology of a protein structure by  using CHIMERA? How? And the second question is about the secondary structure representation of a protein, in my case wiht CHIMERA I am not able to visualize all secondary structure elements, how can I modify the settings for this problem?
> Thank you
> 


Hi Maria,
I don't understand what you are asking, but I will try to answer.

If by topology you mean give you some classification of what fold the protein has, no, Chimera does not do that.  You might try using the "Dali server" or "Cathedral server" (google those) or something similar to compare your structure to a set of other proteins and report back which ones are the most similar.

For the secondary structure, Chimera just uses the information in the input PDB file on which parts are the alpha-helices and beta-strands, and these are shown in the ribbon representation.  If your structure doesn't have HELIX/SHEET information in the input PDB file, Chimera will run the "ksdssp" program to try to identify them.  If you are  not seeing helix and strand where you expect helix and strand, it might be that they HELIX/SHEET information in the PDB file is that way, or that the geometry is irregular/distorted so that "ksdssp" does not identify what you expect.  

EIther way, you could either 

(A) try re-running the secondary structure identification with different parameters (see the "compute SS" function in the Model Panel, which is itself in the Favorites menu, or the command "ksdssp")
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#functions>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html>

(B) just manually change secondary structure assignments.  Several ways are described in this previous post:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2007-April/001514.html>

Elaine

P.S. for Chimera questions the better address is chimera-users at cgl.ucsf.edu  (chimera-dev is for chimera-related python programming questions).
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco


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