[Chimera-users] finding interaction domains

Elaine Meng meng at cgl.ucsf.edu
Tue Oct 15 16:29:20 PDT 2013


Hi Edward,
I'm not sure exactly what you mean. If you mean you have a structure in which one chain is interacting with another and you want to find which atoms are interacting, you could use the Find Contacts/Clashes tool  (in menu under Tools… Structure Analysis) or the "findclash" command:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>

There are examples of using findclash in tutorials:
(1) Opened Interface image tutorial, the command is used in the "Background and Setup" section
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.html>
(2) Structure Analysis and Comparison tutorial, the tool is used in the "Distances, H-Bonds, Contacts" section
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>

If you mean that some chain of your structure has different domains and you just want to see which parts of the chain are which domains, you may need to look up that information outside of Chimera.  If the protein is annotated with domains in UniProt, there is a convenient way in Chimera:
(a) start PDB/Uniprot Info (in Chimera menu under Tools… Sequence) and choose the chain of interest.  Two additional windows should appear, the sequence of the chain and the Region Browser listing annotations of the chain.  
(b) In the Region Browser, scroll to find the domain annotation of interest, check its Shown box to show it as a colored box on the sequence
(b) In the sequence window, click on the colored box to select all the corresponding residues in the structure
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/uniprot/uniprot.html>

If UniProt doesn't have domain annotations for that protein, however, you may need to look in some other resource outside of Chimera.  For example, you could search for the structure in the SCOP database <http://scop.mrc-lmb.cam.ac.uk/scop/> and then manually enter residue ranges in the Chimera command line to color or select that part of the structure.

I hope this helps.  If I answered something different than you were asking, you need to provide more information in your question.
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 Oct 13, 2013, at 3:32 PM, edward el chamy <edward_elchamy at hotmail.com> wrote:

> Hey
> i am a student using chimera 1.8
> i have a question: how we find on a specific chain the different interaction domains?
> Thanks a lot




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