[Chimera-users] How to find a specific motif from a protein structure?

Elaine Meng meng at cgl.ucsf.edu
Wed Aug 5 14:36:51 PDT 2015

Hi Jing,
To search for a motif in the sequence of a structure you already have open, first show the sequence of the structure (main Chimera menu: Favorites… Sequence), then in the sequence window’s menu, choose Edit… Find Subsequence (exact match), or Find Regular Expression, or Find PROSITE Pattern.  Any matches to your search will be highlighted with boxes on the alignment and you can click on the box to select the corresponding structure residues.


To find other structure features such as activation loop, in general it may be necessary to read the paper that goes with the structure to find out which residues are in that feature.  Then you would specify the residue numbers in Chimera. 

However, if the features are included in the UniProt annotations for that structure’s sequence, another way is using the PDB/UniProt Info tool (in menu under Tools… Sequence).  That works for structures that are in the RCSB PDB database; it looks up the UniProt sequence and annotations for the structure and opens a sequence window including the annotations.  The “region browser” window that will automatically open along with the sequence will list the different annotations, and you can click a checkbox in that list to display each annotation of interest as a box on the sequence.


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

On Aug 5, 2015, at 4:30 AM, Jing Tang <jing.tang at helsinki.fi> wrote:

> Hi,
> I would like to know how to identify a given motif such as DFG in a protein kinase structure.  I have thought to use “select: asp,phe,gly” but it found all the residues rather than the motif.
> A related question would be then how to identify the activation loop or other more specific domains such as p-loop p+1 loop etc. from a structure.
> Thanks,
> Jing

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