[Chimera-users] hydrophobic pocket

[Elaine Meng]

Hi Bala,
There are several possibilities, but one easy thing is to use  
"Presets... Interactive 3 (hydrophobicity surface)" in the Chimera  
menu.  This will display a molecular surface and color it by amino  
acid hydrophobicity (Kyte-Doolittle scale) from dodger blue at the  
most polar end, to white, to orange for the most hydrophobic.  You  
can then visually inspect the surface for orange-ish pockets.
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/menu.html#menupresets

A figure showing a hydrophobic pocket is included in the new  
"Structure Analysis and Comparison" tutorial:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ 
squalene.html#surfaces

You can use Render by Attribute to map different coloring schemes to  
Kyte-Doolittle hydrophobicity, as described in that tutorial.  You  
can also read in different hydrophobicity scales as described here:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html

That covers the "what is hydrophobic?" part of the question.  As for  
"what is a pocket?", you may wish to simply use visual inspection, as  
described above.  Another approach is to use the CASTp database of  
pockets - very useful, but it does not include everything in the  
PDB.  You can open a structure and its CASTp pocket data in Chimera  
using "File... Fetch by ID"  or the command "open", for example:

open castp:2gbp
or
open castp:4enl

Just use the PDB ID of your structure.  However, you may get a  
message saying your structure is not in that database.  Here is the  
documentation on viewing CASTp data in Chimera:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/castp.html

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html