[Chimera-users] how to find hydrophobic interaction

[Elaine Meng]

Hi Bishwajit,
There is nothing specifically for hydrophobic interactions.  Instead you could use the Find Clashes/Contacts tool (or findclash) command to find all kinds of contacts, both polar and nonpolar (hydrophobic).  Or, in using that tool or command, you could specify only the hydrophobic atoms to check for contacts. In that case, your results would only include hydrophobic contacts.

Find Contacts/Clashes is in the menu under Tools... Structure Analysis.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html>

Findclash command:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>

This tutorial includes finding contacts:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.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 Feb 8, 2012, at 5:16 AM, Bishwajit Das wrote:

> how to find hydrophobic interaction in a docked protein structure......please help me....
> 
> -- 
> BISHWAJIT DAS
> +91-9433237920
> KOLKATA,West Bengal
> INDIA
>