[Chimera-users] Receptor-Ligand bonding at the LBP

Elaine Meng meng at cgl.ucsf.edu
Thu Feb 13 09:39:44 PST 2014


Hi Graziella,
There is no need to search amino acids one by one.  You can find all contacts of the ligand using "Find Contacts/Clashes," or all H-bonds using "FindHBond", both in the menu under Tools… Structure Analysis. 
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html>

For examples of using these tools, see the Structure Analysis and Comparison tutorial:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>

Or, you can just use a simple distance cutoff around the ligand: if you first select the ligand, you can then use menu "Select… Zone" to also select atoms or residues within a cutoff, which can then be displayed, labeled etc. using the Actions menu.

All of the above could also be done with commands instead of menus/tools.
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 13, 2014, at 7:26 AM, Graziella Portelli <graziellaportelli at gmail.com> wrote:

> To whom it may concern
> 
> I would like to ask if there is a function where the bonds with which the ligand binds inside the LBP of the receptor would be visualised, or whether one has to search the amino acids involved in binding with the ligand one by one?
> 
> I thank you in advance for your time
> 
> Graziella Portelli




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