[Chimera-users] Identifying surface residues

Elaine Meng meng at cgl.ucsf.edu
Fri May 29 12:36:24 PDT 2009

On May 29, 2009, at 11:34 AM, Soumya Ghosh (Systembiologie) wrote:
> Dear Dr. Elaine Meng,
> Thanks a lot for your kind help.Your suggestions helped me a lot. I  
> tried to ask you another question. If I want to see the  
> Vanderwaal's interaction between the two molecules, is it also  
> possible with this software? Can you kindly suggest me how I should  
> proceed further. Also if I want to see different type of bondings  
> like intramolecular / intermolecular: covalent or ionic or any  
> sorts is it possible to see with this CHIMERA.
> Eagerly waiting for your kind reply,
> Thanks with regards,
> Soumya

Dear Soumya,
It is better to send Chimera questions to chimera-users at cgl.ucsf.edu  
instead of to me directly, unless you are including private data.

You can use Chimera to show all kinds of interactions, but it may be  
necessary to take a little time to become familiar with the tools and  
with Chimera in general.  You can use "Help... Search Documentation"  
to look for topics such as "find interactions".

See the tools "FindHBond" (equivalent command "findhbond") and "Find  
Contacts/Clashes."   Both tools are under "Tools... Structure  
Analysis" in the menu.  You can click the "Help" button on each tool  
to see its manual page.  Both tools provide ways to control whether  
you are looking at intermolecular or intramolecular interactions.

These tools are also used in the Structure Analysis and Comparison  

Of course, covalent bonds are shown as connections in the graphics  
window.  Metal coordination bonds are shown with dashed pseudobonds.

FindHBond identifies hydrogen bonds, which could include both polar  
and charged groups.  To only find salt bridges (H-bonds between  
charged groups), you could either get the total results and filter  
them yourself, or you can select only charged groups beforehand and  
then tell FindHBond to only use the selected atoms.  More detailed  
instructions can be found in this previous post:

Find Contacts/Clashes finds contacts of all kinds.  To only find some  
subset of those, you could either filter the output, or limit the  
input, similar to the situation for FindHBond described above.

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

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