[Chimera-users] how to find clashes/contacts for residue of our interest?

Elaine Meng meng at cgl.ucsf.edu
Wed Nov 23 08:25:16 PST 2016

Hi Surya,
This sounds more like a question about selection.  There are many ways to select, not just the menu. For example, you can select using the mouse (Ctrl-click) in the main window.  If you select one atom or bond, then you can use the keyboard up arrow to increase the selection to the whole residue.  Or, you can use a command like “select :32.A” (select residue 32 in chain A; first show the Command Line from the Favorites menu).  Or, you can show Sequence (also in Favorites menu) and then select the residue in the sequence window.  Here is the page about selection:

There is an example of using Find Clashes/Contacts in this tutorial:

Or instead of using the Find Clashes/Contacts graphical interface, you can use the “findclash” command and just name the residue directly instead of selecting it, for example to find clashes and other contacts:

findclash :32.A test other overlap -0.4 hb 0 reveal true

…or to find only the clashes, if any (unfavorable because they are too close):

findclash :32.A test other overlap 0.6 hb 0.4 reveal true

See manual for additional command options.

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 Nov 22, 2016, at 6:59 PM, Seera Suryanarayana <palusoori at gmail.com> wrote:

> Dear chimera users,
> I am new to chimera and I looked into the manual. But I did not get
> perfectly that how to use find clashes command. I would like to know
> clashes/contacts of residue of my interest. But I am not able to
> select the residue in graphical interface under select tool. Kindly
> tell me how to find clashes/contacts ASP32 in a protein.
> Thanks in advance
> Surya
> Graduate student
> India.

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