[Chimera-users] Hydrogen bonds for specific residues

Elaine Meng meng at cgl.ucsf.edu
Sat Feb 10 14:47:40 PST 2018


Hi Surya,
You can select residues with the mouse or with the “select” command, as outlined here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html>

You can specify residues in commands by their numbers, and also by their chain IDs if you have more than one chain, as explained here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#hierarchy>

For example, command: select :20-50.a,:95
(there are many more examples in the link given above)

You can also specify residues directly in commands like “color” and “hbonds” without having to select them.

One approach is to use the “hbonds” command (maybe also “select” if you use hbond’s “selrestrict” option) to calculate only the H-bonds for specific residues.  An alternative approach would be to just calculate a larger set of H-bonds (or even all H-bonds) and then process the results to pick out the lines you care about.  The “hbonds” command has options to send results to the Reply Log and/or save them in a text file.  You will have to spend some time trying commands and seeing if they give what you want.

The manual pages explain the options:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/select.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html>

After you figure out the right command(s) to give you what you want for a single frame, then you could get even more fancy and make a script to to automatically execute at each frame during trajectory playback, as in this tutorial:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Feb 9, 2018, at 10:52 PM, Seera Suryanarayana <palusoori at gmail.com> wrote:
> 
> Dear users,
> I have done simulations for 100ns and I generated clusters. I want know the hydrogen bonding during simulations for specific residues. Kindly let me know how do we select particular residues for hydrogen bonding in chimera.
> Thanks in advance, 
> Surya




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