[Chimera-users] FINDING SALT BRIDGE

Elaine Meng meng at cgl.ucsf.edu
Sat Apr 8 09:07:00 PDT 2017


Hi Qistina,
(1) For finding salt bridges, basically you would use the “findhbond” command or the FIndHBond tool, but limit it to only the formally charged atoms instead of all H-bonding atoms.  For details, please see this previous post and links therein:

<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-April/006218.html>

That describes selecting only formally charged H-bonding atoms, but in all residues.  In your case there would be an extra step after that to unselect atoms not in your 50 residues of interest, for example command:

~sel ~ :10-34.a,51-75.a

(unselect atoms that are NOT in 10-34 in chain A or 51-75 in chain A)… and then find H-bonds only for the remaining selected atoms.

(2) You can measure distances with Ctrl-click one atom, Shift-Ctrl-doubleclick a second atom and then choosing to “Show Distance”.  Or, select two atoms and use the Distances tool (in menu under Tools… Structure Analysis).  Or, use the “distance” command with “sel” (if two atoms selected) or command-line specifiers of those two atoms.

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#distances>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html> 

This tutorial includes examples of measuring distances and finding H-bonds:
<http://www.rbvi.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 Apr 8, 2017, at 4:45 AM, Qistina Hassan <qistina8005 at gmail.com> wrote:
> 
> Hi,
> 1. How to find salt bridges of 50 selected residues in a protein using Chimera? 
> 2. How to measure distances of one residue to another residues to determine if the residues could form salt bridge or not? 
> 
> Thank you,
> Qistina




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