[Chimera-users] finding salt bridges

[Elaine Meng]

On Feb 24, 2009, at 1:51 PM, Jeremy Schmit wrote:

> Does Chimera have a tool for identifying salt bridges?  I was able  
> to use the findHbond tool to count intermolecular H-bonds in the  
> lysozyme crystal, but I can't seem to find an analogous tool for  
> salt bridges.  In fact, the term "salt bridge" does not yield a  
> single result on the Chimera site.
> Thanks,
> Jeremy


Hi Jeremy,
There isn't a tool for specifically finding salt bridges, but you can  
consider them as a subset of hydrogen bonds.  You could select only  
atoms in charged functional groups and then limit H-bond detection to  
that selection.

Example commands to first select by atom type and then find the H-bonds:

sel O2- | O3- | N3+ | Ng+
findhbond selRestrict both saveFile ~/mydir/myfile

If the subunits of interest are different chains in the same model  
(same input file), you could then postprocess the output (for example,  
with "grep" on unix) to count only those between the chains.  If each  
subunit is opened as a different model, you could add "intramodel  
false" to the findhbond command.  There are analogous options on the  
FindHBond graphical interface:  "Only find H-bonds with both ends  
selected" and find just the "inter-model" bonds.

findhbond command:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html>
findhbond GUI:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html 
 >
atom types:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/idatm.html>

I hope this helps,
Elaine
-----
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
                      http://www.cgl.ucsf.edu/home/meng/index.html