[Chimera-users] finding salt bridges

Elaine Meng meng at cgl.ucsf.edu
Sat Feb 28 12:40:43 PST 2009

Hi everybody,
At long last, a complete explanation of using "findhbond" to find only  
salt bridges:

> Select charged functional groups and then use the FindHBond option  
> to find only H-bonds with both ends selected.  This option is in the  
> GUI and is also available as a keyword of the findhbond command:
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html 
> >
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html>
> Selecting charged functional groups:
> The following command selects atom types in charged groups commonly  
> found in amino acids and nucleotides, excluding histidines:
> select Ng+ | N3+ | N2+ | O2- | O3-
> That's better than using residue names, because it also gets the  
> free N-term and C-term and most charged ligand functional groups,  
> and it is not necessary to specify "side chain only" to exclude  
> neutral backbone hydrogen-bonding groups.  However, we don't have a  
> thiolate sulfur atom type; if there is specific Cys thiolate you  
> wish to consider, you would have to add that sulfur to the selection  
> manually.
> Another caveat is that the selection command above does not include  
> histidines. You could use
> select Ng+ | N3+ | N2+ | O2- | O3- | :his at nd1,ne2
> but that would get nitrogens in neutral histidine sidechains as well  
> as the positively charged.  A more correct possibility with more  
> steps is to: add hydrogens (AddH tool or command addh), add charge  
> (Add Charge tool or command addcharge), and then use
> select Ng+ | N3+ | N2+ | O2- | O3- | :/amberName=HIP & @nd1,ne2
> (The charge assignment process identifies which histidines are  
> doubly protonated and assigns them the AMBER residue name HIP.)

There are additional atom types for charged functional groups, but  
they would not occur in proteins.  If manmade ligands are involved,  
however, you may want to take a look at the list of atom types and  
possibly add N1+,P3+,S3+,S3- (no, that's not thiolate even though it  
sounds like it) to the selection command.

Apologies for the earlier incomplete explanation.
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Feb 27, 2009, at 12:50 PM, Elaine Meng wrote:
> I just realized my previous suggestion would not include the
> positively charged histidines, and I have not been able to think of a
> selector for just those nitrogens.
>> 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

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