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...
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@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. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/idatm.html Apologies for the earlier incomplete explanation. Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html 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