Jmol users,
This might be a popular option.... I don't know of any other program that
can do this. Correct me if I'm wrong!
We had an idea yesterday and decided to give it a try, and --- what do you
know, it worked...
version=12.1.51_dev
# new feature: set pdbAddHydrogens
# -- for file loading
# -- adds hydrogens to ALL groups, including HET groups
# -- also adds all multiple bonds to PDB files
# -- for altlocs you should use load option FILTER "CONF 1" (or some other
specific configuration)
# -- atom numbers are appended to maximum number in file
# -- hydrogen addition is saved in the state in the form of DATA commands
that store the RCSB ligand files for nonstandard and HETATM groups.
For example: see http://stolaf.edu/people/hansonr/jmol/hydrogen/examples.htm
Notice -- all the protein and DNA residues have proper multiple bonding and
hydrogens.
Of course, there are a few caveats. HIS is displayed with two H atoms
(protonated). I figure if you don't want one, you can always use the model
kit to delete it.
Placement of H atoms on oxygens is not optimized.
If not from a saved state, it can take some time to transfer files from RCSB
to complete the ligands; the algorithm itself is virtually instantaneous, as
observable if you do this from a saved state, but that first load of ligands
takes (for me) a few seconds per ligand type.
You can try this for yourself at the RCSB site using:
http://www.rcsb.org/pdb/explore/jmol.do?structureId=3HZ3&bionumber=1&JMOLJAR=http://stolaf.edu/people/hansonr/jmol/JmolAppletSigned.jar
and entering, for example:
set pdbAddHydrogens; load ""
Comments, suggestions, feedback appreciated!
Bob Hanson
Erik Wyatt
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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