Still working out the minor bugs in this, but I think we are on to
something. You can try this out yourself at
http://chemapps.stolaf.edu/jmol/docs/examples-12/simple.htm
On Sat, Jul 2, 2011 at 2:23 AM, Robert Hanson <[email protected]> wrote:
> 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
>
--
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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