From: Robert H. <ha...@st...> - 2013-06-23 22:59:40
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Eric, I'm glad to see you like the idea. It's a rather interesting mechanism of adding H atoms, as you have noticed. It is correct that it works only if the structure has no H atoms. The idea being that if a structure has H atoms, then we shouldn't mess with it EVEN if pdbAddHydrogens is set. As you point out, there are convenient ways around that -- removing H atoms during the load with load FILTER "!_H" is a great solution to that. The way to do this allowing H on water, if you really think that is meaningful (convince me!) is to load the file first with no H atoms but with set pdbAddHydrogens TRUE, then do set pdbAddHydrogens TRUE load =1lcd 1 filter "!_H" delete HOH set appendnew FALSE load append "" 1 FILTER "[HOH]" Notice that I'm just loading one model. For all three it looks like there is a bug. I can't get it to work myself. On Sun, Jun 23, 2013 at 5:32 PM, Eric Martz <em...@mi...>wrote: > I am very pleased with pdbAddHydrogens and the resulting double bonds > on HETATM as well as ATOM. Wow! I would like to make this the default > load for all PDB files in FirstGlance in Jmol. > > I find that Jmol does not add hydrogens if the model already contains > hydrogen. For example > > set pdbAddHydrogens true > load =1lfa > > does NOT add the missing hydrogens and the double bonds are NOT > installed. (1lfa has hydrogens only on oxygens and nitrogens.) > > So I found that this works: > > set pdbAddHydrogens true > load =1lfa filter "!_H" > > Now it appears that all the hydrogens are added and double bonds are > installed. > > However, this mode does not add hydrogen to water, quite understandably. > > Some PDB files have hydrogen on water, e.g. 1lcd. Even if all the > hydrogen in present in the PDB file, I want the double bonds to be > installed. So here is my question: > > Can I load, filtering out all hydrogen that is NOT on water? I've > tried what I can think of without success. > > Alternatively, perhaps we need a setting that will make > pdbAddHydrogens work even when there are hydrogens in the data file > (leaving any hydrogen on water untouched). > > Thanks, Eric > > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Windows: > > Build for Windows Store. > > http://p.sf.net/sfu/windows-dev2dev > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 |