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 [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
