> I have added jmol capability to webmineral.com
> (http://www.webmineral.com/jmol/index.shtml). There are about 12,000 .c=
> files I need to go through and convert to .pdb format. Perhaps the grou=
> can comment on some of the problems I have been having.
I strongly advise that you not convert to .pdb format ... it is terrible.=
Jmol supports .cif format.
Q: Are you having problems reading your .cif files with Jmol ?
> 1. Mineral structure data commonly contain references to atoms composed=
> =22OH=22 (hydroxyl) and =22Wat=22 (Water).
Sounds like your .pdb files are invalid.
You probably do not have the proper element symbol in column 70-something=
If you are using =22OH=22 or =22WAT=22 as the atom name without an elemen=
then Jmol cannot figure out what the element is.
Perhaps we could explicitly support =22OH=22 and =22WAT=22 as special ato=
... but I don't want to go down that path yet.
> These appear on jmolapplet as UNK for
> Wat http://www.webmineral.com/jmol/structure.php?id=3DAlunogen
> or has hydrogens for OH
> Any Ideas to get the proper =22atom=22 to show up?
Use .cif format.
If Jmol has problems with properly-formatted .cif files then we will
improve the .cif reader.