Hi Miguel,
Thanks for the advice on using .cif format. I can use the .cif format
rather than the .pdb format.
HOWEVER
Raw .cif files for minerals only contain information on the empirical
formula. Halite (rock salt) is NaCl. The .cif file for Halite only contains
two atoms, Na, and Cl and the jmolapplet depiction of halite shows the 2
atoms which look "incomplete" and do not represent the mineral structure.
What Jmol needs is to be able to take the symmetry operators and "pack" the
unit cell with more NaCl elements to illustrate the cubic array.
The following example illustrates this "packing" ability. I used Mercury to
generate the .cif files.
1. Raw cif of Diopside http://www.webmineral.com/jmol/raw.html
2. Expanded cif of Diopside http://www.webmineral.com/jmol/global.html
3. 2x Expanded cif of Diopside http://www.webmineral.com/jmol/global1.html
This is the reason why I can't use the raw cif files.
Dave,
> I have added jmol capability to webmineral.com
> (http://www.webmineral.com/jmol/index.shtml). There are about 12,000 .cif
> files I need to go through and convert to .pdb format. Perhaps the group
> 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 of
> "OH" (hydroxyl) and "Wat" (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 "OH" or "WAT" as the atom name without an element symbol
then Jmol cannot figure out what the element is.
Perhaps we could explicitly support "OH" and "WAT" as special atom names
... 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=Alunogen
> or has hydrogens for OH
> http://www.webmineral.com/jmol/structure.php?id=Aksaite.
>
> Any Ideas to get the proper "atom" to show up?
Use .cif format.
If Jmol has problems with properly-formatted .cif files then we will
improve the .cif reader.
Miguel
Dave Barthelmy <[EMAIL PROTECTED]>
http://web.wt.net/~daba
3607 Aldergrove Dr.
Spring, TX 77388
(281) 350-4120 (home)
(281) 288-9410 (fax)
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