Sorry, Peter. This is where email communication tends to break down. Here we go:
a) Some time ago I noted that some CIF files obtained from ICSD were unreadable in Jmol, though read perfectly well by some other readers, including that from CCSD. I discovered that there were mistakes in the atom coordinate specifications. In these particular files, there were atoms listed without coordinates, and there was no placeholder such as "?" or "." or "-". Thus there was a whitespace error. An example was (and still is, at least in this release):
CC=39800
http://icsdweb.fiz-karlsruhe.de/index.php?action=Search&authors=39800
http://icsdweb.fiz-karlsruhe.de/index.php?action=Details&id%5B%5D=18424
Title Crystal structure and thermal stability of barium perrhenate tetrahydrate Ba(ReO4)2*4H2O.
Authors Khrustalev, V.N.;Varfolomeev, M.B.;Shamrai, N.B.;Pisarevskii, A.P.;Struchkov, Yu.T.
Reference Koordinatsionnaya Khimiya (1994) 20, 362-365
and
CC=88086
Title Crystal structure of copper perrhenate tetrahydrate, Cu (Re O4)2 . 4(H2 O).
Authors Varfolomeev, M.B.;Zemenkova, A.N.;Chrustalev, V.N.;Struckov, Yu.T.;Lunk, H.-J.;Ziemer, B.
b) I notified ICSD of this, and they realized that there was an error and got rid of the whitespace error, placing "-" in the place of missing coordinates at my suggestion. (They asked me what character I wanted.) This was my mistake, as I didn't realize there was a standard placeholder. Neither I nor the programmer for ICSD realized that "-" was not the official placeholder. I've notified them that "." is correct, and I have no doubt that they will correct this. The important thing for us is that Jmol needs to be able to handle these "nonvalue" possibilities with "." or "?" present, but, I guess, if you like, not "-".
c) OK, then you made the point, Peter, that some CIF files do not contain the symmetry-equivalent atoms. I wasn't aware of any CIF files like that, and I agree completely that we should think about that. So I asked for examples. Thanks for the link. Yes, I see now at
http://scripts.iucr.org/cgi-bin/sendcif?hb6095sup1
that here is a great example. There are 36 equivalent positions, yet only three atoms listed. Sure makes sense to me. I agree completely that Jmol should
read these files and probably also fill out the unit cell, or possibly the "molecule". (In fact, Jmol does not read this file at all, but that's a different problem; see another message.)
Here is the strategy that I suggest:
1) Jmol must recognize whether all atoms are being shown or just those at the primary positions (x,y,z). This will take some thinking.
2) If it is found that not all positions are represented, then there needs to be
some option that would either leave it as is or "turn on" a symmetry-equivalent display.
3) If symmetry is "enabled" then an algorithm must be in place to set those positions. I suggest:
a) If _symmetry_equiv_pos_as_xyz is present, then use it. Ignore (x,y,z), if
present, as we have those positions already. b) If _symmetry_equiv_pos_as_xyz is not present but if _space_group_name_Hall
is present, then that will do fine. Somehow we should be able to encode
those. c) If neither of these are present, but data_symmetry_space_group_name_H-M
is present, the symmetry possibly may not be read unambiguously. I guess we
could write a correlation table for unambiguous names back to Hall names.For a first-try, we could only implement (a), as it is would be relatively easy.
d) origin of files
>>> Make ABSOLUTELY sure they are direct from ICSD. Then I will send them >>> to David Brown (one of the authors of CIF) and I am sure he will get >>> ICSD to change them. But I have to be sure they came direct from ICSD.
> I would guess that you have got coordinates from somewhere else and > should be very careful of asserting that they came from ICSD.
OK, so I'm absolutely sure they are from ICSD. I think you see, I'm not making any claim here that ICSD is not already working on. These files come directly from their web site. The programmer at ICSD is onto this whitespace/"-" problem.
It's a problem specifically at their web site, and they are aware of it.
Peter, you gave an example from ICSD with symmetry equivilent position (x,y,z) listed. I agree, some are like that. But also see
http://icsdweb.fiz-karlsruhe.de/index.php?action=Details&id%5B%5D=60092
This is from ICSD today. We have:
loop_ _symmetry_equiv_pos_site_id _symmetry_equiv_pos_as_xyz 1 '-y, -x+1/2, z+1/4' 2 'y, -x, -z' 3 'y, x+1/2, z+1/4' loop_ _atom_type_symbol _atom_type_oxidation_number Zn2+ 2. C4+ 4. N3- -3.
No (x,y,z) there. So there's no doubt in my mind that some preparations by ICSD don't include (x,y,z).
Bob
-- Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 mailto:[EMAIL PROTECTED] http://www.stolaf.edu/people/hansonr
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