Sorry, they aren't that radically wrong. I was just excising pieces and I didn't grab all the lines. For example, you will see:
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'
So the loop business is all there correctly. There are no "serious problems" with these files. Jmol reads them just fine. They are certainly not doing us a disservice.
I'm sure if you can find the place in the CIF format description that specifies that the trivial "x, y, z" must be present, they will see to it that it gets in there. But it shouldn't be a big deal. I wouldn't obsess over it.
Oh, I see now. ICSD does not report the (trivial) 'x, y, z'. I think it's safe to say 'x, y, z' is implied and not necessary.
1 I think it is extremely unsafe for ICSD to omit it.
Why would you say that, if every possible space group has this? These entries would be used to take the starting positions and generate the symmetry-equivalent positions. You always start with the primary (x,y,z)
coordinates in hand. It's not like it's a programming dilemma, right?
But, I agree, it would be SMART to have 'x,y,z' there somewhere.
I'm guessing that any CIF file showing only fractional coordinates must contain this record.
Strictly not. All crystals implicit have 'x,y,z' and that would be the default. Rather more difficult, you can specify the spacegroup and look the positions up in Int. Tab. for Cryst. unfortunately there don't seem to be any open collections of space group operators
Amazing. All CIF files should (IMHO) be required to specify the symmetry-equivalent positions irrespective of what the space group is named, at least if only the primary coordinates are provided. I would have thought that these operations would be the key set of information, not the name.
I'm sure web can get this list from IUCr.
No - I asked on Monday
But it's a BIG list. There are
230 space groups and about 40 optional origins/coordinate systems (see ftp://ftp.iucr.org/pub/cif_sym_1.0.dic).
This is the dictionary governing the symmetry, not the operations themselves.
right, you need them all.
Several of the 230 groups have 96 equivalent positions, and some have 192.
Correct.
You want to list all of these somewhere in Jmol code? I think this is going to be a big burden on Jmol.
It isn't unreasonable for a crystallographically aware program (like SHELX and now Jmol) to have access to a lookup-table of space groups. This need only be accessed if the author includes the space group symbol but not the positions. Also if the space group is Hall it is possible to calculate the operators from the symbols.
Personally, I think this is a flaw in the CIF standard.
I'd regard it as a problem in conformance. Theoretically it is perfectly allowable to give just the spacegroup and refer the reader to International tables but it makes it difficult for program writers. I think some authors for some journals do not include the operators and should be strongly urged to do so
This business is SO tricky, it only seems reasonable to include all positions.
I agree. There are shortcuts in some listings where the operators deducible from centre of symmetry and also the lattice centering are omitted. This reduces 192 in (say Fm3m) to 24 (192 = 24*2(centre)*4(lattice)
Don't atoms with different equivalent positions have different labels, anyway?
Sometimes, but they are not normally included in the CIF.
Am I understanding correctly that what we are after here is being able to read CIF files that contain only
loop_ _atom_site_label _atom_site_type_symbol _atom_site_symmetry_multiplicity _atom_site_Wyckoff_symbol _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_B_iso_or_equiv _atom_site_occupancy
information for the (x,y,z) identity operation? For example, buckyball with one single atom listed?
Buckyball would actually require more atoms as crystals do not support icosahedral symmetry. But the logic is correct. Thus an octahedron of B atoms (B6) might just have one atom reported.
I'm not familiar with such files, although I understand that "in the old days" this is how just about all crystal files were delivered.
Correct
Where are they arising from? Peter, maybe you sent us some copies. I think I missed that. Is this possibly something we can avoid?
No. I am currently starting discussions on the CIF discussion group as to how to manage symmetry and disorder
I have implemented code in Molecular Origami that ALMOST does this. But I had trouble with identifying the origins. My solution was to identify a set of "minimum operations" that defined each point
group. It was very compact. For example,
Fd-3m(origin at CxCyCz)=227,192,F 4102/d1 -3111 2023/m Fd-3m(origin at i)=227,192,F 4131/d -3 2022/m1 Fd-3c(origin at CxCyCz)=228,192,F 4102/d3 -3333 2023/c Fd-3c(origin at i)=228,192,F 4113/d -3 2020/c1 Im-3m=229,96,I 4/m -3 2/m Ia-3d=230,96,I 4120/a2 -3 2021/d
(Don't ask what all this means. I simply give these as examples of how 192 or 96
equivalent positions can be coded into a single short expression.)
They can actually be completely encoded in the Hall space group symbol and this should be the preferred way of doing this. If you create code that translates Hall symbols that would be very useful. From what you say, it shouldn't be too hard to adapt your code
Unfortunately that won't be enough. We have from the specs:
; Hermann-Mauguin space-group symbol. Note that the H-M symbol does
not necessarily contain complete information about the symmetry
and the space-group origin. If used always supply the FULL symbol
from International Tables for Crystallography, Vol. A (1987) and
indicate the origin and the setting if it is not implicit. If
there is any doubt that the equivalent positions can be uniquely
deduced from this symbol specify the _symmetry_equiv_pos_as_xyz
or *_Hall data items as well. Leave spaces between symbols
referring to different axes.
;
ftp://ftp.iucr.org/pub/cif_core.dic
Be aware that if you are going to do this right, you also have to take into account (ah, so fun!) trigonal and hexagonal coordinates.
Yes
I have spent enough time on this problem to know it is a VERY serious project.
Yes.
OTOH it is formally completable. I can give you encouragement!
me? not me...
If you have some ICSD CIFs that you think are broken, please send them to me (though I can't do much for ca 2 weeks). 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.
again, download any file from their www interface. None have (x,y,z)
If you want CIFs certified to be correct, look at (say)
http://journals.iucr.org/e/issues/2004/10/00/EAtxtisscontsbdy.html
and click on any link denoted by CIF. The inorganic ones should give you an idea of how to manage highly symmetric structures
P.
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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