Peter Murray-Rust wrote:
At 08:06 15/10/2004 -0500, [EMAIL PROTECTED] wrote:
I am in Chicago and don't have full access to my data, but I'd like to contribute to this discussion.
CIF Symmetry: The key here should be
loop_ _symmetry_equiv_pos_site_id _symmetry_equiv_pos_as_xyz 1 '-x, y, -z+1/2'
this is probably illegal. The identity operation is always required
Sorry. I wasn't listing the whole set. I had to work from a hotel computer. The whole set was:
1 '-x, y, -z+1/2' 2 '-x, -y, z+1/2' 3 '-x, y, z' 4 '-x, -y, -z' 5 'x, -y, z+1/2'
But, still, 'x, y, z' is not there, is it? A quick look turns up the following without 'x, y, z':
ic30516.cif _symmetry_equiv_pos_as_xyz 1 '-x, y, -z+1/2' 2 '-x, -y, z+1/2' 3 '-x, y, z' 4 '-x, -y, -z' 5 'x, -y, z+1/2' loop_
ic26060.cif _symmetry_equiv_pos_as_xyz 1 'x+1/2, y, -z+1/2' 2 'x, -y+1/2, z+1/2' 3 '-x+1/2, y+1/2, z' 4 '-x, -y, -z' 5 '-x+1/2, -y, z+1/2' 6 '-x, y+1/2, -z+1/2' 7 'x+1/2, -y+1/2, -z' loop_
ic66547.cif _symmetry_equiv_pos_as_xyz 1 '-z, -x, -y' 2 '-y, -z, -x' 3 '-x, -y, -z' 4 'z, x, y' 5 'y, z, x' loop_
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.
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
I'm sure web can get this list from IUCr. 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). Several of the 230 groups have
96 equivalent positions, and some have 192. You want to list all of these somewhere in Jmol code? I think this is going to be a big burden on Jmol. Personally, I think this is a flaw in the CIF standard. This business is SO tricky, it only seems reasonable to include all positions. Don't atoms with
different equivalent positions have different labels, anyway?
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?
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. Where are they arising from? Peter, maybe you sent us some copies. I think I missed that. Is this possibly something we can avoid? 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.)
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.
I have spent enough time on this problem to know it is a VERY serious project.
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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