On Oct 17 2004, SourceForge.net wrote:
Bugs item #1032542, was opened at 2004-09-22 13:20 Message generated for change (Comment added) made by migueljmol You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1032542&group_id=23629
Category: File Input/Output Group: None >Status: Closed >Resolution: Fixed Priority: 5 Submitted By: Bob Hanson (hansonr) Assigned to: Miguel (migueljmol) Summary: cif file read error
Initial Comment:
We need a quick cif fix. ICSD has fixed their CIF
problem; now Jmol needs to adapt a bit to handle an odd
situation. CIF files exist that have no coordinate
value for some atoms, even though they are listed in
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
specifically, it is possible to have undetermined-position atoms here. Recommend Jmol simply skip these as though they were comments. They are being listed as:
H1 H1+ 4 e - - - 0. 8.
(formerly there were no hyphens there, so the whitespace parsing of course threw the reader off)
Attached is a new file Jmol needs to be able to read.
Bob Hanson
This is something I am taking up with CoreChemCif... I think the semantics are that the atom is known to be present somewhere but hasn't been determined. Certainly for the present it should be omitted from the display. But if Jmol caluclates the MWt or other properties it may need to be included.
P.
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>Comment By: Miguel (migueljmol) Date: 2004-10-17 22:47
Message:
Logged In: YES user_id=1050060
Per our discussions on the mailing list, instead of hyphen these should be '?' or '.'
In either case, the CifReader now deals with it and discards
cif atoms with unrecognized/invalid coordinates.
Jmol can read attached file
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Comment By: Miguel (migueljmol) Date: 2004-09-29 19:52
Message:
Logged In: YES user_id=1050060
Good grief :-(
I suppose that ignoring these lines won�t be difficult ...
... but I wonder whether or note these files are valid .cif files ? :-/
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