From: SourceForge.net <no...@so...> - 2008-09-13 16:42:00
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Bugs item #2107269, was opened at 2008-09-12 06:13 Message generated for change (Comment added) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=2107269&group_id=23629 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: File Input/Output Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: dan (danwilson4) Assigned to: Miguel (migueljmol) Summary: CML reader loses crystal lattice information if no symmetry Initial Comment: Jmol (11.6RC14) seems to lose the lattice parameters information if space group information isn't present. In the attached CML file (UO3.cml), the system has a primitive cell, and hence it's not valid to attach a spaceGroup="..." attribute to the <symmetry> tag. However, in such cases, Jmol doesn't read or display the lattice parameters, assuming the system is molecular. ---------------------------------------------------------------------- >Comment By: Bob Hanson (hansonr) Date: 2008-09-13 11:41 Message: Are you saying that the system is no known space group? I see in that file: <symmetry> <transform3> 1.000000000000e0 0.000000000000e0 0.000000000000e0 0.000000000000e0 0.000000000000e0 1.000000000000e0 0.000000000000e0 0.000000000000e0 0.000000000000e0 0.000000000000e0 1.000000000000e0 0.000000000000e0 0.000000000000e0 0.000000000000e0 0.000000000000e0 1.000000000000e0</transform3> <transform3> 1.000000000000e0 0.000000000000e0 0.000000000000e0 0.000000000000e0 0.000000000000e0 -1.000000000000e0 0.000000000000e0 0.000000000000e0 0.000000000000e0 0.000000000000e0 -1.000000000000e0 0.000000000000e0 0.000000000000e0 0.000000000000e0 0.000000000000e0 1.000000000000e0</transform3> <transform3> 1.000000000000e0 0.000000000000e0 0.000000000000e0 0.000000000000e0 0.000000000000e0 -1.000000000000e0 0.000000000000e0 0.000000000000e0 0.000000000000e0 0.000000000000e0 1.000000000000e0 0.000000000000e0 0.000000000000e0 0.000000000000e0 0.000000000000e0 1.000000000000e0</transform3> <transform3> 1.000000000000e0 0.000000000000e0 0.000000000000e0 0.000000000000e0 0.000000000000e0 1.000000000000e0 0.000000000000e0 0.000000000000e0 0.000000000000e0 0.000000000000e0 -1.000000000000e0 0.000000000000e0 0.000000000000e0 0.000000000000e0 0.000000000000e0 1.000000000000e0</transform3> </symmetry> That to me reads: x,y,z;x,-y,-z;x,-y,z;x,y,-z; But when I use those symmetry operators with this data set I get nonsense. In the wurtzite example you sent, these transformation matrices are very odd they are in fractional coordinates, but the rotational components use angles defined in terms of cartesian coordinates. So they are useless to Jmol. Since Jmol then cannot read the transform3 entries, it must depend upon a defined unit cell and proper spacegroup name. Say again why it would be inappropriate to have a spacegroup defined here. Bob ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=2107269&group_id=23629 |