Bugs item #2948071, was opened at 2010-02-08 15:07 Message generated for change (Comment added) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=2948071&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: Application Group: None Status: Open Resolution: Fixed Priority: 5 Private: No Submitted By: Nobody/Anonymous (nobody) Assigned to: Nobody/Anonymous (nobody) Summary: CIF symmetry operation Initial Comment: I downloaded the latest development code and built JMol - version 11.9.25_dev The following crystal structure is not built correctly in JMol. I will follow-up with further examples. ---start example.cif data_test _cell_length_a 21.710433 _cell_length_b 9.601242 _cell_length_c 9.601044 _cell_angle_alpha 90.000000 _cell_angle_beta 27.813288 _cell_angle_gamma 90.000000 _symmetry_space_group_name_H-M 'P 2' _symmetry_Int_Tables_number 3 loop_ _atom_site_type_symbol _atom_site_label _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z Si Si1 0.874997 0.339960 0.661085 Si Si2 0.125000 0.017818 0.661076 Si Si3 0.625003 0.517817 0.838915 Si Si4 0.625003 0.839960 0.838915 Si Si5 0.875000 0.339959 0.338924 Si Si6 0.375000 0.839959 0.838924 Si Si7 0.125003 0.017817 0.338915 Si Si8 0.375000 0.517818 0.838924 O O1 0.907653 0.368165 0.434694 O O2 0.000000 0.389867 0.500000 O O3 0.842338 0.178889 0.754622 O O4 0.750000 0.428893 0.960986 O O5 0.157656 0.178889 0.623990 O O6 0.250000 0.928893 0.460986 O O7 0.092347 0.989612 0.565306 O O8 0.000000 0.967900 0.000000 O O9 0.657662 0.678889 0.745378 O O10 0.750000 0.428885 0.539014 O O11 0.500000 0.467910 0.000000 O O12 0.592347 0.489612 0.065306 O O13 0.500000 0.889867 0.000000 O O14 0.592347 0.868165 0.065306 O O15 0.000000 0.389877 0.000000 O O16 0.500000 0.889877 0.500000 O O17 0.342344 0.678889 0.876010 O O18 0.250000 0.928885 0.039014 O O19 0.000000 0.967910 0.500000 O O20 0.500000 0.467900 0.500000 ---end example.cif ---------------------------------------------------------------------- >Comment By: Bob Hanson (hansonr) Date: 2010-02-09 08:54 Message: files are in http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2010-02-09 08:54 Message: This is fixed for Jmol 11.9.27 and Jmol 11.8.19 ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2010-02-08 21:46 Message: I'm not surprised -- this file contains no symmetry operator information. All we have to go by is "H-M P2". But there are two settings of P2 -- one with unique axis b and one with unique axis c. Since Jmol has nothing more than "P2" to go with, one should not be surprised if it picks the undesired axis. Loading this model using: load t.cif {1 1 1} spacegroup "-x,y,-z" or load t.cif {1 1 1} spacegroup "P2:b" solves the problem. But, tell me: Is it possible to know from the unit cell dimensions which unique axis is correct? If so, I'll program that in. Bob Hanson ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=2948071&group_id=23629 ------------------------------------------------------------------------------ The Planet: dedicated and managed hosting, cloud storage, colocation Stay online with enterprise data centers and the best network in the business Choose flexible plans and management services without long-term contracts Personal 24x7 support from experience hosting pros just a phone call away. http://p.sf.net/sfu/theplanet-com _______________________________________________ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
