[Jmol-developers] [ jmol-Bugs-2948071 ] CIF symmetry operation

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Bugs item #2948071, was opened at 2010-02-08 15:07
Message generated for change (Comment added) made by hansonr
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Category: Application
Group: None
Status: Open
Resolution: None
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

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>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


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