Take your c2 cell, go to niggli setting, double the c axis. apply
transform (-x+z,y-z,-z). now you end up with your P2 cell in the
niggli setting. you might have stromng pseudo translational symmetry
(or your unit cell is too big)
phenix.explore_metric_symmetry --unit_cell=145,44,67,90,110.5,90
--space_group=C2 --other_unit_cell=67,44,136,90,96,90
--other_space_group=p2
.
.
.
.
.
Unit cell comparison
--------------------
The unit cells will be compared. The smallest niggli cell,
will be used as a (semi-flexible) lego-block to see if it
can construct the larger Niggli cell.
Crystal symmetries in supplied setting
Target crystal symmetry:
Unit cell: (67, 44, 136, 90, 96, 90)
Space group: P 1 2 1 (No. 3)
Building block crystal symmetry:
Unit cell: (145, 44, 67, 90, 110.5, 90)
Space group: C 1 2 1 (No. 5)
Crystal symmetries in Niggli setting
Target crystal symmetry:
Unit cell: (44, 67, 136, 96, 90, 90)
Space group: P 2 1 1 (No. 3)
Building block (lego cell) crystal symmetry:
Unit cell: (44, 67, 75.7644, 109.58, 106.88, 90)
Space group: C 1 2 1 (x+y,z,2*x) (No. 5)
Volume ratio between target and lego cell: 1.99
Cartesian basis (column) vectors of lego cell:
/ 44.0 0.0 -22.0 \
| 0.0 67.0 -25.4 |
\ 0.0 0.0 67.9 /
Cartesian basis (column) vectors of target cell:
/ 44.0 0.0 0.0 \
| 0.0 67.0 -14.2 |
\ 0.0 0.0 135.3 /
A total of 8 matrices in the hermite normal form have been generated.
The volume changes they cause lie between 2 and 1.
Trying all matrices
1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0
. * . . . . . .
Listing all possible solutions
Solution 1
--------------------------------------------------------------
Target unit cell : 44.0 67.0 136.0 96.0 90.0 90.0
Lego cell : 44.0 67.0 75.8 109.6 106.9 90.0
/ 1 0 0 \
matrix : M = | 0 1 0 |
\ 0 0 2 /
Additional Niggli transform: -x+z,y-z,-z
Additional similarity transform: x,y,z
Resulting unit cell : 44.0 67.0 136.8 96.8 90.0 90.0
Deviations : 0.0 0.0 -0.6 -0.8 -0.0 -0.0
Deviations for unit cell lengths are listed in %.
Angular deviations are listed in degrees.
--------------------------------------------------------------
2008/5/1 Junyu Xiao <[log in to unmask]>:
> Hi all,
>
> We run into an interesting space group problem. The same diffraction image
> can be either indexed into space group C2, with a=145, b=44, c=67, and
> beta=110.5; or space group P2 (should be P21 after scaling), with a=67,
> b=44, c=136, and beta=96.8. Both are refined ok during index. These two must
> somehow be related. Can anyone give some comments on that?
>
> Thanks a lot,
> Junyu
>
>
> =================================
> Junyu Xiao
> Department of Biological Chemistry,
> University of Michigan
>
> Lab address:
> 3163 Life Sciences Institute,
> University of Michigan,
> 210 Washtenaw Avenue
> Ann Arbor, MI, 48109-2216
> Phone: 734-615-2078
> ==================================
>
>
>
>
--
-----------------------------------------------------------------
P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
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PHENIX: http://www.phenix-online.org
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