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Re: [ccp4bb] space group problem |
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CCP4bb navigationCCP4bb <-- 2008 <-- May 2008 <-- 01 May 2008Subject: Re: space group problem From: Peter Zwart PHZwart {- at -} LBL {- dot -} GOV Date: 2008-05-01 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 > 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 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net ----------------------------------------------------------------- CCP4bb navigationCCP4bb <-- 2008 <-- May 2008 <-- 01 May 2008 |
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