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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: Junyu Xiao JUNYU {- at -} UMICH {- dot -} EDU Date: 2008-05-01 Thanks for all the advices. I am especially grateful to Dr. Clemens Vonrhein, now I am clear about the relationship between this two choices. Dr. Zwart raises another interesting point, which of course is my major concern. C2 will have the advantage for phasing, since it has a smaller ASU; but incomplete data won't help. Can I get more education on this? Thanks a lot, Junyu On May 1, 2008, at 1:07 PM, Peter Zwart wrote: > Clemens is right of course. If you ignore the lattice centring in C2, > the cells are the same. > > I was however under the impression that auto-indexing goes via the > primitive cell. Which makes the two solutions unique. > Ignoring the possible lattice translation in P2 will show up in a > Patterson function (at 1/2,1/2,0 i think) . The lattice translation > might of course be a pseudo translation. In the C2 case, you would > miss weak reflections if P2 would be the right answer. > > > P > > > > > > 2008/5/1 Clemens Vonrhein >> Dear Junyu, >> >> it looks to me like you encounter a classical monoclinic feature: >> one >> can index monoclinic always in two ways >> >> >> origin >> >> V >> >> A' ---------------------------------- A >> / / >> / / >> / / >> / / >> / / >> / / >> / / >> / / >> /________________/ >> >> C C' >> >> One cell (A,B,C) has B coming towards you and the other >> (A',B',C') has >> B' pointing away from you. The two axes A and A' have identical >> length >> as have B and B'. But C' is the diagonal in the AC-plane. >> >> In your case you can just swap the A and C axis of the C2 (to follow >> the above picture) and then calculate the C' (diagonal) to 136.8. >> >> So to summarize: these are identical cells - just different choice >> of axes (and nothing to do with the C2 versus P2 choice ... I >> think). >> >> Cheers >> >> Clemens >> >> >> >> >> On Thu, May 01, 2008 at 12:03:16PM -0400, Junyu Xiao wrote: >>> 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 >>> ================================== >>> >>> >>> >> >> -- >> >> *************************************************************** >> * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com >> * >> * Global Phasing Ltd. >> * Sheraton House, Castle Park >> * Cambridge CB3 0AX, UK >> *-------------------------------------------------------------- >> * BUSTER Development Group (http://www.globalphasing.com) >> *************************************************************** >> > > > > -- > ----------------------------------------------------------------- > 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 > ----------------------------------------------------------------- > > ================================= 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 ================================== CCP4bb navigationCCP4bb <-- 2008 <-- May 2008 <-- 01 May 2008 |
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