pseudo C2 centering in P21 will result in C2 systematic absenses being weak.
you can check this with e.g. dataman (parity check of even and odd
reflections of that type). and you will have that native patterson peak as
mentioned. this will make life bit more complicated of course since large
portion of the data maybe quite weak. also if its really P21 but because of
some reason you dont count the weaker reflections in indexing that will lead
you to _misindex_ the data in C2 and you are missing the weak data that
would tell you some details about it in realite _differs_ from C2.
(it is not a matter of incompleteness in either space group/lattice per se.)
-i believe this was the point..?
hth,
-tommi
Quoting Junyu Xiao <[log in to unmask]>:
> Dear all,
>
> 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 <[log in to unmask]>:
> >> 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
> ==================================
>
>
>
>
--
Tommi Kajander, Ph.D.
Macromolecular X-ray Crystallography
Research Program in Structural Biology and Biophysics
Institute of Biotechnology
P.O. Box 65 (Street address: Viikinkaari 1, 4th floor)
University of Helsinki
FIN-00014 Helsinki, Finland
Tel. +358-9-191 58903
Fax +358-9-191 59940
|
