Quick navigation:        Home   |    Site Map   ||    References   |    Biography   ||    Copyright   |    Other copyright   |    Contact us   |   
Protein structure
 

Re: [ccp4bb] space group problem
 

Basic tutorials: 		 
 

CCP4bb navigation

CCP4bb <-- 2008 <-- May 2008 <-- 01 May 2008
Previous message:
Subject: Re: space group problem
From: James Holton JMHolton {- at -} LBL {- dot -} GOV
Date: 2008-05-01 		Next message:
Subject: Re: Bacterial induction at 18C
From: Juergen Bosch jbosch {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2008-05-01


Subject: Re: space group problem
From: Peter Zwart PHZwart {- at -} LBL {- dot -} GOV
Date: 2008-05-01
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
-----------------------------------------------------------------
ProteinCrystallography.org: Copyright 2006-2007 by Quid United Ltd