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 <[EMAIL PROTECTED]>:
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
==================================
