If the two molecules are related by translational symmetry, at least
Phaser is not happy.
Since in the second rotation function it removes contribution from the
first orientation,
if the orientation/rotations of the two molecules in identical, it
will fail to see the
second rotation applies.
Thus if you have pure translation symmetry, which must be manifested
with a very high peak
in the native Patterson map, you can either:
1. RTFM of Phaser and supply a list with the first solution and the an
identical rotation, and ask
it to find the second translation
2. Apply the second translation by hand from the native Patterson (as
you more or less did empirically)
3. 'Fool' Phaser by telling it you look for two different molecules,
first the one and then the other.
Tassos
On Dec 7, 2010, at 22:38, Arnon Lavie wrote:
Hi there:
The situation: We are facing difficult molecular replacement: we
believe
we have two molecules in the ASU, but phaser/molrep find only one.
Using
the electron density calculated using this single molecule, we have
manually placed the 2nd molecule, albeit not good enough for rigid
body
refinement.
Our strategy: We are looking for a program to do a 3 dimensional
search
around the current position of the 2nd molecule. Maybe one that
calculates R-factor at the different positions, to allow to identify
the
correct one. ...
Does anyone know of such a program, or an alternative approach?
Thanks.
Arnon
--
***********************************************************
Arnon Lavie, Professor
Dept. of Biochemistry and Molecular Genetics
University of Illinois at Chicago
900 S. Ashland Ave.
Molecular Biology Research Building, Room 1108 (M/C 669)
Chicago, IL 60607
U.S.A.
Tel: (312) 355-5029
Fax: (312) 355-4535
E-mail: la...@uic.edu
http://www.uic.edu/labs/lavie/
***********************************************************
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Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member
Department of Biochemistry (B8)
Netherlands Cancer Institute,
Dept. B8, 1066 CX Amsterdam, The Netherlands
Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791
