Dear Lisa,
It is actually reasonably common that a clear solution (large TFZ) is found in
Phaser with a negative LLG. The negative LLG tells you that the model doesn't
agree with the data as well as one would expect, given what you have told
Phaser about the completeness of the model and its accuracy. So, if the
solution is correct, either the model is less complete than you said (e.g.
there are more copies in the asymmetric unit than you expected) or the
coordinates are less accurate than one would expect from your specification of
model quality (which is given either as a sequence identity, from which an RMSD
is estimated, or directly as an RMSD).
You'll want to sort out which of these explains the result. One of the most
common causes is unanticipated domain motion. Look at the model you are using
for molecular replacement and see whether there are domains that could move
relative to each other. If there are, the molecular replacement solution can
only place one domain correctly at a time. The easiest solution is to search
for the individual domains as separate models (ensembles), which often
succeeds. If this doesn't work, then you can take advantage of the expectation
that the domain movement will be relatively small and do a local orientation
search. The use of the ROTATE AROUND command to do this is explained briefly
on our web page:
http://www.phaser.cimr.cam.ac.uk/index.php/Molecular_Replacement#What_to_do_in_Difficult_Cases.
This requires you to break the Phaser run into several separate jobs,
brute-force rotation, translation search, packing, then rigid-body refinement.
Note that the latest versions of Phaser (available in the recent Phenix release
and also in the imminent CCP4 release) will carry out a refinement of the
estimated RMSD at the end of the automated search, so the negative LLG should
become positive or, at worst, zero.
Best wishes,
Randy Read
On 19 Jun 2012, at 09:43, LISA wrote:
Hi all,
does anyone solve their structure by molecular replacement with phaser with
LLG 0?
Thanks
lisa
--
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: + 44 1223 336500
Wellcome Trust/MRC Building Fax: + 44 1223 336827
Hills RoadE-mail: rj...@cam.ac.uk
Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
