Does this mean that, when placing the first (or only) copy of a model,
the score will not be elevated by presence of tNCS (Unless the model contains
domains separated by more or less exactly the distance of the tNCS vector)?
(In general, using a generic MR program that does not correct for TNS.)
So a good score at the first step is likely to be correct, even if there is
tNCS?
eab
Randy Read wrote:
Dear Yurong,
I just wanted to check that you're using an up-to-date version of Phaser, which
will account for the presence of
translational NCS (tNCS). With older versions of Phaser, you could get apparent
solutions that were incorrect but would
give a high LLG just because they satisfied the tNCS. However, even with the
current version of Phaser there's a
potential problem here. Phaser will only take account of the tNCS if you're
looking for an even number of copies (so
that it can look for pairs related by the tNCS). I'm wondering if, in your
case, the tNCS is generated in the model by
placing the heterotetramer with its internal 2-fold parallel to the 2(1) screw
axis along y. If that's the case, and
you're only looking for one copy of the heterotetramer, then I'm afraid Phaser
will ignore the tNCS. If indeed you're
only looking for one copy of the heterotetramer, could you try looking for two
copies of the half-tetramer instead (in
the new version of Phaser)? That may give a clearer indication of the true
symmetry and, if the solution is correct, the
combination of translational symmetry and the screw axis should generate a full
tetramer.
In cases like this, there's always a potential issue with twinning. I'd be
interested in seeing the logfile (off-list)
for the Phaser run, which should give an indication of whether the intensity
moments suggest twinning, once the
statistical effect of tNCS has been accounted for.
Best wishes,
Randy Read
On 3 Dec 2012, at 11:49, Yurong Wen wrote:
Dear All,
Recently, I collected a dataset of a protein-DNA complex and indexed in
spacegroup P212121 to 3.4 Å. However,
Phenix.Xtriage indicated the presence of a very high pseudotranslational
symmetry peak. I scaled the data in
spacegroup P222. When I used the protein heterotetramer as search model to do
the MR, solutions are suggested in
P22121, P212121, P2212, P21212 and all with a TFZ score higher than 15, LLG
higher than 570. Then I used phenix.refine
to refine those solutions; however the Rfree is as high as 0.54-0.56. The
refinement strategy that I used for the
refinement is rigid body, group B-factors and XYZ coordinates.
How to deal with this pseudotranslational symmetry problem? Does a solution
with such high TFZ scores mean that the
correct one has been found? How to solve the spacegroup problem in such
situation?
Do you have any suggestions?
Thank you very much.
Greetings,
Yurong
------
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 Road E-mail: rj...@cam.ac.uk <mailto:rj...@cam.ac.uk>
Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
