Hi Esko,
thanks for the paper - very interesting!
Perhaps accounting for ptNCS matters a lot for structure solution
or/and refinement/model building at early stages, however I did not
see any problem with refinement in this particular example.
Here is what I did:
1) Get model and data from PDB:
phenix.fetch_pdb 1yup --mtz
2) Get initial statistics: R-factors from PDB file header, geometry
using command:
phenix.pdbtools model_stat=true 1yup.pdb
Rwork=0.235 Rfree=0.311
all-atom clashscore : 8.21
ramachandran plot:
outliers : 1.52 %
allowed : 7.43 %
favored : 91.05 %
rotamer outliers : 14.11 %
cbeta deviations : 3
3) Then I perturbed the model and refined it with phenix.refine
(restrained coordinates and B-factors, water update, weights
optimization, local real-space refinement). Here is the statistics
for refined model:
Rwork=0.2380 Rfree=0.2709
all-atom clashscore : 10.61
ramachandran plot:
outliers : 0.80 %
allowed : 5.20 %
favored : 94.00 %
rotamer outliers : 2.38 %
cbeta deviations : 0
Just to make it clear: I'm *not* saying we shouldn't account for
ptNCS in refinement; in fact, we really should especially given that
Randy Read et al worked out all the methods for this!
I will re-visit this once we implement ptNCS in phenix.refine.
All the best,
Pavel
On 4/3/15 9:01 AM, Esko Oksanen wrote:
Hi Mark,
I believe at least part of the problem arises already in the
scaling stage, where the programs assume a unimodal distribution
which is not the case in the presence of pseudo-translations. We
encountered a similar issue with refinement and
pseudo-translation, where I simply scaled the systematically
weak data separately from the strong and did rigid body
refinement against the weak data and restrained against the
strong. The details can be found in
http://scripts.iucr.org/cgi-bin/paper?ea5052.
Best,
Esko
_____________________
Esko
Oksanen, PhD
Instrument
Scientist - Neutron Macromolecular
Crystallography
European
Spallation Source ESS AB
P.O Box 176,
SE-221 00 Lund, Sweden
Visiting
address: Tunavägen 24, Lund
Switchboard:
+46 46 888 00 00
Phone: +46 46
888 30 36
Mobile: +46
721 79 20 36
I know that Phaser takes account of
NCS translation in the likelihood statistics ( Read, Adams,
McCoy (2013) Intensity statistics in the presence of
translational non crystallographic symmetry”). Has this also
been incorporated into phenix.refine? I have a structure
with pseudo NCS translations because of NCS rotational
symmetry. One suggestion that I found in the archives, was
to explicitly LS target refinement rather than ML. Any
comments?
Mark
_________________________________
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry, University of
Michigan
Ann Arbor MI 48109-1055 U.S.A.
saper@umich.edu
phone (734) 764-3353 fax (734) 764-3323
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