Hi Pavel,
I think the scaling issue only occurs with pseudo-centering where a significant number of reflections would be systematically weak, which should not be the case with rotational NCS I suppose.
Best,
Esko
Sent from my iPhone
On 3 apr 2015, at 20:58, Pavel Afonine mailto:[email protected]> wrote:
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
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Instrument Scientist - Neutron Macromolecular Crystallography
European Spallation Source ESS AB
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On 03 Apr 2015, at 15:59, Mark A Saper mailto:[email protected]> wrote:
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.
[email protected]mailto:[email protected] phone (734) 764-3353 fax (734) 764-3323
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