[phenixbb] Structure with pseudo-NCS translation
Pavel Afonine
pafonine at lbl.gov
Fri Apr 3 10:58:35 PDT 2015
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
>
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>
>
>
>
> On 03 Apr 2015, at 15:59, Mark A Saper <saper at umich.edu
> <mailto:saper at umich.edu>> 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.
>> saper at umich.edu <mailto:saper at umich.edu> phone (734) 764-3353
>> fax (734) 764-3323
>>
>>
>>
>>
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