[phenixbb] Structure with pseudo-NCS translation

[Pavel Afonine]

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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