[phenixbb] Structure with pseudo-NCS translation

[Esko Oksanen]

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 <pafonine at lbl.gov<mailto:pafonine at lbl.gov>> 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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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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