[phenixbb] Structure with pseudo-NCS translation

Mark Saper saper at umich.edu
Fri Apr 3 14:40:39 PDT 2015


My R-factors are similar to what Pavel obtained.   My Patterson peak was 43% of origin. 

Haven't read Esko's response yet. 

Mark Saper
3040 & 3250 Chemistry Building
Dept of Biological Chemistry
saper at umich.edu
734 764 3353 office   734 276 6505 mobile

> On Apr 3, 2015, at 1:58 PM, Pavel Afonine <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
>> _____________________
>> 
>> 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
>> E-mail: esko.oksanen at esss.se
>> 
>> www.esss.se
>> 
>> 
>> 
>> 
>>> On 03 Apr 2015, at 15:59, Mark A Saper <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     phone (734) 764-3353     fax (734) 764-3323
>>> 
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>> Unsubscribe: phenixbb-leave at phenix-online.org
>> 
>> 
>> 
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>> Unsubscribe: phenixbb-leave at phenix-online.org
> 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20150403/83818d3b/attachment.htm>


More information about the phenixbb mailing list