[phenixbb] inputing tNCS into phenix?
amadrona at uci.edu
Tue Apr 22 11:52:42 PDT 2014
I guess my next question is whether, a stalled Rfree of 40% for data with
otherwise good processing stats and a P21 space group could possibly be due
to tNCS or if another reason is also likely?
On Tue, Apr 22, 2014 at 7:34 AM, Randy Read <rjr27 at cam.ac.uk> wrote:
> Dear Yarrow,
> Phenix.refine can impose NCS restraints for general NCS, and that is
> handled pretty automatically without having to specify a rotation and
> translation, but that’s probably not what you’re asking. In the particular
> case of tNCS, there are problems arising from the fact that there is an
> overall modulation to give systematically strong and systematically weak
> intensities, whereas the refinement likelihood targets implicitly assume
> that all the intensities (and, more importantly, the errors in predicting
> the intensities from the model) have a smooth distribution.
> For molecular replacement, the performance of Phaser has been improved
> significantly by accounting for these tNCS effects and, in principle, it
> would be great to do the same in refinement. That’s pretty high up on the
> to-do list — and the same theory used in Phaser would apply, but at the
> moment there isn’t any way yet to account for this in refinement.
> Best wishes,
> Randy Read
> On 22 Apr 2014, at 14:51, Yarrow Madrona <amadrona at uci.edu> wrote:
> > Hello,
> > I recently posted a question about stalled R-factors and and obtained
> excellent help resulting in the realization that I have tNCS even though
> it is not picked up by X-triage. I know the transformation matrix of one
> molecule onto another but I am not sure how to input this into phenix (both
> the translation and the rotation) to improve refinement. Is there a way to
> do this? I'm sorry if this has already been covered.
> > -Yarrow
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> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical Research Tel: + 44 1223 336500
> Wellcome Trust/MRC Building Fax: + 44 1223 336827
> Hills Road E-mail: rjr27 at cam.ac.uk
> Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
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