[phenixbb] inputing tNCS into phenix?

Yarrow Madrona amadrona at uci.edu
Tue Apr 22 11:52:42 PDT 2014

Thanks Randy,

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
> > _______________________________________________
> > phenixbb mailing list
> > phenixbb at phenix-online.org
> > http://phenix-online.org/mailman/listinfo/phenixbb
> ------
> 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20140422/bc6d99fb/attachment.htm>

More information about the phenixbb mailing list