[phenixbb] inputing tNCS into phenix?

Randy Read rjr27 at cam.ac.uk
Tue Apr 22 07:34:29 PDT 2014

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
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