<div dir="ltr">Thanks Randy,<div><br></div><div>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?<div>
<br></div><div>-Yarrow</div></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Apr 22, 2014 at 7:34 AM, Randy Read <span dir="ltr"><<a href="mailto:rjr27@cam.ac.uk" target="_blank">rjr27@cam.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear Yarrow,<br>
<br>
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.<br>
<br>
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.<br>
<br>
Best wishes,<br>
<br>
Randy Read<br>
<div><div class="h5"><br>
On 22 Apr 2014, at 14:51, Yarrow Madrona <<a href="mailto:amadrona@uci.edu">amadrona@uci.edu</a>> wrote:<br>
<br>
> Hello,<br>
><br>
> 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.<br>
><br>
> -Yarrow<br>
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<br>
------<br>
Randy J. Read<br>
Department of Haematology, University of Cambridge<br>
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<br>
</blockquote></div><br></div>