[phenixbb] inputing tNCS into phenix?
amadrona at uci.edu
Wed Apr 23 07:42:58 PDT 2014
Oh yea, I ran Phaser in both P2 and P21 but was unable to find a solution
in P2. I tried this using only default parameters however. I also did not
try it after I removed bad images from my data set.
On Wednesday, April 23, 2014, Randy Read <rjr27 at cam.ac.uk> wrote:
> There could be a number of things going on, depending on other factors.
> If you had a relatively poor starting model and relatively low resolution,
> then that could be responsible. However, if you’ve got a reasonably good
> (high sequence identity) starting model and reasonable resolution, then I’d
> expect to do better even in the presence of tNCS — especially if the
> Patterson peak was weak enough that xtriage didn’t clearly flag it as
> indicating tNCS.
> tNCS often arises when a local symmetry operator (e.g. a dimer axis) is
> parallel to a crystallographic symmetry axis. In a subset of these cases,
> the NCS symmetry is close to crystallographic and sometimes it’s not
> obvious which is the NCS and which is the crystallographic symmetry. The
> old version of Phaser (before the tNCS analysis and correction) often made
> the wrong choice, but the new version is usually pretty good at making the
> right choice, at least if it is asked to check all possible space groups
> and the tNCS is being accounted for in the search. Did you let Phaser try
> both P2 and P21 when you ran the molecular replacement search?
> Best wishes,
> 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?
> > 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
>> > 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
>> > 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
>> Cambridge CB2 0XY, U.K.
> 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
> Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
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