Does this mean that, when placing the first (or only) copy of a model,
the score will not be elevated by presence of tNCS (Unless the model contains
domains separated by more or less exactly the distance of the tNCS vector)?
(In general, using a generic MR program that does not correct for TNS.)
So a good score at the first step is likely to be correct, even if there is tNCS?
eab
Randy Read wrote:
> Dear Yurong,
>
> I just wanted to check that you're using an up-to-date version of Phaser, which will account for the presence of
> translational NCS (tNCS). With older versions of Phaser, you could get apparent solutions that were incorrect but would
> give a high LLG just because they satisfied the tNCS. However, even with the current version of Phaser there's a
> potential problem here. Phaser will only take account of the tNCS if you're looking for an even number of copies (so
> that it can look for pairs related by the tNCS). I'm wondering if, in your case, the tNCS is generated in the model by
> placing the heterotetramer with its internal 2-fold parallel to the 2(1) screw axis along y. If that's the case, and
> you're only looking for one copy of the heterotetramer, then I'm afraid Phaser will ignore the tNCS. If indeed you're
> only looking for one copy of the heterotetramer, could you try looking for two copies of the half-tetramer instead (in
> the new version of Phaser)? That may give a clearer indication of the true symmetry and, if the solution is correct, the
> combination of translational symmetry and the screw axis should generate a full tetramer.
>
> In cases like this, there's always a potential issue with twinning. I'd be interested in seeing the logfile (off-list)
> for the Phaser run, which should give an indication of whether the intensity moments suggest twinning, once the
> statistical effect of tNCS has been accounted for.
>
> Best wishes,
>
> Randy Read
>
> On 3 Dec 2012, at 11:49, Yurong Wen wrote:
>
>> Dear All,
>>
>> Recently, I collected a dataset of a protein-DNA complex and indexed in spacegroup P212121 to 3.4 Å. However,
>> Phenix.Xtriage indicated the presence of a very high pseudotranslational symmetry peak. I scaled the data in
>> spacegroup P222. When I used the protein heterotetramer as search model to do the MR, solutions are suggested in
>> P22121, P212121, P2212, P21212 and all with a TFZ score higher than 15, LLG higher than 570. Then I used phenix.refine
>> to refine those solutions; however the Rfree is as high as 0.54-0.56. The refinement strategy that I used for the
>> refinement is rigid body, group B-factors and XYZ coordinates.
>>
>> How to deal with this pseudotranslational symmetry problem? Does a solution with such high TFZ scores mean that the
>> correct one has been found? How to solve the spacegroup problem in such situation?
>>
>> Do you have any suggestions?
>>
>> Thank you very much.
>> Greetings,
>> Yurong
>
> ------
> 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: [log in to unmask] <mailto:[log in to unmask]>
> Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
>
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