[phenixbb] twinning

Tue Mar 31 20:46:09 PDT 2015

The main reason for the r-factor dropping is due to the fact the the
'bandwidth' of possible sqrt(I) values is radically reduced, resulting in
the observed reduction.

On 31 March 2015 at 13:48, Tim Gruene <tg at shelx.uni-ac.gwdg.de> wrote:

> Dear Shun,
>
> as you provide a twin law you basically half the data to parameter
> ratio, your R-factor usually drops irrespective of whether your model
> improved or not. You need to judge by yourself, e.g. by the quality of
> the map, whether or not the twin operator actually caused an improvement
> of your model.
>
> Best,
> Tim
>
> On 03/31/2015 06:47 PM, Shun Liu wrote:
> > Dear Randy,
> > Thank you so much for your suggestion. Phenix.xtriage indicated that
> there are 3 possible twin operators, (-h, -k, l; h, -h-k, -l; -k, -h, -l).
> When I provided twin law=-h,-k,l to phenix.refine (as it seemed that only
> one operator can be provided), I got lower R-factors than before. Now the
> question is that: should I provide all the three twin operators at the same
> time? And how? Thanks!
> >
> > Best,
> > Shun
> >
> > On Mar 31, 2015, at 3:26 AM, Randy Read <rjr27 at cam.ac.uk> wrote:
> >
> >> Dear Shun,
> >>
> >> Phaser does a test based on the moments of the intensity distribution,
> after correcting for anisotropy and (if present) translational
> non-crystallographic symmetry.  However, once a test like that has
> indicated that twinning is probably present, you will get a better result
> from running a program like phenix.xtriage, which will compare reflections
> related by possible twin operators and give a more precise idea of the twin
> fraction.
> >>
> >> Since you’ve managed to get reasonable R-factors (even if they are
> higher than expected for 1.7A), the twin fraction is probably not too
> high.  The best thing to do now is probably to run phenix.xtriage to get a
> suggestion for what the twin operator is, then you can provide that twin
> operator to phenix.refine, which will then: a) refine the twin fraction to
> give a much more precise estimate; b) correct for twinning in the
> refinement.  Detwinning is not recommended any more, because it is better
> to refine against the original data.
> >>
> >> Best wishes,
> >>
> >> Randy Read
> >>
> >> -----
> >> 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
> >>
> >> On 31 Mar 2015, at 06:18, Shun Liu <sliu.xtal at gmail.com> wrote:
> >>
> >>> Dear all,
> >>> Recently I have got a data set that diffracts to 1.7 angstrom. Images
> look good. During data processing I did not find anything that looks
> strange. However, when I was doing Phaser-MR, I got a  warning: “ Intensity
> moments suggest significant twinning (>5%). Tests based on possible twin
> laws will be more definitive.” What does this mean? A twinning data set? I
> still found a solution and refined the model step by step, using the data
> (20-1.7 angstrom). It seems that the final model and map are acceptable.
> But R-factors are 0.24/0.28, very high. Does the twin cause the high
> R-factors? Is there a solution to detwin? Or are the R-factors acceptable
> for a twinning data set? Any suggestions are appreciated and thanks in
> advance!
> >>>
> >>> Best,
> >>>
> >>> Shun
> >>> _______________________________________________
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> >>
> >
> >
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>
> --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
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