Hello
Space groups with point groups 622 and 432 merohedral twinning is not possible
(they are the highest groups possible for proteins).
If you could merge in 622 it means that Rmerge was very small. It is very
likely that point group is either 622 or 6 with very strong rotational symmetry
that is perpendicular to 6 fold axis. In these cases H test (sfcheck based on
this) and N(z) test (truncate is based on this) will overestimate (H) or
underestimate (N(z)) if twin is present. At the moment better test for these
cases seems to be L-test (that is in ctruncate I think).
Solving structure using molecular replacement in the presence of twinning does
not seem to be a problem (unless data are very noisy and/or model is too far).
Pointless gives very good idea about "true" space group.
I would solve in P6_{x} space groups and then run zanuda (from ysbl server) to
correct space group.
I hope it helps
regards
Garib
On 30 Aug 2011, at 20:31, john peter wrote:
> Hello All,
>
> This is regarding twinning in a data set.
>
> I collected a native data set to resolution, 1.8 A. I used XDS suite
> to process and scale the data set. It scaled well in P622 and I found
> systematic absence (l=6n present).
>
> Hence thought the space group may be P6122/P6522. SFCHECK did not
> show any twinning and also it did not detect pseudo-translation. Twin
> test in http://nihserver.mbi.ucla.edu/pystats/ ( Merohedral Twin
> Detector: Padilla-Yeates Algorithm ) showed perfect twinning.
>
> Scaled in P61/65 and SFCHECK reported twinning fraction 0.272 & no
> pseudo-translation.
> http://nihserver.mbi.ucla.edu/pystats/ ( Merohedral Twin Detector:
> Padilla-Yeates Algorithm ) showed perfect twinning.
> Another server from ucla http://nihserver.mbi.ucla.edu/Twinning/
> showed partial twinning with twin fraction 0.23 as follows.
>
> 2 along a, b, a*, b*
>
> No. Twin Law Related Reflections = 18033 (pairs)
> No. Twin Law Pairs Considered = 9016
>
> <H> = 0.266149
> <H2> = 0.095303
>
> Twin Fraction = 0.233249 +/- 0.000602
>
> (SHELXL Commands: TWIN 1 0 0 -1 -1 0 0 0 -1 and BASF 0.233249)
>
>
> In P61/65, I got the following matthews-coeffs
>
> mol/asym Matthews Coeff %solvent P(1.73) P(tot)
> _____________________________________________________________
> 1 9.75 87.39 .00 .00
> 2 4.88 74.79 .00 .01
> 3 3.25 62.18 .06 .14
> 4 2.44 49.57 .57 .63
> 5 1.95 36.97 .36 .21
> 6 1.63 24.36 .00 .00
> 7 1.39 11.75 .00 .00
> _____________________________________________________________
>
>
> May I ask what could be the real twin fraction and what is the
> likelihood of solving the structure by molecular replacement by models
> with 25 % sequence identity and 30 % sequence similarity.
>
> Thank you so much for reading this mail during your busy hours and
> all suggestions, comments would be gratefully welcome & appreciated.
>
> thank you ccp4 mailing list.
>
> John
Garib N Murshudov
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk
Web http://www.mrc-lmb.cam.ac.uk
