PHZwart at lbl.gov
Thu Jun 26 20:56:31 PDT 2008
Did you try processing in P4 and refining in that spacegroup? That
would my naive first choice.
The twin law in your P2 trial twin refinement is actaully
perpendicular to the pseudo four fold (which is equal to the
crystallographic two fold along b), indicating that P4 is a realistic
When entering total desperation mode, you could try the following:
1. reprocess your data in P1
2. solve it with MR
3. feed data and model into xtriage and look at the rvsr stats.
4 note down the 'twin laws' for which Robs and Rcalc both are close to zero.
5. Feed these operators into this webpage, in the section "Additional
In the line 'Space group symbol', give P1
click "get space group information"; look in output for
'conventional herman maugain symbol' or so.
This is the space group you want to have your data processed in.
Possible point groups under P422 are
P1,P211,P121,P112,C2, P222, C222, P4. The last three lie
'directly' under P422.
Let me know if this works out.
yes, the total desparation mode is automate-able and will be at some
point I suspect.
please download the latest cci_apps release
2008/6/26 Michael Gorman <mgorman at svi.edu.au>:
> Dear all,
> After over 15 years solving structures I have (knowingly) encountered my
> first twinned data set.
> Short history..
> Processed synchrotron data with HKL2000
> SG P 42 21 2 ( Cell 105.485, 105.485, 62.445, 90, 90, 90)
> Rmerge 6% to 2A
> Solved MR using Phaser ( 1 mol in ASU) and built using COOT
> Refined using Phenix to a 'final' Rwork 29.4% Rfree 31.7%
> The maps look good but not great. Spurious peaks in difference maps.
> Couldn't get R's down any further.
> Xtriage suggested 'Overmerging pseudo-symmetric or twinned data'
> Re-processed in P2 ( cell 105.299, 62.385, 105.548, 90, 90.021, 90)
> Two molecules in ASU
> Xtriage suggested the presence of 3 pseudo-merohedral twin operators
> (one 4-fold and two 2-folds)
> Refined with twin law h,-k,-l (one of the pseudo 2-folds) using Phenix
> Rwork 26% Rfree 28% (no further building carried out at the moment)
> Wondered if it was a higher space group so....
> re-processed in P222 (again Rmerge 6% to 2A) and did MR with Phaser in
> all the alternative space groups.
> The highest LL-gain was for P 21 21 21 (cell 62.377 105.297 105.546 90
> 90 90)
> I re-processed the data in P 21 21 21, all the systematic absences
> looked 'absent'.
> Xtriage suggested the presence of only one 4-fold Pseudo-merohedral twin
> law h,l,-k, R obs 5.1%
> Simulated annealing and ADP refinement in Phenix with twin law h,l,-k
> gave Rwork 33% Rfree 40%.
> Here are my questions...
> 1) Should I go for P2 due to the low R-factors and build from my good
> model ( beta angle of 90.021 seems unlikely )
> 2) Should I try other possible SG ( HKL2000 suggested, primitive
> tetragonal, primitive orthorhombic, C centred orthorhombic, and
> 3) I'm concerned that my free-R reflections will be screwed-up since I
> have pseudo-merohedral twinning and some Rwork reflections may be the
> same as Rfree ones. I have read that Phenix is rather clever and chooses
> the highest observed symmetry to ovoid this problem but I can't see it
> being reported in the log-file that, in the case of P2, pseudo P42 21 2
> is used for Rfree calculations.
> All help is much appreciated
> Michael Gorman PhD
> St. Vincent's Institute of Medical Research
> 9 Princes Street
> Victoria 3065
> Tel : (03) 9288 2519
> phenixbb mailing list
> phenixbb at phenix-online.org
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