[phenixbb] Pseudo-merohedral twinning refinement in C2, when beta = 94 degrees

Peter Zwart PHZwart at lbl.gov
Tue Sep 20 00:26:51 PDT 2011

Hi John,

Did you try and process the data in P1?
When 50% twinned and no twin laws, one typically tries to go down in
symmetry ...


On 20 September 2011 00:20, John Pak <john.pak at msg.ucsf.edu> wrote:
> Hi all,
> I currently have a dataset that scales well in C2.  (a = 224,b = 129,c =
> 392. beta= 94.5 degrees).  Previously, I had thought that these crystals
> were in P6322 (posted this a few months ago), but I've since grown better
> crystals, where the beta angle is now 94.5, and not close to 90.0.  I'm
> reasonably confident with the scaling - however, it has always been really
> difficult to index these crystals in HKL2000.
> Like the previous crystals, this new C2 dataset looks like it might be
> perfectly twinned, based on Xtriage's L test.
> I've solved the structure by MR, and refined it to 3.0 angstroms to R=30%,
> Rfree=33%, but I am running out of things to fix.  I'd like to perform
> twinning refinement, based on this Xtriage L test result.
> The problem is that Xtriage cannot find any pseudomerohedral twinning laws,
> likely because the beta angle is too far from 90 degrees??  For kicks and
> giggles, I started to enter arbitrary beta angles in Xtriage, and at a beta
> angle below 93.4, Xtriage can find two twinning laws (closer to 90 degrees,
> Xtriage can find 5 twin laws).  Using "-1/2*h+3/2*k, 1/2*h+1/2*k, -l" in
> Phenix refine (the beta angle is still 94.5 degrees, I haven't changed this)
> results in the R and Rfree dropping a lot to 25.5 and 28.6, respectively.
>  Used the same random seed as previous runs to generate the test set from
> the scalepack file, with the "use lattice symmetry to generate test set"
> flag enabled.  The maps look a lot noisier.
> So my questions are:
> 1. Is this twinning refinement valid?  I'm really thinking no - since the
> maps didn't improve.   Suppose the maps didn't get worse though - would this
> twinning refinement then be valid?
> 2. How do I go about reindexing this dataset in I2? i.e. to see if the beta
> angle with this unit cell selection is closer to 90 degrees.  Would this
> even help, with respect to pseudomerohedral twinning refinement?
> Thanks!
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P.H. Zwart
Research Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB:      http://bcsb.als.lbl.gov
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