[phenixbb] Twin refinement issues?

[Peter Zwart]

Hi Phil,

twinning with a twin fraction of 1-alpha is the same as twinning by
alpha and reindexing your data (with the twin law for instance).
Not a bug, but a consequence of structure solution, indexing
ambiguities. Did you run MR, or did you have 'old' model already?

0.59 is the same as 0.41 (after reindexing), pretty close to the
britton and H test (0.35). The ML test typically is lower then the
other two estimates, as it tries to incorporate experimental errors.

HTH

Peter



2009/4/9 Phil Jeffrey <pjeffrey at princeton.edu>:
> While experimenting with twin refinement for a crystal in P321 that
> approximates P622 to varying extents, I noticed:
>
> | twin fraction: 0.59  twin operator: -h,-k,l
>       |
>
> A bug, perhaps ?
>
> This twin fraction would seem to be unlikely, since twin fractions > 0.5
> have no meaning.  Since this data does not scale well in p622 compared
> to some more heavily-twinned datasets on this xtal form I think the twin
> fraction is certainly less than 0.5.
>
> Xtriage estimates:
> Statistics depending on twin laws
> -----------------------------------------------------------------
> | Operator | type | R obs. | Britton alpha | H alpha | ML alpha |
> -----------------------------------------------------------------
> | -h,-k,l  |   M  | 0.150  | 0.343         | 0.347   | 0.283    |
> -----------------------------------------------------------------
>
>
> Unless of course phenix.refine is reporting 2*alpha.
>
> Phenix v1.4-3  Intel Mac OSX 10.5.6
>
> This particular run with:
>
> phenix.refine model-08.pdb pz7e_truncate-unique.mtz
> refinement.main.ncs=true strategy=individual_sites+group_adp --overwrite
> xray_data.r_free_flags.generate=True twin_law="-h,-k,l"
>
> This is a very early non-finessed model.
>
> Phil Jeffrey
> Princeton
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> phenixbb at phenix-online.org
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>



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P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
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