[phenixbb] Twin refinement issues?

Peter Zwart phzwart at gmail.com
Fri Apr 10 08:19:37 PDT 2009


Hi Phil,

>
> The reasons I consider this behavior to be a bad thing are:
>
> 1.  Twin fractions > 0.5 are not physically reasonable and I would
> expect default behavior should be to clamp them to the range 0.-0.5.
> (caveat: I'm not sure what CNS or REFMAC do).

Twin fractions above 0.5  are physically reasonable! the twin fraction
is the size of the twin domain.
When you have a twin fraction of alpha, you always have a twin
fraction of 1-alpha that goes with it.
I wouldn't be surprised to see shelxl and refmac behave in a similar manner.

>
> 2.  I have mixed feelings about "stealth reindexings", especially since
> I didn't set refinement.second_guess=True  (see below)

I don't like a program to reindex data or model unless i ask to .

> 3.  The stealth reindexing behavior is inconsistent across refinement
> without twinning set (no stealth indexing) and when it is set, for
> exactly the same mtz and pdb files.
>
> Auto-reindexing might be a time-saving feature (especially in point
> group 3) but should be consistent w/ and w/o twinning enabled and needs
> to be much more prominently advertised in the output, and a new MTZ file
> written.

no reindexing was done in phenix.refine. we could do so, but I have my
reservations on that.

Cheers

P

>
> Aside: this structure was the result of a MAD dataset at 3.5 Angstrom
> with a lower twin fraction (~0.2) so of course the relative indexing
> problem comes into play when I switched datasets.  In the case of the
> MAD dataset SHARP made a radical difference in phase quality compared to
>  the uninterpretable map straight out of SHELX - perhaps the largest
> improvement I have ever seen.



>
> Cheers
> Phil Jeffrey
>
> Peter Zwart wrote:
>> 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
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>>
>>
>>
>>
>
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P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
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