[phenixbb] another difficult space group

[Peter Zwart]

Hi Maia,

Two points:

1) :

Given that fact that you can process the data in p622, you can expand
the data to p1:

phenix.reflection_file_converter mydata.sca --sca=p1.sca --expand_to_p1

Eventhough this is not the same as having 'real' p1 data, you know
that the data merges well in p622, so no harm is done (or at least not
a lot).

Do you have pseudo translational symmetry by any chance? I wasn't able
to find any relation between the two provided unit cells. It is very
curious that their volume are equal though.



2):

The fact that you cannot solve it might also be due to the fact that
your MR model is incorrect for some obscure reason.


HTH

Peter








2009/8/25 Maia Cherney <chern at ualberta.ca>:
> Hi everybody,
>
> I have two types of hexagonal crystals: rods and bipyramids with
> dimensions 150x150x83 (rods) and 142x142x93 (bipyramids). Both types of
> crystals give the same spacegroup P6222. However, the rods gave a good
> solution and refined to low R factors, whereas the bipyramids give a
> solution with high LLG and Z-score, but don't refine at all (R factors
> around 50%). The xtriage does not indicate any twinning. Lower symmetry
> spacegroups (trigonal and monoclinic) have the same problem: give
> solutions with high scores that would not refine. The resolution is
> 2.3A. Unfortunately, the dataset processed in p1 has only 60%
> completeness (as it was collected according to p3 strategy). Should I
> try to solve in p1 with this low completeness? What  can be a problem?
>
> Maia
>
>
>
> Peter Zwart wrote:
>> Good point.
>>
>> For now the best thing to do is to read the RvsR paper cited in the text.
>> I'll add a section to the manual as well.
>>
>> Ideally of course, xtriage should make its own judgement. Some code is
>> there, but I took it out as it is not well-tested (and didn't do the
>> job)
>>
>> P
>>
>>
>> 2009/8/25 Pavel Afonine <PAfonine at lbl.gov>:
>>
>>> Hi Peter,
>>>
>>> do you have any guidance to how interpret this table summarized
>>> somewhere in the documentation? Otherwise it looks a bit cryptic to me
>>> (I tried it while ago, may be it is improved now). Alternatively, it
>>> would be nice if Xtriage prints out its own verdict based on that table.
>>>
>>> Thanks!
>>> Pavel.
>>>
>>>
>>> On 8/25/09 10:47 AM, Peter Zwart wrote:
>>>
>>>> Subsequently, run
>>>>
>>>> phenix.xtriage p1data.mtz reference.structure.file=MR.1.pdb
>>>>
>>>> and start interpreting the RvsR tables.
>>>>
>>>>
>>>>
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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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