[phenixbb] another difficult space group

Peter Zwart phzwart at gmail.com
Tue Aug 25 12:31:52 PDT 2009

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.


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



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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P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
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