[phenixbb] another difficult space group

[Maia Cherney]

Thank you Peter for your reply.

I will try the p1 expansion. Thank you for the suggestion. And really 
data look very good, the Rmerge is very low, chi squares are around one, 
looked like a perfect data set to me;

 one molecule in AU (in p6222). The model is exactly  the same protein 
solved in two other space groups.

And it's not one crystal, all these bipyramids are like this. I can send 
you my p1.sca if you are curious to look at it.

Maia


Peter Zwart wrote:
> 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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>>     
>
>
>
>