[phenixbb] another difficult space group

Maia Cherney chern at ualberta.ca
Tue Aug 25 12:13:13 PDT 2009


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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