[phenixbb] another difficult space group

Maia Cherney chern at ualberta.ca
Wed Aug 26 08:33:42 PDT 2009


Hi Randy,

thank you for your help. Today we collected at the CLS two newer 
crystals of this form. I will process them and see, if they give me 
better results.

For the dataset that I have done mor. rep, here is information from the 
headers of solutions

P6222: LLG 2194

in p32: LLG 6840

C222:  LLG=5252

C2:  LLG 7942

P62:  LLG 4058

Z-scores are very high, too, between 40 and 60.

Refinement of any of these solutions gives Rfree around 50-55%, 
actually, it goes up at every cycle of refinement.

Randy, what is the best  file to send to you: which space group for the 
sca or mtz file , which solution?

Maia

Randy J. Read wrote:
> Hi Maia,
>
> If it's a molecular replacement issue, we might be able to help. I'd 
> be happy to look at your data.
>
> All the best,
>
> Randy
>
> On Aug 25 2009, Maia Cherney wrote:
>
>> 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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>>>>     
>>>
>>>
>>>
>>>   
>>
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