[phenixbb] Same enzyme, different space groups ?

[Yuri]

When would it be a good idea to remove reflections and process in
higher symmetry?
For my data that was processed in P 4 2 2, the fact that xtriage sees
absence violations tells me it probably really is in P 4 2 2, correct?
For the data set processed in P 43 21 2, how is its refinement
affected? 



On Mon, 28 Mar 2011 16:42:13 -0700, Peter Zwart <PHZwart at lbl.gov>
wrote:
> Hi Yuri,
> 
>> Could it all be a function of the space group they were processed in?
> 
> The short answer is yes and a detailed explanation is given below.
> 
> 
> I understand the confusion. The problem however lies with the the fact
> that when data is processed in P43212 there are no systematic absences
> available to test the hypothesis that those reflections you just
> removed are absent ....
> 
> I agree that this might even confuse you more, but here is how it
> works. The scores reported are likelihood scores from wilson
> statistics + experimental error that ariose when assuming a specific
> space group. For instance, if you have the observations (h,k,l,i,sigi)
> 
> 0 1 0   10.0 20.0
> 0 2 0   30.0  3.0
> 0 3 0   -3.0  4.0
> 0 4 0   120.0 3.0
> 
> and possible space groups P2 or P21, you have the following
> assignments of reflection statistic class:
> 
> P2:
> 0 1 0  Centric
> 0 2 0  Centric
> 0 3 0  Centric
> 0 4 0  Centric
> 
> 
> P21
> 0 1 0 Absent
> 0 2 0 Centric
> 0 3 0 Absent
> 0 4 0 Centric
> 
> On the basis of these assignments, the prior distribution of intensity
> changes and a likelihood model that includes experimental errors can
> be obtained in a relatively straightforward manner. This lead to the
> scoring function reported. This method of assigning space groups
> appears to be relatively robust.
> 
> Now once you have removed your absences by choosing your space group
> yourself in scala/scalepack/xscale/xds (i.e. P21 in my example above)
> you end up with the following list for P2 and P21:
> 
> P21 / P2
> 0 2 0 Centric
> 0 4 0 Centric
> 
> Because there is no difference now between these two spacegroups in
> terms of space group symmetry dictated intensity statistics, all space
> group will have the same score. rather then guessing if someone has
> removed these values themselves, I opted for the current scheme: if
> you remove your absences yourself, your probably know what you are
> doing and will ignore the table ;-)
> Perhaps some words in the table are in order that explains what is going on.
> 
> 
> HTH
> 
> Peter
> 
> 
> 
> 
> On 28 March 2011 15:23, Yuri <yuri.pompeu at ufl.edu> wrote:
>> Hello everyone,
>> I was comparing 2 data sets I have and when I run Xtriage I noticed the
>> following:
>> a) for one crystal (data processed in P 4 2 2)
>>
>> | space group | n absent | <Z>_absent | <Z/sigZ>_absent | +++ | ---  | score
>>       |
>> ------------------------------------------------------------------------------------
>> | P 41 21 2   | 24       |     0.03   |     1.30        |  0  |  2   |
>> 0.000e+00  |
>> | P 43 21 2   | 24       |     0.03   |     1.30        |  0  |  2   |
>> 0.000e+00  |
>> | P 42 21 2   | 22       |     0.03   |     1.27        |  0  |  4   |
>> 7.187e-02  |
>> | P 4 21 2    | 18       |     0.01   |     1.21        |  0  |  8   |
>> 3.035e-01  |
>> | P 41 2 2    | 6        |     0.11   |     1.59        |  0  |  20  |
>> 9.065e-01  |
>> | P 43 2 2    | 6        |     0.11   |     1.59        |  0  |  20  |
>> 9.065e-01  |
>> | P 42 2 2    | 4        |     0.13   |     1.57        |  0  |  22  |
>> 9.784e-01  |
>> | P 4 2 2     | 0        |     0.00   |     0.00        |  0  |  26  |
>> 1.210e+00  |
>> ------------------------------------------------------------------------------------
>>
>> b) the other crystal, of the same enzyme (data scaled in P 43 21 2) x triage
>> tells me this crystal is in P 43 21 2.
>>
>> | space group | n absent | <Z>_absent | <Z/sigZ>_absent | +++ | --- | score
>>       |
>> -----------------------------------------------------------------------------------
>> | P 4 2 2     | 0        |     0.00   |     0.00        |  0  |  2  |
>>  0.000e+00  |
>> | P 4 21 2    | 0        |     0.00   |     0.00        |  0  |  2  |
>>  0.000e+00  |
>> | P 41 2 2    | 0        |     0.00   |     0.00        |  0  |  2  |
>>  0.000e+00  |
>> | P 41 21 2   | 0        |     0.00   |     0.00        |  0  |  2  |
>>  0.000e+00  |
>> | P 42 2 2    | 0        |     0.00   |     0.00        |  0  |  2  |
>>  0.000e+00  |
>> | P 42 21 2   | 0        |     0.00   |     0.00        |  0  |  2  |
>>  0.000e+00  |
>> | P 43 2 2    | 0        |     0.00   |     0.00        |  0  |  2  |
>>  0.000e+00  |
>> | P 43 21 2   | 0        |     0.00   |     0.00        |  0  |  2  |
>>  0.000e+00  |
>> -----------------------------------------------------------------------------------
>>
>> My understanding is that P 43 21 2 should have 0 systematic absences (if I
>> am wrong, please point it out)
>>
>> My questions are:
>> what is really my space group? Or should I say space groups, if indeed I
>> have two different space groups.
>> How do I nterpret the scores?
>> Could it all be a function of the space group they were processed in?
>>
>>
>>
>> --
>> Yuri Pompeu
>>
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>>

-- 
Yuri Pompeu