Re: [phenixbb] Same enzyme, different space groups ?

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 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 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 | _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 | _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