[phenixbb] Same enzyme, different space groups ?

[Peter Zwart]

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
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
>



-- 
-----------------------------------------------------------------
P.H. Zwart
Research Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB:      http://bcsb.als.lbl.gov
PHENIX:   http://www.phenix-online.org
SASTBX:  http://sastbx.als.lbl.gov
-----------------------------------------------------------------