[phenixbb] Same enzyme, different space groups ?
Peter Zwart
PHZwart at lbl.gov
Mon Mar 28 21:07:29 PDT 2011
I sense a more fundamental issue has to be explained which hopefully
make things more clear.
When determining the symmetry of a crystal structure, the following
steps are typically followed:
1. Determination of the unit cell and bravais lattice type
(monoclinic, tetratgonal etc)
2. Point group of the data posible in the bravais class; in tetragonal
system, we have the possibilities P4 and P422 (leave alone the
absenses for step 3). You find this out via merging the data and
inspecting merging stats.
3. space group assignment. IN your case (after scaling in P422) you
have to choose between P422, P4122, P4322, P4222, P4212, etc etc etc
this last step is typically done by checking absences, a particular
algorithm was outline in the previous email. when in step 3, there is
no need to rescale the data: you can just change the reflection file
header. I like my absences to be included in the reflection file, even
when one is sure that it is P 43 21 2.
If you cannot find out which space group you have, you typically sort
it out via structure solution or divine inspiration (facilitated by a
database analyses of frequency of spacegroups)
In your case it sounds like your space group is P 43 21 2, confirmed
by the xtriage analyses of your P 4 2 2 data set. The fact that
xtriage suggests that your P43212 could be P422 is a feature
associated with how the space group is determined using wilson
statistics.
HTH
P
On 28 March 2011 19:09, Yuri <yuri.pompeu at ufl.edu> wrote:
> 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
>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>
>
> --
> Yuri Pompeu
>
--
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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
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