I guess you have checked that P43212 is a better match than P41212?
(And that you are running REFMAC against an mtz file with the same
symmetry as the input PDB - you may need to change the SG in the mtz
header by hand.
mtzutils hklin P41212.mtz hklout P43212.mtz
symm P43212
end
Or vice versa..
Sorry - THIS IS CRAZY but there you are..
Re the pseudo translation -Randy summs up the situation very clearly.
I would build my model by hand actually but I am sure PHASER does itwell too!
Something I dont understand but maybe it is to do with your patterson sampling.
Peak 3 is a consequence of Pk 1 and Pk2 -
Pk 5 is the consequence of Pk 1 and Pk4
but the peak heights dont exactly fit..
Eleanor
On 18 November 2013 10:19, Randy Read <[log in to unmask]> wrote:
> Dear Dan,
>
> First, you don't want to reprocess in the smaller cell. What xtriage is
> saying is that, if *and only if* the translation detected in the Patterson
> map were an exact crystallographic translation, then you would get the
> smaller cell. However, in order for that to be a plausible hypothesis, the
> Patterson peaks would have to be near to 100% of the origin peak.
>
> You actually seem to have a very interesting case, where the Patterson peaks
> are related by multiples of approximately the same translation. If you take
> a translation of 1/2,1/2,1/6 and multiply it by 1, 2 and 3, you get
> something close to the three biggest peaks in your Patterson (taking account
> of lattice translations), and these are related by the Patterson inversion
> centre to what you get if you multiply by 4 and 5. So the six molecules
> should be related to each other by something close to a repeated translation
> of 1/2,1/2,1/6. (You should check this in the solution that you already
> have.) If this were exact, you would have a smaller cell, but it's not
> exact, and one way in which it is not exact is that the translations along z
> are not exactly multiples of 1/6.
>
> This is reminiscent of a structure that we recently collaborated with
> Mariusz Jaskolski and Zbyszek Dauter to solve (paper accepted for
> publication in Acta D). In that case, there are seven translations of
> approximately 0,0,1/7. The difficulty with cases like this is figuring out
> how to break the exact symmetry. Any solution that has approximately the
> right translations will basically fit the data, but you need to find the
> right combination of deviations from the exact symmetry to get an optimal
> answer. If you get the wrong deviations from exact symmetry, the refinement
> will stall, and this may be the problem that you're facing.
>
> You can deal with problems like this in Phaser by using the TNCS NMOL 6
> command (to say that there are 6 copies related by repeated applications of
> the same translation). You should tell Phaser to use the 1/2,1/2,0.174
> vector (TNCS TRA VECTOR 0.5 0.5 0.174), and hopefully this will break the
> symmetry in a way that subsequent rigid-body refinement can deal with. I'm
> happy to give you more advice on this, off-line, because this kind of case
> isn't something that we've figured out how to deal with automatically yet.
> The optimal approach probably involves getting a deeper understanding of
> commensurate modulation, which is another way of thinking about
> pseudo-translations.
>
> Best wishes,
>
> Randy Read
>
> On 18 Nov 2013, at 09:19, #CHEN DAN# <[log in to unmask]> wrote:
>
> Dear experts,
>
> I am working on one dataset (2.5A) which was processed using space group
> P43212 ( 107.9, 107.9, 313.7; 90, 90, 90).
> After running MR with 6 molecules in ASU and one round of refmac, the R
> factors are high (38%/45%).
> I ran phenix.xtriage and found that translational pseudo symmetry is likely
> present. It suggested that the space group is I4122 with the unit cell about
> 1/3 smaller (I paste the patterson analyses below).
> I tried to reprocess the data to get the suggested space group and unit cell
> using HKL2000. But the index always gives a long c axis about 313A.
> Could you provide any suggestions on how to proceed?
>
> Patterson analyses
> ------------------
>
> Largest Patterson peak with length larger than 15 Angstrom
>
> Frac. coord. : 0.500 0.500 0.174
> Distance to origin : 93.757
> Height (origin=100) : 55.763
> p_value(height) : 3.018e-05
>
>
> The reported p_value has the following meaning:
> The probability that a peak of the specified height
> or larger is found in a Patterson function of a
> macro molecule that does not have any translational
> pseudo symmetry is equal to 3.018e-05.
> p_values smaller than 0.05 might indicate
> weak translational pseudo symmetry, or the self vector of
> a large anomalous scatterer such as Hg, whereas values
> smaller than 1e-3 are a very strong indication for
> the presence of translational pseudo symmetry.
>
> The full list of Patterson peaks is:
>
> x y z height p-value(height)
> ( 0.500, 0.500, 0.174 ) : 55.763 (3.018e-05)
> ( 0.500, 0.500, 0.500 ) : 51.209 (5.796e-05)
> ( 0.000, 0.000, 0.326 ) : 32.915 (8.699e-04)
> ( 0.000, 0.000, 0.348 ) : 18.765 (1.266e-02)
> ( 0.500, 0.500, 0.151 ) : 11.396 (9.756e-02)
>
> If the observed pseudo translationals are crystallographic
> the following spacegroups and unit cells are possible:
>
> space group operator unit cell of reference setting
> I 41 2 2 (a+1/4,b+1/4,3*c) x+1/2, y+1/2, z+1/6 (107.94, 107.94, 104.58,
> 90.00, 90.00, 90.00)
>
>
> Thanks,
> Dan
>
>
> ------
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical Research Tel: + 44 1223 336500
> Wellcome Trust/MRC Building Fax: + 44 1223 336827
> Hills Road E-mail: [log in to unmask]
> Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
>
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