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 <rj...@cam.ac.uk> 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# <chen0...@e.ntu.edu.sg> 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: rj...@cam.ac.uk > Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk >
