Actually, with a non-origin peak height only 1/4 of the origin and a translation that does not correspond exactly to a centering operator, Phaser has a very good chance of coping with this case. I think that the space group ambiguity of whether the 2-fold parallel to x is a screw axis or a pure 2-fold (as Eleanor discussed) is more likely to be the problem.
Regards, Randy Read On 9 Feb 2011, at 22:08, Jon Schuermann wrote: > Just to add to Phil and Eleanor's response... > > I would NOT use Phaser for MR with PTS present. It doesn't handle it > correctly yet, since the likelihood targets don't account for PTS. Others may > be able to explain it better. > > Its probably not C-centered (as Eleanor mentions) and you should try the > other primitive cell options. > > From what I understand about seeing (or not) the strong/weak reflection > behavior... it is proportional to the size of your off-origin Patterson peak > so it is more difficult to see when the off-origin peak is small (26% in your > case). Crystal orientation, I guess, could also be a reason for not > visualizing it on the diffraction image, but it still should be apparent in > the stats since Xtriage found it. > > If it was me... If your off-origin peak was over 50% of the origin peak > height AND after inspecting the Patterson map to see if it lies at z0.25, > then you MIGHT be able to solve and refine the structure in C-centered > orthorhombic cell. The advantage of this would be that you wouldn't be > refining against a large portion of weak reflection data. In your case, > however, since your weak reflections are not really that weak you shouldn't > have too much of a problem refining. > > Hope this helps. > > Jon > > -- > Jonathan P. Schuermann, Ph. D. > Beamline Scientist > NE-CAT, Building 436E > Advanced Photon Source (APS) > Argonne National Laboratory > 9700 South Cass Avenue > Argonne, IL 60439 > > email: schue...@anl.gov > Tel: (630) 252-0682 > Fax: (630) 252-0687 > > > > > On 02/08/2011 11:49 AM, Francis E Reyes wrote: >> Hi all >> >> I have a case of a dataset that indexed, integrated, and scaled well in P 21 >> 21 21 (55.6410 81.6493 147.1294 90.0000 90.0000 90.0000) . The data >> has an Mn(i/sd) of 2.1 at 3.5 A with a Rpim of about 0.398 at the highest >> resolution shell (3.49-3.58). >> >> Analysis with phenix.xtriage warns of pseudotranslational symmetry (26% of >> origin). >> >> >> x y z height p-value(height) >> ( 0.500, 0.000, 0.233 ) : 26.344 (2.681e-03) >> ( 0.000, 0.338, 0.000 ) : 5.380 (8.476e-01) >> >> If the observed pseudo translationals are crystallographic >> the following spacegroups and unit cells are possible: >> >> space group operator unit cell of reference setting >> C 2 2 21 (b-1/4,c-1/4,2*a) x+1/2, y, z+1/4 (73.64, 55.47, 81.46, >> 90.00, 90.00, 90.00) >> >> From what I've read about pseudo c-centering via pseudotranslational >> symmetry, the problem exhibits itself with alternating weak and strong >> reflections at low resolution, but become consistent at high resolution. >> Inspection of the h+k parity groups via truncate does not show this behavior >> . >> >> Despite the fact the data was collected at the anomalous peak, I do not >> observe any anomalous signal (DelAnom correlation between half-sets is 0.013 >> for all data). >> >> Using a reasonably complete model (>80%) I searched for two molecules in the >> ASU in space group P 21 21 21 and obtained a solution at TFZ=22.1 for two >> molecules related solely by a translation. However the electron density >> maps (after rigid body refinement) are not great (or maybe my expectations >> are too high). I am encouraged by the fact the density is weak for a region >> of the model which should have a different conformation, while strong >> density is maintained for the rest of the molecule. >> >> Is this the proper way to approach pseudotranslation (i.e. is there any >> reason to believe that the solution obtained by MR is not the correct >> solution?). >> >> Is the space group determined? (i.e. does the pseudo c-centering affect >> pointless's ability to analyze the systematic absences?). >> >> Is the lack of a pattern of alternating weak/strong reflections normal >> (would observing this behavior be dependent on the crystal orientation) ? >> >> any advice would be greatly appreciated! (especially from those who have had >> a case like this before) >> >> >> F >> >> >> --------------------------------------------- >> Francis E. Reyes M.Sc. >> 215 UCB >> University of Colorado at Boulder >> >> gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D >> >> 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D ------ 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
