refinement with several twins / modulated data / pseudo-translational symmetry
Dear all, I have a strongly modulated dataset as can be observed in the truncate output below. Specially, the modulation is higher for L odd/even and at lower resolution: !!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Analysis of mean intensity by parity for reflection classes For each class, Mn(I/sig(I)) is given for even and odd parity with respect to the condition, eg group 1: h even & odd; group 7 h+k+l even & odd; group 8 h+k=2n & h+l=2n & k+l=2n or not Range Min_S Dmax Nref 1 2 3 4 5 6 7 8 h k l h+k h+l k+l h+k+l h+k,h+l,k+l 1 0.00018 20.85 519 13.2 8.9 13.9 8.2 22.3 2.4 13.3 8.9 12.5 9.6 12.9 9.0 12.6 9.5 16.5 9.2 2 0.00230 15.04 994 15.9 16.0 15.3 16.5 30.1 2.3 15.7 16.2 15.1 16.7 14.9 16.8 15.1 16.7 13.5 16.6 3 0.00442 12.36 1289 17.2 16.0 17.0 16.2 33.8 3.7 17.2 16.0 14.9 18.0 14.7 18.2 14.9 18.0 13.1 17.4 4 0.00655 10.74 1568 20.7 18.9 20.3 19.2 35.5 4.9 20.4 19.2 18.7 20.7 18.3 21.0 18.5 20.9 17.7 20.3 5 0.00867 9.63 1759 20.3 15.8 20.1 16.0 33.2 4.9 20.1 15.9 18.7 17.3 18.6 17.4 18.8 17.2 21.6 16.9 6 0.01079 8.80 2042 19.6 15.4 19.3 15.7 30.5 5.8 19.5 15.5 17.6 17.3 17.5 17.4 17.6 17.3 19.9 16.7 7 0.01291 8.15 2206 15.9 12.0 15.8 12.1 22.6 5.0 15.5 12.4 14.3 13.5 14.1 13.7 14.0 13.8 16.2 13.2 8 0.01504 7.63 2393 11.8 9.0 11.5 9.3 18.6 3.6 11.7 9.1 10.5 10.2 10.3 10.3 10.4 10.3 12.0 9.9 9 0.01716 7.20 2526 9.8 6.5 9.8 6.5 13.8 3.2 9.8 6.6 9.0 7.3 9.0 7.3 9.0 7.4 11.6 7.1 10 0.01928 6.83 2747 11.1 7.5 11.0 7.6 15.7 3.0 10.8 7.8 10.0 8.5 9.9 8.6 9.8 8.6 12.3 8.3 11 0.02141 6.52 2867 10.3 7.3 10.2 7.3 14.4 3.0 10.3 7.3 9.4 8.1 9.4 8.1 9.4 8.2 11.7 7.9 12 0.02353 6.24 3122 8.6 5.8 8.5 5.8 11.6 3.0 8.4 5.9 7.3 6.9 7.3 6.9 7.2 7.0 8.8 6.6 13 0.02565 6.00 3124 7.9 5.7 7.7 5.9 11.1 2.9 7.7 5.9 6.8 6.7 6.8 6.8 6.8 6.7 7.8 6.5 14 0.02777 5.78 3346 9.8 6.7 9.7 6.7 12.7 3.5 9.6 6.8 8.8 7.7 8.7 7.8 8.6 7.9 10.7 7.5 15 0.02990 5.59 3428 9.0 5.6 8.9 5.7 11.2 3.1 8.8 5.8 7.9 6.7 7.8 6.8 7.7 6.9 9.9 6.4 16 0.03202 5.41 3633 8.3 5.5 8.2 5.5 10.9 3.5 8.2 5.6 7.1 6.6 7.1 6.6 7.1 6.6 8.8 6.2 17 0.03414 5.25 3658 9.6 6.2 9.4 6.3 12.4 3.7 9.4 6.4 8.4 7.3 8.4 7.3 8.2 7.5 10.6 7.0 18 0.03627 5.10 3696 10.2 6.4 10.1 6.5 12.5 4.3 9.8 6.7 8.8 7.8 8.7 7.9 8.6 7.9 10.8 7.4 19 0.03839 4.97 3955 10.1 6.9 9.9 7.0 12.6 4.5 9.8 7.1 8.8 8.2 8.6 8.3 8.6 8.3 10.4 7.9 20 0.04051 4.84 3902 10.9 7.2 10.9 7.2 13.4 4.6 10.7 7.4 9.7 8.4 9.7 8.4 9.7 8.4 12.1 8.0 21 0.04263 4.73 4207 11.4 6.8 11.3 6.9 13.7 4.8 11.1 7.0 9.5 8.5 9.4 8.6 9.5 8.6 12.0 8.1 22 0.04476 4.62 4169 9.7 6.8 9.6 6.9 12.4 4.6 9.5 7.0 8.3 8.1 8.3 8.2 8.2 8.2 9.7 7.8 23 0.04688 4.52 4100 11.1 6.7 11.0 6.8 12.6 5.5 10.8 7.0 9.0 8.8 8.9 8.8 8.9 8.9 11.0 8.2 24 0.04900 4.42 4605 10.8 6.5 10.7 6.5 12.3 4.9 10.5 6.8 9.5 7.8 9.4 7.9 9.3 7.9 12.2 7.5 25 0.05113 4.33 4449 9.6 6.1 9.5 6.2 11.1 4.6 9.4 6.3 8.3 7.4 8.2 7.5 8.2 7.5 10.2 7.0 26 0.05325 4.25 4528 9.1 5.8 9.1 5.8 10.0 4.8 8.8 6.0 7.6 7.2 7.5 7.3 7.5 7.3 9.2 6.8 27 0.05537 4.17 4782 8.6 5.3 8.6 5.3 9.7 4.6 8.5 5.4 7.5 6.5 7.4 6.5 7.4 6.5 9.5 6.1 28 0.05749 4.10 4774 8.3 5.2 8.2 5.3 9.6 3.9 8.0 5.4 7.0 6.4 7.0 6.4 6.9 6.5 8.6 6.1 29 0.05962 4.02 4837 8.1 5.6 8.1 5.7 9.7 4.4 7.9 5.8 7.2 6.6 7.2 6.6 7.2 6.6 8.6 6.4 30 0.06174 3.96 5066 8.2 4.9 8.2 4.9 8.9 4.2 8.0 5.1 6.9 6.2 6.8 6.2 6.7 6.3 8.6 5.8 31 0.06386 3.89 4954 7.4 4.7 7.3 4.8 7.9 4.1 7.2 4.9 6.2 5.9 6.1 6.0 6.2 5.9 7.5 5.6 32 0.06599 3.83 5052 7.6 4.6 7.6 4.6 8.2 4.0 7.4 4.8 6.4 5.8 6.4 5.8 6.3 5.9 8.0 5.5 33 0.06811 3.77 5159 6.9 4.4 6.8 4.5 7.2 4.0 6.6 4.6 5.8 5.4 5.7 5.5 5.6 5.6 6.9 5.2 34 0.07023 3.72 5226 6.7 4.1 6.7 4.2 7.2 3.8 6.6 4.2 5.6 5.2 5.6 5.2 5.6 5.2 7.0 4.9 35 0.07236 3.66 5359 6.6 4.1 6.6 4.2 6.7 4.1 6.4 4.4 5.4 5.3 5.4 5.3 5.3 5.4 6.6 5.0 36 0.07448 3.61 5293 6.4 3.9 6.3 3.9 6.9 3.5 6.2 4.1 5.4 4.8 5.4 4.9 5.4 4.8 6.7 4.6 37 0.07660 3.56 5633 6.7 4.4 6.7 4.4 7.4 3.7 6.6 4.5 5.8 5.3 5.7 5.4 5.7 5.4 7.0 5.1 38 0.07872 3.52 5479 5.9 3.8 5.9 3.8 6.2 3.6 5.8 3.9 5.0 4.7 5.0 4.7 5.0 4.7 6.1 4.5 39 0.08085 3.47 5578 5.2 3.3 5.2 3.3 5.4 3.1 5.0 3.5 4.4 4.0 4.4 4.0 4.3 4.1 5.4 3.8 40 0.08297 3.43 5580 5.3 3.3 5.3 3.3 5.3 3.3 5.2 3.4 4.6 4.0 4.6 4.1 4.6 4.1 5.8 3.8 41 0.08509 3.39 5936 5.3 3.3 5.3 3.2 5.4 3.2 5.1 3.4 4.5 4.0 4.5 4.0 4.4 4.1 5.5 3.8 42 0.08722 3.35 5783 4.7 3.0 4.7 3.0 4.5 3.3 4.6 3.1 3.9 3.8 4.0 3.8 3.9 3.8 4.8 3.6 43 0.08934 3.31 5889 4.4 3.0 4.4 2.9 4.5 2.9 4.3 3.1 3.8 3.6 3.8 3.5 3.7 3.6 4.5 3.4 44 0.09146 3.27 5966 4.4 2.8 4.5 2.8 4.5 2.8 4.3 2.9 3.8 3.5 3.8 3.5 3.8 3.5 4.7 3.3 45 0.09358 3.23 6145 4.0 2.6 4.0 2.6 4.1 2.5 3.9 2.8 3.5 3.2 3.5 3.2 3.5 3.2 4.2 3.0 46 0.09571 3.20 6202 3.6 2.3 3.7 2.3 3.6 2.3 3.6 2.4 3.2 2.8 3.2 2.7 3.2 2.7 4.0 2.6 47 0.09783 3.16 6042 3.7 2.3 3.8 2.2 3.5 2.5 3.7 2.3 3.1 2.9 3.1 2.9 3.1 2.9 4.0 2.7 48 0.09995 3.13 6198 3.5 2.2 3.5 2.1 3.3 2.4 3.4 2.2 2.9 2.8 2.9 2.8 2.9 2.8 3.6 2.6 49 0.10208 3.10 6421 3.3 2.1 3.3 2.1 3.1 2.3 3.2 2.1 2.7 2.6 2.7 2.6 2.7 2.6 3.4 2.4 50 0.10420 3.07 6403 3.2 2.2 3.3 2.1 3.1 2.3 3.2 2.2 2.8 2.6 2.8 2.6 2.8 2.6 3.3 2.5 51 0.10632 3.04 6357 2.9 2.0 3.0 1.9 2.8 2.1 2.9 2.0 2.6 2.4 2.6 2.3 2.6 2.4 3.1 2.2 52 0.10844 3.01 6389 2.6 1.9 2.6 1.9 2.6 2.0 2.6 1.9 2.4 2.2 2.4 2.2 2.3 2.2 2.8 2.1 53 0.11057 2.98 6580 2.8 1.9 2.8 1.9 2.7 2.0 2.8 2.0 2.5 2.3 2.4 2.3 2.4 2.3 2.9 2.2 54 0.11269 2.95 6663 2.8 1.9 2.8 1.8 2.7 1.9 2.7 1.9 2.5 2.1 2.5 2.1 2.5 2.1 3.1 2.0 55 0.11481 2.92 6582 2.6 1.9 2.7 1.8 2.6 1.9 2.6 1.9 2.4 2.1 2.4 2.1 2.4 2.1 2.9 2.0 56 0.11694 2.90 6572 2.6 1.8 2.6 1.8 2.5 1.9 2.6 1.8 2.3 2.1 2.3 2.1 2.3 2.1 2.7 2.0 57 0.11906 2.87 6820 2.4 1.7 2.4 1.7 2.3 1.8 2.4 1.8 2.1 2.0 2.1 2.0 2.1 2.0 2.5 1.9 58 0.12118 2.85 6970 2.3 1.6 2.3 1.6 2.2 1.8 2.3 1.6 2.0 1.9 2.0 1.9 2.0 2.0 2.3 1.8 59 0.12330 2.82 6717 2.4 1.7 2.5 1.6 2.2 1.8 2.4 1.7 2.0 2.0 2.0 2.0 2.0 2.0 2.4 1.9 60 0.12543 2.80 5677 2.1 1.6 2.1 1.6 2.0 1.7 2.0 1.6 1.8 1.8 1.8 1.8 1.8 1.8 2.0 1.8 Totals: 277916 6.4 4.3 6.4 4.3 7.6 3.2 6.3 4.4 5.5 5.2 5.5 5.2 5.5 5.2 6.6 4.9 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! As you can imagine, I have pseudo-translation peaks , the strongest at 48 % height (of the origin peak) at 0.0 0.0 0.5, other two at ~ 30 % height at 0.0 0.5 0.0 and 0.5 0.0 0.0 (and so at 0.5 0.0 0.5, etc.). The cell is large, 229 229 72 90 90 120, data processed at several space group options with good statistics; the highest symmetry is P622. With much struggle, some solutions from molecular replacement came out. Basically, the monomers (~274 residues each) makes "strings" (pack of one monomer over the other in one dimension), then these strings seem to be able to pack themselves in parallel (within them there must be an up/down feature) and parallel to the shorter cell axis. Given the cell dimensions, it seems most probable that I have 48 mol/au, although I cannot discard 36 mol/au (or even something between, depending upon the symmetry). I attach a picture of the supposed pack in case of 48 mol/au, viewed down to the 120 angle. The packing has made me practically rule out space groups P622 and P312, yet the need for a 2-fold axis passing through both 0, 1, 0 and 1, 0 0. Whenever I process the data in a lower space group, xtriage suggests strongly twinning, and close to 50 % in almost any operation. Also, whatever space group I choose for refinement, the results are all some how alike, R-free stucks (with any twinning operation that I can use to refine) at about 40/41 %; non-twinned refinement stucks R-free around 48 %. The investigated space groups include P321, P6, P3, P2, C222, C2 and P1 (besides, of course, at the beginning, P622 and P312), with several combinations of molecules/au (I there might be screw axes, although no systematic absences). With P1, I have the lowest reason between R and R-free (because R is higher). I must add that I have already tested some refinement alternatives, such as bulk solvent models, fix these, etc., but of course not all alternatives. Much information has been produced; one other highlight I think is the fact that most of the time atomic B-factors are refined to the ground, I suppose because of the abnormal intensity distribution/data modulation. I have a couple of questions and other information which I prefer to number since from now. a) Is there a source of information for refinement of such modulated data? Or previous cases reported in the literature? b) I have not tried yet P1 with 48 molecules. I run out of chain ID's, what does phenix accept besides the alphabet and 0-9? c) For P3, with any of the 3 twin operators the result is practically the same. To my knowledge, only shelxl can deal, currently, with more that one twinned domain, but these can only be produced in a iterative fashion. So, what might be the other way round? Is this development expected for phenix? For P1, I would have 11 pseudo-merohedral twin operations... I think the kind of packing is quite prone to twinning. d) Concerning what is raised in c, how necessary is to combine the 3 possible twin operators with the 3 reindexing possibilities.... e) How can I convince phenix to use the suggested twin operation 1/2*h-1/2*k,3/2*h+1/2*k,l in C222 (and some others with the * symbol in C2)? Much more information is available; I think I could pick the main ones. Thanks for any help. Jorge
Hi Jorge, what does phenix.xtriage say about the data processed in P1? Cheers, Paul On Jun 29, 2008, at 6:43 AM, iulek wrote:
Dear all,
I have a strongly modulated dataset as can be observed in the truncate output below. Specially, the modulation is higher for L odd/even and at lower resolution:
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Analysis of mean intensity by parity for reflection classes
For each class, Mn(I/sig(I)) is given for even and odd parity with respect to the condition, eg group 1: h even & odd; group 7 h+k+l even & odd; group 8 h+k=2n & h+l=2n & k+l=2n or not
Range Min_S Dmax Nref 1 2 3 4 5 6 7 8 h k l h+k h+l k+l h+k+l h+k,h+l,k+l 1 0.00018 20.85 519 13.2 8.9 13.9 8.2 22.3 2.4 13.3 8.9 12.5 9.6 12.9 9.0 12.6 9.5 16.5 9.2 2 0.00230 15.04 994 15.9 16.0 15.3 16.5 30.1 2.3 15.7 16.2 15.1 16.7 14.9 16.8 15.1 16.7 13.5 16.6 3 0.00442 12.36 1289 17.2 16.0 17.0 16.2 33.8 3.7 17.2 16.0 14.9 18.0 14.7 18.2 14.9 18.0 13.1 17.4 4 0.00655 10.74 1568 20.7 18.9 20.3 19.2 35.5 4.9 20.4 19.2 18.7 20.7 18.3 21.0 18.5 20.9 17.7 20.3 5 0.00867 9.63 1759 20.3 15.8 20.1 16.0 33.2 4.9 20.1 15.9 18.7 17.3 18.6 17.4 18.8 17.2 21.6 16.9 6 0.01079 8.80 2042 19.6 15.4 19.3 15.7 30.5 5.8 19.5 15.5 17.6 17.3 17.5 17.4 17.6 17.3 19.9 16.7 7 0.01291 8.15 2206 15.9 12.0 15.8 12.1 22.6 5.0 15.5 12.4 14.3 13.5 14.1 13.7 14.0 13.8 16.2 13.2 8 0.01504 7.63 2393 11.8 9.0 11.5 9.3 18.6 3.6 11.7 9.1 10.5 10.2 10.3 10.3 10.4 10.3 12.0 9.9 9 0.01716 7.20 2526 9.8 6.5 9.8 6.5 13.8 3.2 9.8 6.6 9.0 7.3 9.0 7.3 9.0 7.4 11.6 7.1 10 0.01928 6.83 2747 11.1 7.5 11.0 7.6 15.7 3.0 10.8 7.8 10.0 8.5 9.9 8.6 9.8 8.6 12.3 8.3 11 0.02141 6.52 2867 10.3 7.3 10.2 7.3 14.4 3.0 10.3 7.3 9.4 8.1 9.4 8.1 9.4 8.2 11.7 7.9 12 0.02353 6.24 3122 8.6 5.8 8.5 5.8 11.6 3.0 8.4 5.9 7.3 6.9 7.3 6.9 7.2 7.0 8.8 6.6 13 0.02565 6.00 3124 7.9 5.7 7.7 5.9 11.1 2.9 7.7 5.9 6.8 6.7 6.8 6.8 6.8 6.7 7.8 6.5 14 0.02777 5.78 3346 9.8 6.7 9.7 6.7 12.7 3.5 9.6 6.8 8.8 7.7 8.7 7.8 8.6 7.9 10.7 7.5 15 0.02990 5.59 3428 9.0 5.6 8.9 5.7 11.2 3.1 8.8 5.8 7.9 6.7 7.8 6.8 7.7 6.9 9.9 6.4 16 0.03202 5.41 3633 8.3 5.5 8.2 5.5 10.9 3.5 8.2 5.6 7.1 6.6 7.1 6.6 7.1 6.6 8.8 6.2 17 0.03414 5.25 3658 9.6 6.2 9.4 6.3 12.4 3.7 9.4 6.4 8.4 7.3 8.4 7.3 8.2 7.5 10.6 7.0 18 0.03627 5.10 3696 10.2 6.4 10.1 6.5 12.5 4.3 9.8 6.7 8.8 7.8 8.7 7.9 8.6 7.9 10.8 7.4 19 0.03839 4.97 3955 10.1 6.9 9.9 7.0 12.6 4.5 9.8 7.1 8.8 8.2 8.6 8.3 8.6 8.3 10.4 7.9 20 0.04051 4.84 3902 10.9 7.2 10.9 7.2 13.4 4.6 10.7 7.4 9.7 8.4 9.7 8.4 9.7 8.4 12.1 8.0 21 0.04263 4.73 4207 11.4 6.8 11.3 6.9 13.7 4.8 11.1 7.0 9.5 8.5 9.4 8.6 9.5 8.6 12.0 8.1 22 0.04476 4.62 4169 9.7 6.8 9.6 6.9 12.4 4.6 9.5 7.0 8.3 8.1 8.3 8.2 8.2 8.2 9.7 7.8 23 0.04688 4.52 4100 11.1 6.7 11.0 6.8 12.6 5.5 10.8 7.0 9.0 8.8 8.9 8.8 8.9 8.9 11.0 8.2 24 0.04900 4.42 4605 10.8 6.5 10.7 6.5 12.3 4.9 10.5 6.8 9.5 7.8 9.4 7.9 9.3 7.9 12.2 7.5 25 0.05113 4.33 4449 9.6 6.1 9.5 6.2 11.1 4.6 9.4 6.3 8.3 7.4 8.2 7.5 8.2 7.5 10.2 7.0 26 0.05325 4.25 4528 9.1 5.8 9.1 5.8 10.0 4.8 8.8 6.0 7.6 7.2 7.5 7.3 7.5 7.3 9.2 6.8 27 0.05537 4.17 4782 8.6 5.3 8.6 5.3 9.7 4.6 8.5 5.4 7.5 6.5 7.4 6.5 7.4 6.5 9.5 6.1 28 0.05749 4.10 4774 8.3 5.2 8.2 5.3 9.6 3.9 8.0 5.4 7.0 6.4 7.0 6.4 6.9 6.5 8.6 6.1 29 0.05962 4.02 4837 8.1 5.6 8.1 5.7 9.7 4.4 7.9 5.8 7.2 6.6 7.2 6.6 7.2 6.6 8.6 6.4 30 0.06174 3.96 5066 8.2 4.9 8.2 4.9 8.9 4.2 8.0 5.1 6.9 6.2 6.8 6.2 6.7 6.3 8.6 5.8 31 0.06386 3.89 4954 7.4 4.7 7.3 4.8 7.9 4.1 7.2 4.9 6.2 5.9 6.1 6.0 6.2 5.9 7.5 5.6 32 0.06599 3.83 5052 7.6 4.6 7.6 4.6 8.2 4.0 7.4 4.8 6.4 5.8 6.4 5.8 6.3 5.9 8.0 5.5 33 0.06811 3.77 5159 6.9 4.4 6.8 4.5 7.2 4.0 6.6 4.6 5.8 5.4 5.7 5.5 5.6 5.6 6.9 5.2 34 0.07023 3.72 5226 6.7 4.1 6.7 4.2 7.2 3.8 6.6 4.2 5.6 5.2 5.6 5.2 5.6 5.2 7.0 4.9 35 0.07236 3.66 5359 6.6 4.1 6.6 4.2 6.7 4.1 6.4 4.4 5.4 5.3 5.4 5.3 5.3 5.4 6.6 5.0 36 0.07448 3.61 5293 6.4 3.9 6.3 3.9 6.9 3.5 6.2 4.1 5.4 4.8 5.4 4.9 5.4 4.8 6.7 4.6 37 0.07660 3.56 5633 6.7 4.4 6.7 4.4 7.4 3.7 6.6 4.5 5.8 5.3 5.7 5.4 5.7 5.4 7.0 5.1 38 0.07872 3.52 5479 5.9 3.8 5.9 3.8 6.2 3.6 5.8 3.9 5.0 4.7 5.0 4.7 5.0 4.7 6.1 4.5 39 0.08085 3.47 5578 5.2 3.3 5.2 3.3 5.4 3.1 5.0 3.5 4.4 4.0 4.4 4.0 4.3 4.1 5.4 3.8 40 0.08297 3.43 5580 5.3 3.3 5.3 3.3 5.3 3.3 5.2 3.4 4.6 4.0 4.6 4.1 4.6 4.1 5.8 3.8 41 0.08509 3.39 5936 5.3 3.3 5.3 3.2 5.4 3.2 5.1 3.4 4.5 4.0 4.5 4.0 4.4 4.1 5.5 3.8 42 0.08722 3.35 5783 4.7 3.0 4.7 3.0 4.5 3.3 4.6 3.1 3.9 3.8 4.0 3.8 3.9 3.8 4.8 3.6 43 0.08934 3.31 5889 4.4 3.0 4.4 2.9 4.5 2.9 4.3 3.1 3.8 3.6 3.8 3.5 3.7 3.6 4.5 3.4 44 0.09146 3.27 5966 4.4 2.8 4.5 2.8 4.5 2.8 4.3 2.9 3.8 3.5 3.8 3.5 3.8 3.5 4.7 3.3 45 0.09358 3.23 6145 4.0 2.6 4.0 2.6 4.1 2.5 3.9 2.8 3.5 3.2 3.5 3.2 3.5 3.2 4.2 3.0 46 0.09571 3.20 6202 3.6 2.3 3.7 2.3 3.6 2.3 3.6 2.4 3.2 2.8 3.2 2.7 3.2 2.7 4.0 2.6 47 0.09783 3.16 6042 3.7 2.3 3.8 2.2 3.5 2.5 3.7 2.3 3.1 2.9 3.1 2.9 3.1 2.9 4.0 2.7 48 0.09995 3.13 6198 3.5 2.2 3.5 2.1 3.3 2.4 3.4 2.2 2.9 2.8 2.9 2.8 2.9 2.8 3.6 2.6 49 0.10208 3.10 6421 3.3 2.1 3.3 2.1 3.1 2.3 3.2 2.1 2.7 2.6 2.7 2.6 2.7 2.6 3.4 2.4 50 0.10420 3.07 6403 3.2 2.2 3.3 2.1 3.1 2.3 3.2 2.2 2.8 2.6 2.8 2.6 2.8 2.6 3.3 2.5 51 0.10632 3.04 6357 2.9 2.0 3.0 1.9 2.8 2.1 2.9 2.0 2.6 2.4 2.6 2.3 2.6 2.4 3.1 2.2 52 0.10844 3.01 6389 2.6 1.9 2.6 1.9 2.6 2.0 2.6 1.9 2.4 2.2 2.4 2.2 2.3 2.2 2.8 2.1 53 0.11057 2.98 6580 2.8 1.9 2.8 1.9 2.7 2.0 2.8 2.0 2.5 2.3 2.4 2.3 2.4 2.3 2.9 2.2 54 0.11269 2.95 6663 2.8 1.9 2.8 1.8 2.7 1.9 2.7 1.9 2.5 2.1 2.5 2.1 2.5 2.1 3.1 2.0 55 0.11481 2.92 6582 2.6 1.9 2.7 1.8 2.6 1.9 2.6 1.9 2.4 2.1 2.4 2.1 2.4 2.1 2.9 2.0 56 0.11694 2.90 6572 2.6 1.8 2.6 1.8 2.5 1.9 2.6 1.8 2.3 2.1 2.3 2.1 2.3 2.1 2.7 2.0 57 0.11906 2.87 6820 2.4 1.7 2.4 1.7 2.3 1.8 2.4 1.8 2.1 2.0 2.1 2.0 2.1 2.0 2.5 1.9 58 0.12118 2.85 6970 2.3 1.6 2.3 1.6 2.2 1.8 2.3 1.6 2.0 1.9 2.0 1.9 2.0 2.0 2.3 1.8 59 0.12330 2.82 6717 2.4 1.7 2.5 1.6 2.2 1.8 2.4 1.7 2.0 2.0 2.0 2.0 2.0 2.0 2.4 1.9 60 0.12543 2.80 5677 2.1 1.6 2.1 1.6 2.0 1.7 2.0 1.6 1.8 1.8 1.8 1.8 1.8 1.8 2.0 1.8
Totals: 277916 6.4 4.3 6.4 4.3 7.6 3.2 6.3 4.4 5.5 5.2 5.5 5.2 5.5 5.2 6.6 4.9
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !
As you can imagine, I have pseudo-translation peaks , the strongest at 48 % height (of the origin peak) at 0.0 0.0 0.5, other two at ~ 30 % height at 0.0 0.5 0.0 and 0.5 0.0 0.0 (and so at 0.5 0.0 0.5, etc.). The cell is large, 229 229 72 90 90 120, data processed at several space group options with good statistics; the highest symmetry is P622. With much struggle, some solutions from molecular replacement came out. Basically, the monomers (~274 residues each) makes "strings" (pack of one monomer over the other in one dimension), then these strings seem to be able to pack themselves in parallel (within them there must be an up/down feature) and parallel to the shorter cell axis. Given the cell dimensions, it seems most probable that I have 48 mol/au, although I cannot discard 36 mol/au (or even something between, depending upon the symmetry). I attach a picture of the supposed pack in case of 48 mol/au, viewed down to the 120 angle. The packing has made me practically rule out space groups P622 and P312, yet the need for a 2-fold axis passing through both 0, 1, 0 and 1, 0 0. Whenever I process the data in a lower space group, xtriage suggests strongly twinning, and close to 50 % in almost any operation. Also, whatever space group I choose for refinement, the results are all some how alike, R-free stucks (with any twinning operation that I can use to refine) at about 40/41 %; non-twinned refinement stucks R-free around 48 %. The investigated space groups include P321, P6, P3, P2, C222, C2 and P1 (besides, of course, at the beginning, P622 and P312), with several combinations of molecules/au (I there might be screw axes, although no systematic absences). With P1, I have the lowest reason between R and R-free (because R is higher). I must add that I have already tested some refinement alternatives, such as bulk solvent models, fix these, etc., but of course not all alternatives. Much information has been produced; one other highlight I think is the fact that most of the time atomic B- factors are refined to the ground, I suppose because of the abnormal intensity distribution/data modulation. I have a couple of questions and other information which I prefer to number since from now. a) Is there a source of information for refinement of such modulated data? Or previous cases reported in the literature? b) I have not tried yet P1 with 48 molecules. I run out of chain ID's, what does phenix accept besides the alphabet and 0-9? c) For P3, with any of the 3 twin operators the result is practically the same. To my knowledge, only shelxl can deal, currently, with more that one twinned domain, but these can only be produced in a iterative fashion. So, what might be the other way round? Is this development expected for phenix? For P1, I would have 11 pseudo-merohedral twin operations... I think the kind of packing is quite prone to twinning. d) Concerning what is raised in c, how necessary is to combine the 3 possible twin operators with the 3 reindexing possibilities.... e) How can I convince phenix to use the suggested twin operation 1/2*h-1/2*k,3/2*h+1/2*k,l in C222 (and some others with the * symbol in C2)? Much more information is available; I think I could pick the main ones. Thanks for any help.
Jorge
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
-- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Administrator: Delia Clark [ [email protected] ][ 1-510-486-6331 ] --
Hi, Paul, Thanks four you reply. In summary, some warnings, I think the main ones are the off-origin peaks in the native Patterson and the twinning operators. I can send you the whole output (or snipping the intermediate twin analyses) if you like, or post to the bb if appropriate. Concerning twin, I have below: Statistics depending on twin laws ------------------------------------------------------------------ | Operator | type | R obs. | Britton alpha | H alpha | ML alpha | ------------------------------------------------------------------ | -k,h+k,l | PM | 0.120 | 0.380 | 0.388 | 0.385 | | h+k,-h,l | PM | 0.120 | 0.376 | 0.388 | 0.349 | | -h-k,h,l | PM | 0.120 | 0.371 | 0.388 | 0.350 | | k,-h-k,l | PM | 0.120 | 0.379 | 0.388 | 0.370 | | -h,-k,l | PM | 0.106 | 0.391 | 0.408 | 0.392 | | k,h,-l | PM | 0.108 | 0.382 | 0.399 | 0.401 | | h,-h-k,-l | PM | 0.121 | 0.372 | 0.388 | 0.370 | | h+k,-k,-l | PM | 0.124 | 0.377 | 0.388 | 0.362 | | -h-k,k,-l | PM | 0.123 | 0.377 | 0.387 | 0.373 | | -k,-h,-l | PM | 0.109 | 0.390 | 0.399 | 0.430 | | -h,h+k,-l | PM | 0.122 | 0.377 | 0.387 | 0.370 | ------------------------------------------------------------------ Please, let me know if appropriate to send the whole output or ask for any further information you find necessary. Many thanks once again. Jorge
Hi Jorge,
what does phenix.xtriage say about the data processed in P1?
Cheers, Paul
On Jun 29, 2008, at 6:43 AM, iulek wrote:
Dear all,
I have a strongly modulated dataset as can be observed in the truncate output below. Specially, the modulation is higher for L odd/even and at lower resolution:
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Analysis of mean intensity by parity for reflection classes
For each class, Mn(I/sig(I)) is given for even and odd parity with respect to the condition, eg group 1: h even & odd; group 7 h+k+l even & odd; group 8 h+k=2n & h+l=2n & k+l=2n or not
Range Min_S Dmax Nref 1 2 3 4 5 6 7 8 h k l h+k h+l k+l h+k+l h+k,h+l,k+l 1 0.00018 20.85 519 13.2 8.9 13.9 8.2 22.3 2.4 13.3 8.9 12.5 9.6 12.9 9.0 12.6 9.5 16.5 9.2 2 0.00230 15.04 994 15.9 16.0 15.3 16.5 30.1 2.3 15.7 16.2 15.1 16.7 14.9 16.8 15.1 16.7 13.5 16.6 3 0.00442 12.36 1289 17.2 16.0 17.0 16.2 33.8 3.7 17.2 16.0 14.9 18.0 14.7 18.2 14.9 18.0 13.1 17.4 4 0.00655 10.74 1568 20.7 18.9 20.3 19.2 35.5 4.9 20.4 19.2 18.7 20.7 18.3 21.0 18.5 20.9 17.7 20.3 5 0.00867 9.63 1759 20.3 15.8 20.1 16.0 33.2 4.9 20.1 15.9 18.7 17.3 18.6 17.4 18.8 17.2 21.6 16.9 6 0.01079 8.80 2042 19.6 15.4 19.3 15.7 30.5 5.8 19.5 15.5 17.6 17.3 17.5 17.4 17.6 17.3 19.9 16.7 7 0.01291 8.15 2206 15.9 12.0 15.8 12.1 22.6 5.0 15.5 12.4 14.3 13.5 14.1 13.7 14.0 13.8 16.2 13.2 8 0.01504 7.63 2393 11.8 9.0 11.5 9.3 18.6 3.6 11.7 9.1 10.5 10.2 10.3 10.3 10.4 10.3 12.0 9.9 9 0.01716 7.20 2526 9.8 6.5 9.8 6.5 13.8 3.2 9.8 6.6 9.0 7.3 9.0 7.3 9.0 7.4 11.6 7.1 10 0.01928 6.83 2747 11.1 7.5 11.0 7.6 15.7 3.0 10.8 7.8 10.0 8.5 9.9 8.6 9.8 8.6 12.3 8.3 11 0.02141 6.52 2867 10.3 7.3 10.2 7.3 14.4 3.0 10.3 7.3 9.4 8.1 9.4 8.1 9.4 8.2 11.7 7.9 12 0.02353 6.24 3122 8.6 5.8 8.5 5.8 11.6 3.0 8.4 5.9 7.3 6.9 7.3 6.9 7.2 7.0 8.8 6.6 13 0.02565 6.00 3124 7.9 5.7 7.7 5.9 11.1 2.9 7.7 5.9 6.8 6.7 6.8 6.8 6.8 6.7 7.8 6.5 14 0.02777 5.78 3346 9.8 6.7 9.7 6.7 12.7 3.5 9.6 6.8 8.8 7.7 8.7 7.8 8.6 7.9 10.7 7.5 15 0.02990 5.59 3428 9.0 5.6 8.9 5.7 11.2 3.1 8.8 5.8 7.9 6.7 7.8 6.8 7.7 6.9 9.9 6.4 16 0.03202 5.41 3633 8.3 5.5 8.2 5.5 10.9 3.5 8.2 5.6 7.1 6.6 7.1 6.6 7.1 6.6 8.8 6.2 17 0.03414 5.25 3658 9.6 6.2 9.4 6.3 12.4 3.7 9.4 6.4 8.4 7.3 8.4 7.3 8.2 7.5 10.6 7.0 18 0.03627 5.10 3696 10.2 6.4 10.1 6.5 12.5 4.3 9.8 6.7 8.8 7.8 8.7 7.9 8.6 7.9 10.8 7.4 19 0.03839 4.97 3955 10.1 6.9 9.9 7.0 12.6 4.5 9.8 7.1 8.8 8.2 8.6 8.3 8.6 8.3 10.4 7.9 20 0.04051 4.84 3902 10.9 7.2 10.9 7.2 13.4 4.6 10.7 7.4 9.7 8.4 9.7 8.4 9.7 8.4 12.1 8.0 21 0.04263 4.73 4207 11.4 6.8 11.3 6.9 13.7 4.8 11.1 7.0 9.5 8.5 9.4 8.6 9.5 8.6 12.0 8.1 22 0.04476 4.62 4169 9.7 6.8 9.6 6.9 12.4 4.6 9.5 7.0 8.3 8.1 8.3 8.2 8.2 8.2 9.7 7.8 23 0.04688 4.52 4100 11.1 6.7 11.0 6.8 12.6 5.5 10.8 7.0 9.0 8.8 8.9 8.8 8.9 8.9 11.0 8.2 24 0.04900 4.42 4605 10.8 6.5 10.7 6.5 12.3 4.9 10.5 6.8 9.5 7.8 9.4 7.9 9.3 7.9 12.2 7.5 25 0.05113 4.33 4449 9.6 6.1 9.5 6.2 11.1 4.6 9.4 6.3 8.3 7.4 8.2 7.5 8.2 7.5 10.2 7.0 26 0.05325 4.25 4528 9.1 5.8 9.1 5.8 10.0 4.8 8.8 6.0 7.6 7.2 7.5 7.3 7.5 7.3 9.2 6.8 27 0.05537 4.17 4782 8.6 5.3 8.6 5.3 9.7 4.6 8.5 5.4 7.5 6.5 7.4 6.5 7.4 6.5 9.5 6.1 28 0.05749 4.10 4774 8.3 5.2 8.2 5.3 9.6 3.9 8.0 5.4 7.0 6.4 7.0 6.4 6.9 6.5 8.6 6.1 29 0.05962 4.02 4837 8.1 5.6 8.1 5.7 9.7 4.4 7.9 5.8 7.2 6.6 7.2 6.6 7.2 6.6 8.6 6.4 30 0.06174 3.96 5066 8.2 4.9 8.2 4.9 8.9 4.2 8.0 5.1 6.9 6.2 6.8 6.2 6.7 6.3 8.6 5.8 31 0.06386 3.89 4954 7.4 4.7 7.3 4.8 7.9 4.1 7.2 4.9 6.2 5.9 6.1 6.0 6.2 5.9 7.5 5.6 32 0.06599 3.83 5052 7.6 4.6 7.6 4.6 8.2 4.0 7.4 4.8 6.4 5.8 6.4 5.8 6.3 5.9 8.0 5.5 33 0.06811 3.77 5159 6.9 4.4 6.8 4.5 7.2 4.0 6.6 4.6 5.8 5.4 5.7 5.5 5.6 5.6 6.9 5.2 34 0.07023 3.72 5226 6.7 4.1 6.7 4.2 7.2 3.8 6.6 4.2 5.6 5.2 5.6 5.2 5.6 5.2 7.0 4.9 35 0.07236 3.66 5359 6.6 4.1 6.6 4.2 6.7 4.1 6.4 4.4 5.4 5.3 5.4 5.3 5.3 5.4 6.6 5.0 36 0.07448 3.61 5293 6.4 3.9 6.3 3.9 6.9 3.5 6.2 4.1 5.4 4.8 5.4 4.9 5.4 4.8 6.7 4.6 37 0.07660 3.56 5633 6.7 4.4 6.7 4.4 7.4 3.7 6.6 4.5 5.8 5.3 5.7 5.4 5.7 5.4 7.0 5.1 38 0.07872 3.52 5479 5.9 3.8 5.9 3.8 6.2 3.6 5.8 3.9 5.0 4.7 5.0 4.7 5.0 4.7 6.1 4.5 39 0.08085 3.47 5578 5.2 3.3 5.2 3.3 5.4 3.1 5.0 3.5 4.4 4.0 4.4 4.0 4.3 4.1 5.4 3.8 40 0.08297 3.43 5580 5.3 3.3 5.3 3.3 5.3 3.3 5.2 3.4 4.6 4.0 4.6 4.1 4.6 4.1 5.8 3.8 41 0.08509 3.39 5936 5.3 3.3 5.3 3.2 5.4 3.2 5.1 3.4 4.5 4.0 4.5 4.0 4.4 4.1 5.5 3.8 42 0.08722 3.35 5783 4.7 3.0 4.7 3.0 4.5 3.3 4.6 3.1 3.9 3.8 4.0 3.8 3.9 3.8 4.8 3.6 43 0.08934 3.31 5889 4.4 3.0 4.4 2.9 4.5 2.9 4.3 3.1 3.8 3.6 3.8 3.5 3.7 3.6 4.5 3.4 44 0.09146 3.27 5966 4.4 2.8 4.5 2.8 4.5 2.8 4.3 2.9 3.8 3.5 3.8 3.5 3.8 3.5 4.7 3.3 45 0.09358 3.23 6145 4.0 2.6 4.0 2.6 4.1 2.5 3.9 2.8 3.5 3.2 3.5 3.2 3.5 3.2 4.2 3.0 46 0.09571 3.20 6202 3.6 2.3 3.7 2.3 3.6 2.3 3.6 2.4 3.2 2.8 3.2 2.7 3.2 2.7 4.0 2.6 47 0.09783 3.16 6042 3.7 2.3 3.8 2.2 3.5 2.5 3.7 2.3 3.1 2.9 3.1 2.9 3.1 2.9 4.0 2.7 48 0.09995 3.13 6198 3.5 2.2 3.5 2.1 3.3 2.4 3.4 2.2 2.9 2.8 2.9 2.8 2.9 2.8 3.6 2.6 49 0.10208 3.10 6421 3.3 2.1 3.3 2.1 3.1 2.3 3.2 2.1 2.7 2.6 2.7 2.6 2.7 2.6 3.4 2.4 50 0.10420 3.07 6403 3.2 2.2 3.3 2.1 3.1 2.3 3.2 2.2 2.8 2.6 2.8 2.6 2.8 2.6 3.3 2.5 51 0.10632 3.04 6357 2.9 2.0 3.0 1.9 2.8 2.1 2.9 2.0 2.6 2.4 2.6 2.3 2.6 2.4 3.1 2.2 52 0.10844 3.01 6389 2.6 1.9 2.6 1.9 2.6 2.0 2.6 1.9 2.4 2.2 2.4 2.2 2.3 2.2 2.8 2.1 53 0.11057 2.98 6580 2.8 1.9 2.8 1.9 2.7 2.0 2.8 2.0 2.5 2.3 2.4 2.3 2.4 2.3 2.9 2.2 54 0.11269 2.95 6663 2.8 1.9 2.8 1.8 2.7 1.9 2.7 1.9 2.5 2.1 2.5 2.1 2.5 2.1 3.1 2.0 55 0.11481 2.92 6582 2.6 1.9 2.7 1.8 2.6 1.9 2.6 1.9 2.4 2.1 2.4 2.1 2.4 2.1 2.9 2.0 56 0.11694 2.90 6572 2.6 1.8 2.6 1.8 2.5 1.9 2.6 1.8 2.3 2.1 2.3 2.1 2.3 2.1 2.7 2.0 57 0.11906 2.87 6820 2.4 1.7 2.4 1.7 2.3 1.8 2.4 1.8 2.1 2.0 2.1 2.0 2.1 2.0 2.5 1.9 58 0.12118 2.85 6970 2.3 1.6 2.3 1.6 2.2 1.8 2.3 1.6 2.0 1.9 2.0 1.9 2.0 2.0 2.3 1.8 59 0.12330 2.82 6717 2.4 1.7 2.5 1.6 2.2 1.8 2.4 1.7 2.0 2.0 2.0 2.0 2.0 2.0 2.4 1.9 60 0.12543 2.80 5677 2.1 1.6 2.1 1.6 2.0 1.7 2.0 1.6 1.8 1.8 1.8 1.8 1.8 1.8 2.0 1.8
Totals: 277916 6.4 4.3 6.4 4.3 7.6 3.2 6.3 4.4 5.5 5.2 5.5 5.2 5.5 5.2 6.6 4.9
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !
As you can imagine, I have pseudo-translation peaks , the strongest at 48 % height (of the origin peak) at 0.0 0.0 0.5, other two at ~ 30 % height at 0.0 0.5 0.0 and 0.5 0.0 0.0 (and so at 0.5 0.0 0.5, etc.). The cell is large, 229 229 72 90 90 120, data processed at several space group options with good statistics; the highest symmetry is P622. With much struggle, some solutions from molecular replacement came out. Basically, the monomers (~274 residues each) makes "strings" (pack of one monomer over the other in one dimension), then these strings seem to be able to pack themselves in parallel (within them there must be an up/down feature) and parallel to the shorter cell axis. Given the cell dimensions, it seems most probable that I have 48 mol/au, although I cannot discard 36 mol/au (or even something between, depending upon the symmetry). I attach a picture of the supposed pack in case of 48 mol/au, viewed down to the 120 angle. The packing has made me practically rule out space groups P622 and P312, yet the need for a 2-fold axis passing through both 0, 1, 0 and 1, 0 0. Whenever I process the data in a lower space group, xtriage suggests strongly twinning, and close to 50 % in almost any operation. Also, whatever space group I choose for refinement, the results are all some how alike, R-free stucks (with any twinning operation that I can use to refine) at about 40/41 %; non-twinned refinement stucks R-free around 48 %. The investigated space groups include P321, P6, P3, P2, C222, C2 and P1 (besides, of course, at the beginning, P622 and P312), with several combinations of molecules/au (I there might be screw axes, although no systematic absences). With P1, I have the lowest reason between R and R-free (because R is higher). I must add that I have already tested some refinement alternatives, such as bulk solvent models, fix these, etc., but of course not all alternatives. Much information has been produced; one other highlight I think is the fact that most of the time atomic B- factors are refined to the ground, I suppose because of the abnormal intensity distribution/data modulation. I have a couple of questions and other information which I prefer to number since from now. a) Is there a source of information for refinement of such modulated data? Or previous cases reported in the literature? b) I have not tried yet P1 with 48 molecules. I run out of chain ID's, what does phenix accept besides the alphabet and 0-9? c) For P3, with any of the 3 twin operators the result is practically the same. To my knowledge, only shelxl can deal, currently, with more that one twinned domain, but these can only be produced in a iterative fashion. So, what might be the other way round? Is this development expected for phenix? For P1, I would have 11 pseudo-merohedral twin operations... I think the kind of packing is quite prone to twinning. d) Concerning what is raised in c, how necessary is to combine the 3 possible twin operators with the 3 reindexing possibilities.... e) How can I convince phenix to use the suggested twin operation 1/2*h-1/2*k,3/2*h+1/2*k,l in C222 (and some others with the * symbol in C2)? Much more information is available; I think I could pick the main ones. Thanks for any help.
Jorge
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
participants (2)
-
iulek -
Paul Adams