[phenixbb] refinement with several twins / modulated data / pseudo-translational symmetry
Paul Adams
PDAdams at lbl.gov
Sun Jun 29 08:36:59 PDT 2008
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
>
> <snapshot35_ed.png>
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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
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