[phenixbb] refinement with several twins / modulated data / pseudo-translational symmetry
iulek
iulek at interponta.com.br
Sun Jun 29 06:43:52 PDT 2008
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
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