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