[phenixbb] refinement with several twins / modulated data / pseudo-translational symmetry
iulek
iulek at interponta.com.br
Sun Jun 29 09:24:14 PDT 2008
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
>>
>> <snapshot35_ed.png>
>> _______________________________________________
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>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>
>
>
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