Hi Jürgen, Kelly and Nat,
I tried XDS and MosFilm, they simply cannot index the data.
I reprocessed the data yesterday with HKL2000 starting from frame #30 (splitting 1-29, 30-360), I did get it indexed to I4 and refined to very nice x/y chi^2 and covering most spots, I then used the index/refinement numbers for the whole data set. it seems that other spots were from a “nicely” positioned secondary crystal which fooled the program to pick P4 space group.
I scaled the data as I4 and I422 to see which one is better. The I4 data set, ~95% complete overall, 9.2% R-sym. Xtriage suggested it should have higher symmetry I422 or twin (-k, -h, -l, almost 50%). MR sent well and best SG is I4, 2 mol/ASU, r and r-free went to about 27% and 32%, but if I used the twin-law in phenix.refine and ask phenix to generate r-free-flags with twinning in mind, the numbers went to ~22% and 27%.
Shell Lower Upper Average Average Norm. Linear Square
limit Angstrom I error stat. Chi**2 R-fac R-fac
50.00 7.32 440.7 8.8 5.1 1.481 0.027 0.030
7.32 5.81 167.2 4.2 3.2 1.868 0.045 0.048
5.81 5.08 196.3 5.1 3.9 2.130 0.053 0.058
5.08 4.62 243.1 6.2 4.7 2.264 0.056 0.061
4.62 4.29 236.7 6.4 4.9 2.057 0.055 0.055
4.29 4.03 167.6 5.6 4.7 1.819 0.067 0.066
4.03 3.83 139.5 5.6 5.0 1.740 0.083 0.075
3.83 3.66 110.2 5.5 5.1 1.645 0.102 0.091
3.66 3.52 92.5 5.6 5.3 1.459 0.117 0.101
3.52 3.40 76.5 5.7 5.4 1.372 0.143 0.124
3.40 3.30 59.3 5.7 5.5 1.278 0.179 0.146
3.30 3.20 47.3 5.7 5.6 1.161 0.212 0.179
3.20 3.12 40.7 5.8 5.7 1.103 0.241 0.201
3.12 3.04 31.6 5.8 5.8 1.057 0.298 0.254
3.04 2.97 28.9 5.9 5.9 1.031 0.331 0.271
2.97 2.91 22.6 5.9 5.9 0.985 0.400 0.340
2.91 2.85 19.0 6.0 6.0 0.991 0.484 0.405
2.85 2.80 17.1 6.1 6.1 0.957 0.518 0.437
2.80 2.75 14.6 6.2 6.2 0.908 0.577 0.485
2.75 2.70 13.0 6.4 6.3 0.931 0.645 0.550
All reflections 112.9 5.9 5.3 1.455 0.092 0.066
The I422 data (below), 1 mol/ASU, r and r-free were about 27% and 32%.
Shell Lower Upper Average Average Norm. Linear Square
limit Angstrom I error stat. Chi**2 R-fac R-fac
50.00 7.32 430.0 8.4 5.0 1.344 0.025 0.028
7.32 5.81 163.4 4.0 3.0 1.489 0.040 0.042
5.81 5.08 192.4 4.8 3.6 1.694 0.046 0.052
5.08 4.62 231.6 5.6 4.3 1.790 0.049 0.053
4.62 4.29 227.8 5.8 4.5 1.534 0.045 0.043
4.29 4.03 161.3 5.0 4.2 1.401 0.055 0.052
4.03 3.83 135.3 5.0 4.4 1.367 0.066 0.059
3.83 3.66 106.2 4.9 4.4 1.302 0.082 0.071
3.66 3.52 88.1 4.8 4.5 1.253 0.097 0.082
3.52 3.40 75.0 4.9 4.6 1.193 0.113 0.096
3.40 3.30 56.7 4.8 4.6 1.121 0.144 0.115
3.30 3.20 44.8 4.8 4.7 1.061 0.172 0.141
3.20 3.12 38.0 4.8 4.7 1.011 0.203 0.166
3.12 3.04 29.1 4.7 4.7 1.029 0.253 0.209
3.04 2.97 27.7 4.8 4.8 0.985 0.261 0.209
2.97 2.91 21.4 4.9 4.8 0.917 0.320 0.266
2.91 2.85 18.3 4.9 4.8 0.949 0.380 0.316
2.85 2.80 16.1 4.9 4.9 0.955 0.431 0.358
2.80 2.75 14.2 5.0 5.0 0.940 0.483 0.399
2.75 2.70 12.6 5.2 5.2 0.886 0.536 0.462
All reflections 110.9 5.1 4.5 1.236 0.076 0.054
So my questions are:
1. Is it really twinned since including twin-law in refinment gave much better numbers?
2. When refining with twin-law, Are the maps by phenix.refine output already “corrected” mtz/map?
3. If I use xray_data.r_free_flags.generate=True, can I write the data mtz out with the generated r-free-flags so that each round of refinement uses the same CV set?
Thnaks,
Tongqing
Tongqing Zhou, Ph.D.
Staff Scientist
Structural Biology Section
Vaccine Research Center, NIAID/NIH
Building 40, Room 4609B
40 Convent Drive, MSC3027
Bethesda, MD 20892
(301) 594-8710 (Tel)
(301) 793-0794 (Cell)
(301) 480-2658 (Fax)
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From: Bosch, Juergen [mailto:[email protected]]
Sent: Monday, May 07, 2012 1:34 PM
To: PHENIX user mailing list
Subject: Re: [phenixbb] Difficult dataset and refinement--P422? I422?Twinning?
Why don't you index over the whole dataset (XDS) ?
Or at least over a couple of images (Mosflm)
On May 7, 2012, at 12:50 PM, Kelly Daughtry wrote:
I agree.
The fact that two "crystals forms" appear, with related unit cells:
P422 data:
unit_cell = 191.6999969 191.6999969 311.0539856 90 90 90
space_group = "P 4 2 2"
I422 data:
unit_cell = 191.783 191.783 103.775 90 90 90
space_group = "I 4 2 2"
indicated to me you have mis-indexed the P422 data. It is likely I422.
Kelly
*******************************************************
Kelly Daughtry, Ph.D.
Post-Doctoral Fellow, Raetz Lab
Biochemistry Department
Duke University
Alex H. Sands, Jr. Building
303 Research Drive
RM 250
Durham, NC 27710
P: 919-684-5178
*******************************************************
On Mon, May 7, 2012 at 12:18 PM, Nathaniel Echols <
[email protected]> wrote:
Looking at the P422 data, it look like you have pseudo translational symmetry.
Did you try processing this data as I422?
From the P422_xtriage.log:
The full list of Patterson peaks is:
x y z height p-value(height)
( 0.500, 0.500, 0.165 ) : 78.635 (6.634e-07)
( 0.000, 0.000, 0.330 ) : 56.292 (2.795e-05)
( 0.500, 0.500, 0.497 ) : 30.920 (1.207e-03)
One word of caution: an exceptionally high off-origin peak can mean
that the unit cell was measured too large, and you've integrated extra
reflections that are really non-existent. (I'm not sure what the
threshold for this is, but 80% seems pretty large.) Splitting and
various indexing artifacts can sometimes lead to this. I'd recommend
running labelit.index on the images and seeing what it thinks the
lattice should be.
-Nat
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Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
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Lab: +1-410-614-4894
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