[phenixbb] UPDATE-- Difficult dataset and refinement--P422? I422?Twinning?

Kelly Daughtry kddaught at bu.edu
Tue May 8 10:08:04 PDT 2012


> 1.    Is it really twinned since including twin-law in refinment gave much
> better numbers?
   I would say, it likely is twinned. But as Jürgen pointed out, if
the twin domain is close to 50%, you are likely in too low of
symmetry. Compare the maps between both by eye and use your best
judgement.
Both set of stats (R and Rfree) are pretty good, so I'm leaning
towards the higher symmetry model as being correct.
Question: Do you have 1mol/ASU in the I422 model? (You mention 2 mol/ASU in I4).

> 2.    When refining with twin-law, Are the maps by phenix.refine output
> already “corrected” mtz/map?

YES.

> 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?

NO! You presumably already have an Rfree set. When you run your first
round of phenix.refine, it will generate an mtz file labelled
"refine_data.mtz" or something similar. This file contains your
experimental data (and rfree). Use the same file for each round of
phenix.refine.
You do not want to select a new set of Rfree during each refinement,
which I believe is what the xray_data.r_free_flags.generate=True
command will do, as that can increase bias (by including reflections
in rfree that have been used to refine the model)

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 Tue, May 8, 2012 at 11:11 AM, Zhou, Tongqing (NIH/VRC) [E]
<tzhou at mail.nih.gov> wrote:
> 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:jubosch at jhsph.edu]
> 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)
>
>
>
> Jürgen
>
>
>
> 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 <nechols at lbl.gov> wrote:
>
> On Mon, May 7, 2012 at 8:46 AM, Kelly Daughtry <kddaught at bu.edu> 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
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