[phenixbb] phenix.refine using anomalous concepts for neutron data?
Pavel Afonine
pafonine at lbl.gov
Wed May 29 07:29:08 PDT 2013
Hi Derek,
did you really collected anomalous neutron data? I doubt. Then how you
ended up having anomalous data set for your neutron observations:
FO,SIGFO,DANO,SIGDANO,ISYM ?
By default phenix.refine will always take anomalous data set if there is
a choice anomalous versus non-anomalous. This is because anomalous data
is a) richer source of information, and b) less manipulated compared to
non-anomalous Fmean=(F+ + F-)/2 or Imean=(I+ + I-)/2.
In refinement Bijvoet mates F+ and F- are counted as two reflections,
not one. So don't get surprised to see "doubled" number of reflections.
It's not really doubled, it's what you actually have.
All in all, if you don't have anomalous data make sure your inputs files
do not have spurious (anomalous) arrays: phenix.refine can't read your
mind to see what you have done in your diffraction experiment - it's
beyond the scope of what it's supposed to do!
All the best,
Pavel
On 5/29/13 4:18 AM, Derek Logan wrote:
> Hi,
>
> I'm doing a joint X-ray neutron refinement in Phenix and have run into
> some behaviour that puzzles me. I had not been paying any attention to
> the use or non-use of anomalous signal in the neutron dataset, as
>
> This is what I get if I let phenix.refine itself decide whether or not
> to use anomalous data:
>
> ================================= Neutron data
> ================================
>
> F-obs:
> neutron.mtz:FO,SIGFO,DANO,SIGDANO,ISYM
>
> Miller array info: neutron.mtz:FO,SIGFO,DANO,SIGDANO,ISYM
> *Observation type: xray.reconstructed_amplitude*
> Type of data: double, size=16672
> Type of sigmas: double, size=16672
> Number of Miller indices: 16672
> Anomalous flag: True
> Unit cell: (removed)
> Space group: P 21 21 21 (No. 19)
> Systematic absences: 0
> Centric reflections: 1258
> Resolution range: 29.22 1.89826
> Completeness in resolution range: 0.785008
> Completeness with d_max=infinity: 0.78486
> Bijvoet pairs: 6832
> Lone Bijvoet mates: 1750
> Anomalous signal: 0.0876
>
> Number of F-obs in resolution range: 16672
> Number of F-obs<0 (these reflections will be rejected): 0
> Number of F-obs=0 (these reflections will be used in refinement): 0
> Refinement resolution range: d_max = 29.2200
> d_min = 1.8983
>
> and this is what I get if I forcibly switch off use of anomalous data
> in the phenix.refine GUI:
>
> ================================= Neutron data
> ================================
>
> F-obs:
> neutron.mtz:FO,SIGFO,DANO,SIGDANO,ISYM
>
> Miller array info: neutron.mtz:FO,SIGFO,DANO,SIGDANO,ISYM
> Observation type: xray.reconstructed_amplitude
> Type of data: double, size=16672
> Type of sigmas: double, size=16672
> Number of Miller indices: 16672
> Anomalous flag: True
> Unit cell: (removed)
> Space group: P 21 21 21 (No. 19)
> Systematic absences: 0
> Centric reflections: 1258
> Resolution range: 29.22 1.89826
> Completeness in resolution range: 0.785008
> Completeness with d_max=infinity: 0.78486
> Bijvoet pairs: 6832
> Lone Bijvoet mates: 1750
> Anomalous signal: 0.0876
>
> force_anomalous_flag_to_be_equal_to=False
> Reducing data to non-anomalous array.
> R-linear = sum(abs(data - mean(data))) / sum(abs(data))
> R-square = sum((data - mean(data))**2) / sum(data**2)
> In these sums single measurements are excluded.
> Redundancy Mean Mean
> Min Max Mean R-linear R-square
> unused: - 29.2234
> bin 1: 29.2234 - 4.0863 1 2 1.699 0.0240 0.0011
> bin 2: 4.0863 - 3.2448 1 2 1.793 0.0302 0.0022
> bin 3: 3.2448 - 2.8350 1 2 1.800 0.0417 0.0041
> bin 4: 2.8350 - 2.5760 1 2 1.764 0.0486 0.0054
> bin 5: 2.5760 - 2.3914 1 2 1.745 0.0505 0.0051
> bin 6: 2.3914 - 2.2505 1 2 1.717 0.0513 0.0051
> bin 7: 2.2505 - 2.1378 1 2 1.658 0.0533 0.0056
> bin 8: 2.1378 - 2.0448 1 2 1.614 0.0611 0.0074
> bin 9: 2.0448 - 1.9661 1 2 1.575 0.0634 0.0075
> bin 10: 1.9661 - 1.8983 1 2 1.485 0.0736 0.0097
> unused: 1.8983 -
>
> Fobs statistics after all cutoffs applied:
>
> Miller array info: None
> *Observation type: xray.amplitude*
> Type of data: double, size=9840
> Type of sigmas: double, size=9840
> Number of Miller indices: 9840
> Anomalous flag: False
> Unit cell: (removed)
> Space group: P 21 21 21 (No. 19)
> Systematic absences: 0
> Centric reflections: 1258
> Resolution range: 29.22 1.89826
> Completeness in resolution range: 0.855801
> Completeness with d_max=infinity: 0.855503
>
> What's going on here? If I let phenix.refine decide automatically, it
> looks like it's reading in F+ and F- separately and regarding them as
> independent in the refinement. If I force "no anomalous" it merges
> them. However I can't work out whether in either case it has actually
> read FOBS instead of the Friedel mates. According to the SCALA manual
> the I+ and I- columns will always be written out even if the keyword
> ANOMALOUS OFF is used, so this is a potential pitfall for many. In
> addition, phenix.refine seems to identify the neutron data first as
> xray.reconstructed_amplitude then as xray.amplitude even though the
> data are explicitly defined as neutron data in the GUI.
>
> I can send more information if required!
>
> Thanks
> Derek
>
>
>
> ________________________________________________________________________
> Derek Logan tel: +46 46 222 1443
> Associate Professor mob: +46 76 8585 707
> Dept. of Biochemistry and Structural Biology www.cmps.lu.se
> <http://www.cmps.lu.se>
> Centre for Molecular Protein Science www.maxlab.lu.se/node/307
> <http://www.maxlab.lu.se/node/307>
> Lund University, Box 124, 221 00 Lund, Sweden www.saromics.com
> <http://www.saromics.com>
>
>
>
>
>
>
>
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