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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