Hi Pavel, did you really collected anomalous neutron data? I doubt. No, I'm unfortunately not yet developing methods for phasing neutron structures :-) Maybe I should actually have finished the second sentence in my mail, as it looked like I was implying that neutron anomalous signal might be something worth caring about, when what I really meant was "I wonder why phenix.refine is even considering this option". I was sitting in a conference at the time... Then how you ended up having anomalous data set for your neutron observations: FO,SIGFO,DANO,SIGDANO,ISYM ? As I mentioned in my original mail, I've discovered that SCALA always outputs I+ and I- no matter what you do. From the manual: "Normally anomalous scattering is ignored during the scale determination (I+ & I- observations are treated together), but the merged file always contains I+ & I-, even if the ANOMALOUS OFF command is used." Thus if you don't take special precautions, e.g. in TRUNCATE, these will be converted to F+ and F- and (I now know) phenix.refine will use them. However I've now discovered that the keyword ANOMALOUS NO in TRUNCATE will prevent output of the anomalous columns altogether. 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! Fine, I've now learned an important lesson in input/output checking! But could I politely suggest that an improvement in phenix.refine's mind-reading capabilities: if the user mistakenly inputs a file as neutron data with anomalous columns in, then these should be ignored, as the concept is by default incompatible with neutron data? As I've discovered, the default behaviour of SCALA and TRUNCATE is to leave these columns in... Finally, it would also be nice if the neutron maps and not just the X-ray maps were displayed in Coot during refinement and if the summary panel at the end of refinement showed statistics for the neutron data as well as for the X-ray data. But having said that, thanks for a powerful and user-friendly program! Best wishes Derek 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