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Hi Pavel,
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<div class="moz-cite-prefix">did you really collected anomalous neutron data? I doubt.
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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...</div>
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<div class="moz-cite-prefix">Then how you ended up having anomalous data set for your neutron observations: FO,SIGFO,DANO,SIGDANO,ISYM ?<br>
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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:</div>
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<div>"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."</div>
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<div>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.</div>
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<div class="moz-cite-prefix">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!<br>
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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...</div>
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<div>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!</div>
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<div>Best wishes</div>
<div>Derek</div>
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<div class="moz-cite-prefix">On 5/29/13 4:18 AM, Derek Logan wrote:<br>
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<div>Hi,</div>
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<div>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 </div>
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<div>This is what I get if I let phenix.refine itself decide whether or not to use anomalous data:</div>
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<div style="font-family: Courier; ">================================= Neutron data ================================</div>
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<div style="font-family: Courier; ">F-obs:</div>
<div style="font-family: Courier; "> neutron.mtz:FO,SIGFO,DANO,SIGDANO,ISYM</div>
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<div style="font-family: Courier; ">Miller array info: neutron.mtz:FO,SIGFO,DANO,SIGDANO,ISYM</div>
<div style="font-family: Courier; "><b>Observation type: xray.reconstructed_amplitude</b></div>
<div style="font-family: Courier; ">Type of data: double, size=16672</div>
<div style="font-family: Courier; ">Type of sigmas: double, size=16672</div>
<div style="font-family: Courier; ">Number of Miller indices: 16672</div>
<div style="font-family: Courier; ">Anomalous flag: True</div>
<div style="font-family: Courier; ">Unit cell: (removed)</div>
<div style="font-family: Courier; ">Space group: P 21 21 21 (No. 19)</div>
<div style="font-family: Courier; ">Systematic absences: 0</div>
<div style="font-family: Courier; ">Centric reflections: 1258</div>
<div style="font-family: Courier; ">Resolution range: 29.22 1.89826</div>
<div style="font-family: Courier; ">Completeness in resolution range: 0.785008</div>
<div style="font-family: Courier; ">Completeness with d_max=infinity: 0.78486</div>
<div style="font-family: Courier; ">Bijvoet pairs: 6832</div>
<div style="font-family: Courier; ">Lone Bijvoet mates: 1750</div>
<div style="font-family: Courier; ">Anomalous signal: 0.0876</div>
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<div style="font-family: Courier; ">Number of F-obs in resolution range: 16672</div>
<div style="font-family: Courier; ">Number of F-obs<0 (these reflections will be rejected): 0</div>
<div style="font-family: Courier; ">Number of F-obs=0 (these reflections will be used in refinement): 0</div>
<div style="font-family: Courier; ">Refinement resolution range: d_max = 29.2200</div>
<div style="font-family: Courier; "> d_min = 1.8983</div>
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<div>and this is what I get if I forcibly switch off use of anomalous data in the phenix.refine GUI:</div>
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<div><font face="Courier">================================= Neutron data ================================</font></div>
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<div><font face="Courier">F-obs:</font></div>
<div><font face="Courier"> neutron.mtz:FO,SIGFO,DANO,SIGDANO,ISYM</font></div>
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<div><font face="Courier">Miller array info: neutron.mtz:FO,SIGFO,DANO,SIGDANO,ISYM</font></div>
<div><font face="Courier">Observation type: xray.reconstructed_amplitude</font></div>
<div><font face="Courier">Type of data: double, size=16672</font></div>
<div><font face="Courier">Type of sigmas: double, size=16672</font></div>
<div><font face="Courier">Number of Miller indices: 16672</font></div>
<div><font face="Courier">Anomalous flag: True</font></div>
<div><font face="Courier">Unit cell: (removed)</font></div>
<div><font face="Courier">Space group: P 21 21 21 (No. 19)</font></div>
<div><font face="Courier">Systematic absences: 0</font></div>
<div><font face="Courier">Centric reflections: 1258</font></div>
<div><font face="Courier">Resolution range: 29.22 1.89826</font></div>
<div><font face="Courier">Completeness in resolution range: 0.785008</font></div>
<div><font face="Courier">Completeness with d_max=infinity: 0.78486</font></div>
<div><font face="Courier">Bijvoet pairs: 6832</font></div>
<div><font face="Courier">Lone Bijvoet mates: 1750</font></div>
<div><font face="Courier">Anomalous signal: 0.0876</font></div>
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<div><font face="Courier">force_anomalous_flag_to_be_equal_to=False</font></div>
<div><font face="Courier">Reducing data to non-anomalous array.</font></div>
<div><font face="Courier"> R-linear = sum(abs(data - mean(data))) / sum(abs(data))</font></div>
<div><font face="Courier"> R-square = sum((data - mean(data))**2) / sum(data**2)</font></div>
<div><font face="Courier"> In these sums single measurements are excluded.</font></div>
<div><font face="Courier"> Redundancy Mean Mean</font></div>
<div><font face="Courier"> Min Max Mean R-linear R-square</font></div>
<div><font face="Courier"> unused: - 29.2234</font></div>
<div><font face="Courier"> bin 1: 29.2234 - 4.0863 1 2 1.699 0.0240 0.0011</font></div>
<div><font face="Courier"> bin 2: 4.0863 - 3.2448 1 2 1.793 0.0302 0.0022</font></div>
<div><font face="Courier"> bin 3: 3.2448 - 2.8350 1 2 1.800 0.0417 0.0041</font></div>
<div><font face="Courier"> bin 4: 2.8350 - 2.5760 1 2 1.764 0.0486 0.0054</font></div>
<div><font face="Courier"> bin 5: 2.5760 - 2.3914 1 2 1.745 0.0505 0.0051</font></div>
<div><font face="Courier"> bin 6: 2.3914 - 2.2505 1 2 1.717 0.0513 0.0051</font></div>
<div><font face="Courier"> bin 7: 2.2505 - 2.1378 1 2 1.658 0.0533 0.0056</font></div>
<div><font face="Courier"> bin 8: 2.1378 - 2.0448 1 2 1.614 0.0611 0.0074</font></div>
<div><font face="Courier"> bin 9: 2.0448 - 1.9661 1 2 1.575 0.0634 0.0075</font></div>
<div><font face="Courier"> bin 10: 1.9661 - 1.8983 1 2 1.485 0.0736 0.0097</font></div>
<div><font face="Courier"> unused: 1.8983 -</font></div>
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<div><font face="Courier">Fobs statistics after all cutoffs applied:</font></div>
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<div><font face="Courier">Miller array info: None</font></div>
<div><font face="Courier"><b>Observation type: xray.amplitude</b></font></div>
<div><font face="Courier">Type of data: double, size=9840</font></div>
<div><font face="Courier">Type of sigmas: double, size=9840</font></div>
<div><font face="Courier">Number of Miller indices: 9840</font></div>
<div><font face="Courier">Anomalous flag: False</font></div>
<div><font face="Courier">Unit cell: (removed)</font></div>
<div><font face="Courier">Space group: P 21 21 21 (No. 19)</font></div>
<div><font face="Courier">Systematic absences: 0</font></div>
<div><font face="Courier">Centric reflections: 1258</font></div>
<div><font face="Courier">Resolution range: 29.22 1.89826</font></div>
<div><font face="Courier">Completeness in resolution range: 0.855801</font></div>
<div><font face="Courier">Completeness with d_max=infinity: 0.855503</font></div>
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<div>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 <span style="font-family: Courier; ">xray.reconstructed_amplitude
</span>then as <span style="font-family: Courier; ">xray.amplitude </span>even though the data are explicitly defined as neutron data in the GUI.</div>
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<div>I can send more information if required!</div>
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<div>Thanks</div>
<div>Derek</div>
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