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Hi again,
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<div>Sorry, in my last mail I meant "... it would also be nice if ... the <b>progress panel during refinement</b> showed statistics for the neutron data as well as for the X-ray data". The neutron statistics are of course shown at the end. I'm a bit tired...</div>
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<div>Best wishes</div>
<div>Derek</div>
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<div>On 29 May 2013, at 16:29, Pavel Afonine <<a href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>></div>
<div> wrote:</div>
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<div class="moz-cite-prefix">Hi Derek,<br>
<br>
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 ?<br>
<br>
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.<br>
<br>
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.<br>
<br>
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>
<br>
All the best,<br>
Pavel<br>
<br>
On 5/29/13 4:18 AM, Derek Logan wrote:<br>
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<blockquote cite="mid:2B765EE6-BE04-40E1-8427-08632A047675@biochemistry.lu.se" type="cite">
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<div>Hi,</div>
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</div>
<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>
<div style="font-family: Courier; "><br>
</div>
<div style="font-family: Courier; ">================================= Neutron data ================================</div>
<div style="font-family: Courier; "><br>
</div>
<div style="font-family: Courier; ">F-obs:</div>
<div style="font-family: Courier; "> neutron.mtz:FO,SIGFO,DANO,SIGDANO,ISYM</div>
<div style="font-family: Courier; "><br>
</div>
<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>
<div style="font-family: Courier; "><br>
</div>
<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>
<div style="font-family: Courier; "><br>
</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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</font></div>
<div><font face="Courier">================================= Neutron data ================================</font></div>
<div><font face="Courier"><br>
</font></div>
<div><font face="Courier">F-obs:</font></div>
<div><font face="Courier"> neutron.mtz:FO,SIGFO,DANO,SIGDANO,ISYM</font></div>
<div><font face="Courier"><br>
</font></div>
<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>
<div><font face="Courier"><br>
</font></div>
<div>
<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>
<div><br>
</div>
<div><font face="Courier">Fobs statistics after all cutoffs applied:</font></div>
<div><font face="Courier"><br>
</font></div>
<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>
</div>
<div><br>
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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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<div><font class="Apple-style-span" face="'Courier New'" size="3"><span class="Apple-style-span" style="font-size: 12px; ">________________________________________________________________________<br>
Derek Logan tel: +46 46 222 1443<br>
Associate Professor </span></font><span style="font-family: 'Courier
New'; font-size: 12px; ">mob: +46 76 8585 707</span><font class="Apple-style-span" face="'Courier New'" size="3"><span class="Apple-style-span" style="font-size: 12px; "><br>
Dept. of Biochemistry and Structural Biology </span></font><span style="font-family:
'Courier New'; font-size: 12px; "><a moz-do-not-send="true" href="http://www.cmps.lu.se/">www.cmps.lu.se</a></span><font class="Apple-style-span" face="'Courier New'" size="3"><span class="Apple-style-span" style="font-size: 12px; "><br>
Centre for Molecular Protein Science <a moz-do-not-send="true" href="http://www.maxlab.lu.se/node/307">
www.maxlab.lu.se/node/307</a></span></font><font class="Apple-style-span" face="'Courier New'" size="3"><span class="Apple-style-span" style="font-size: 12px; "><br>
Lund University, Box 124, 221 00 Lund, Sweden <a moz-do-not-send="true" href="http://www.saromics.com/">
www.saromics.com</a></span></font></div>
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