[phenixbb] phenix.refine using anomalous concepts for neutron data?

Derek Logan derek.logan at biochemistry.lu.se
Wed May 29 04:18:51 PDT 2013


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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