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

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.

________________________________________________________________________
Derek Logan tel: +46 46 222 1443
Associate Professor mob: +46 76 8585 707
Dept. of Biochemistry and Structural Biology www.cmps.lu.se
Centre for Molecular Protein Science www.maxlab.lu.se/node/307
Lund University, Box 124, 221 00 Lund, Sweden www.saromics.com