Hi everybody,
 
I used phenix for calculating anomalous Fourier coefficients (script below) and I get the desired file containing columns FANOM PHANOM. When I read this into Coot for displaying the imaginary map, I only get noise, regardless of resolution cutoff etc. When I export the Fcalcs as CNS format and use CNS for the map calculation, I get very high peaks (i.e. excellent signal-to-noise ratio) on the anomalous scatterers.
Inspection of the phenix fcalc file reveals that FOFCWT_no_fill equals FANOM and PHFOFCWT_no_fill is identical to PHANOM . Obviously I am doing something stupidly wrong.
Setting xray_data.force_anomalous_flag_to_be_equal_to=true doesn't change anything, by the way, and i am using the latest Phenix version. I vaguely remember that there were an issue with anomlous data but can't find the thread.
Thank you very much in advance for enlightening me,
 
Ulrich
 
#
source /usr/local/phenix-1.4-3/phenix_env
phenix.refine m226h1_rfree-unique.mtz m226h1_hkl2000_6_waters_001.pdb 
main.number_of_macro_cycles=1 \
refinement.input.xray_data.labels="F(+),SIGF(+),F(-),SIGF(-)" \
xray_data.high_resolution =3.5
strategy=none export_final_f_model=cns output.prefix=sfcalc --overwrite
* Space group = 'P3121' (number     152)

The mapcoeff.mtz looks like

  OVERALL FILE STATISTICS for resolution range   0.000 -   0.319
  =======================


  Col Sort    Min    Max    Num      %     Mean     Mean   Resolution  
  Type Column
  num order               Missing complete          abs.   Low    High 
       label

    1 ASC      0      49      0  100.00     23.7     23.7  88.43   1.77   H  H
    2 NONE     0      28      0  100.00      8.4      8.4  88.43   1.77   H  K
    3 NONE   -69      69      0  100.00      0.6     26.2  88.43   1.77   H  L
    4 NONE    0.0  2220.8     0  100.00   235.55   235.55  88.43   
1.77   F  2FOFCWT
    5 NONE -180.0   180.0     0  100.00     2.65    89.99  88.43   
1.77   P  PH2FOFCWT
    6 NONE    0.0   956.4     0  100.00    72.48    72.48  88.43   
1.77   F  FOFCWT
    7 NONE -180.0   180.0     0  100.00     2.16    89.97  88.43   
1.77   P  PHFOFCWT
    8 NONE    0.0  2202.8   117   99.84   234.51   234.51  37.16   
1.77   F  2FOFCWT_no_fill
    9 NONE -180.0   180.0   117   99.84     2.78    89.99  37.16   
1.77   P  PH2FOFCWT_no_fill
   10 NONE    0.0   961.2   117   99.84    72.39    72.39  37.16   
1.77   F  FOFCWT_no_fill
   11 NONE -180.0   180.0   117   99.84     2.19    89.95  37.16   
1.77   P  PHFOFCWT_no_fill
   12 NONE    0.0   961.2   117   99.84    72.39    72.39  37.16   
1.77   F  ANOM
   13 NONE -180.0   180.0   117   99.84     2.19    89.95  37.16   
1.77   P  PHANOM


  No. of reflections used in FILE STATISTICS    72570

    1   1   3       88.81   -133.90    400.50   -133.90    139.90   -134.31
                    502.82   -134.31    502.82   -134.31
     1   1   4      719.55    109.38    336.98    109.38    703.51    104.61
                    304.13    104.61    304.13    104.61
     1   1   5      987.30    124.20    664.11    124.20    985.68    119.49
                    659.96    119.49    659.96    119.49
     1   1   6      871.35     35.76    152.79     35.76    894.80     36.84
                    198.58     36.84    198.58     36.84
     1   1   7      425.64     38.73    189.77     38.73    419.88     34.24
                    177.78     34.24    177.78     34.24
     1   1   8      406.00   -154.97     53.51     25.03    416.82   -153.85
                     32.47     26.15     32.47     26.15
     1   1   9       73.73    139.84    441.04    139.84     92.83    139.16
                    479.45    139.16    479.45    139.16