Hi Ulrich,

sorry for delayed reply.

I just checked this myself with the latest version. Here is my favorite test case:

http://cci.lbl.gov/~afonine/lysozime_gold/

The files are:

data.mtz - file with Fobs
lysozyme.pdb - best refined model that included gold (Au)
lysozyme_poor_noAU.pdb - unrefined model without Au
maps_001_map_coeffs.mtz - map coefficients file
run - file with phenix.refine command

To test if phenix.refine produces the correct anomalous difference map coefficients, I ran this command ("run" file):

phenix.refine data.mtz lysozyme_poor_noAU.pdb strategy=none main.number_of_mac=1 --overwrite output.prefix=maps

this does not do any refinement but computes maps only.

Use "phenix.mtz.dump maps_001_map_coeffs.mtz" to see the content of maps_001_map_coeffs.mtz file.

Now, if I load in COOT the map coefficients file (maps_001_map_coeffs.mtz, result of the above run) (labels ANOM,PHANOM) and the model (lysozyme.pdb, best refined model), and center on Au, I see very strong density peak (see a screen-shot picture: Au_density.png).

So, this shows me that the option works well... I'm not sure what happens in your case. This map (ANOM,PHANOM) is computed automatically if your input datafile contains Fobs(+) and Fobs(-), so you don't need to use any special command for this.

If you want me to have a look, please send me the data and model files (along with anom. sites) and I will check it myself.

Pavel.


On 3/31/09 9:18 AM, Ulrich Baumann wrote:
 
    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

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