[phenixbb] FreeR label?

[Thomas C. Terwilliger]

Hi Jon,
I would think that  exptl_fobs_phases_freeR_flags_xx.mtz should have the
labels you want. (You don't want to use overall_best_denmod_map_coeffs.mtz
in refinement, only to create maps.)

For example:

 phenix.mtz.dump exptl_fobs_phases_freeR_flags_2.mtz
Processing: exptl_fobs_phases_freeR_flags_2.mtz
Title: Resolve mtz file
Space group symbol from file: C2
Space group number from file: 5
Space group from matrices: C 1 2 1 (No. 5)
Point group symbol from file: PG2
Number of crystals: 2
Number of Miller indices: 2692
Resolution range: 21.3298 2.59408
History:
  From CCP4 20/ 3/2010 19:45:21
Crystal 1:
  Name: HKL_base
  Project: HKL_base
  Id: 1
  Unit cell: (76.08, 27.97, 42.36, 90, 103.2, 90)
  Number of datasets: 1
  Dataset 1:
    Name: HKL_base
    Id: 0
    Wavelength: 0
    Number of columns: 3
    label #valid  %valid    min   max type
    H       2692 100.00% -28.00 27.00 H: index h,k,l
    K       2692 100.00%   0.00 10.00 H: index h,k,l
    L       2692 100.00%   0.00 15.00 H: index h,k,l
Crystal 2:
  Name: crystal
  Project: project
  Id: 2
  Unit cell: (76.08, 27.97, 42.36, 90, 103.2, 90)
  Number of datasets: 1
  Dataset 1:
    Name: dataset
    Id: 1
    Wavelength: 1
    Number of columns: 10
    label      #valid  %valid     min    max type
    FP           2692 100.00%   11.41 902.45 F: amplitude
    SIGFP        2692 100.00%    0.86  17.94 Q: standard deviation
    PHIM         2692 100.00% -179.89 180.00 P: phase angle in degrees
    FOMM         2692 100.00%    0.00   1.00 W: weight (of some sort)
    HLAM         2692 100.00%  -14.26  13.84 A: phase probability
coefficients (Hendrickson/Lattman)
    HLBM         2692 100.00%  -14.36  10.86 A: phase probability
coefficients (Hendrickson/Lattman)
    HLCM         2692 100.00%   -2.83   4.81 A: phase probability
coefficients (Hendrickson/Lattman)
    HLDM         2692 100.00%   -4.71   3.77 A: phase probability
coefficients (Hendrickson/Lattman)
    FreeR_flag   2692 100.00%    0.00   1.00 I: integer
    FC           2692 100.00%    0.00   0.00 F: amplitude

I hope that helps! Please let me know if not.
-Tom T



>> Hello all,
>>
>>   I used AutoSol to generate a model from my Se-Met crystal.  I then used
>> this output model, overall_best.pdb, for AutoBuild1 in which I extended
>> the
>> data to include a set of native data.  At this point I took the
>> exptl_fobs_phases_freeR_flags.mtz output and used it with a different
>> model
>> that I believe to be accurate to carry out AutoBuild2.  The problem I'm
>> having is that I can't run Refmac/Phenix refinements on the output from
>> AutoBuild2: overall_best.pdb and overall_best_denmod_map_coeffs.mtz.  Both
>> pieces of software say the FreeR labels are missing although in the
>> AutoBuild2 output PDB there is a FreeR test set count of ~2,000.   When I
>> list all labels in Refmac I see:
>>
>> F  FP
>> P  PHIM
>> W FOMM
>>
>> Using these labels doesn't work for refinement.  I used default settings
>> for
>> AutoSol/AutoBuild except for the number of Se-Met sites and of course the
>> f'
>> and f'' etc.  I'm assuming the problem is with the MTZ but I'm not sure
>> where to troubleshoot.  Does anyone have any thoughts?
>>
>> Thanks in advance,
>> Jon
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>>