Re: [phenixbb] problems with kicked maps in phenix version 1.4-162

15 Sep 2009

      Hi Sabine,

try this:

refinement.electron_density_maps {
  map {
    mtz_label_amplitudes = 2FOFCWT_kick
    mtz_label_phases = PH2FOFCWT_kick
    likelihood_weighted = True
    obs_factor = 2
    calc_factor = 1
    kicked = True
    fill_missing_f_obs_with_weighted_f_model = true
  }
  map {
    mtz_label_amplitudes = FOFCWT_kick
    mtz_label_phases = PHFOFCWT_kick
    likelihood_weighted = True
    obs_factor = 1
    calc_factor = 1
    kicked = True
    fill_missing_f_obs_with_weighted_f_model = true
  }
}

where I added "refinement." to correctly define the parameter scope.

Please let me know if it still does not work.

Pavel.

On 9/15/09 8:04 AM, Sabine Schneider wrote:
...
Hello,
Im trying to generate kicked maps in phenix1.4-162 using the following 
comand:
phenix.refine junk.mtz  xray_data.labels=F_XDSdataset,SIGF_XDSdataset \
coot-1.pdb strategy=individual_sites simulated_annealing=true 
refine2.params
where refine2.params is:
electron_density_maps {
  map {
    mtz_label_amplitudes = 2FOFCWT_kick
    mtz_label_phases = PH2FOFCWT_kick
    likelihood_weighted = True
    obs_factor = 2
    calc_factor = 1
    kicked = True
    fill_missing_f_obs_with_weighted_f_model = true
  }
  map {
    mtz_label_amplitudes = FOFCWT_kick
    mtz_label_phases = PHFOFCWT_kick
    likelihood_weighted = True
    obs_factor = 1
    calc_factor = 1
    kicked = True
    fill_missing_f_obs_with_weighted_f_model = true
  }
}
I get the following error message:
refinement.input.xray_data.labels = F_XDSdataset,SIGF_XDSdataset
  refinement.refine.strategy = individual_sites
  refinement.main.simulated_annealing = true
*******************************************************************************
ERROR: Unused parameter definitions:
  electron_density_maps.map.mtz_label_amplitudes (file "refine2.params", 
line 3)
  electron_density_maps.map.mtz_label_phases (file "refine2.params", line 4)
  electron_density_maps.map.likelihood_weighted (file "refine2.params", 
line 5)
  electron_density_maps.map.obs_factor (file "refine2.params", line 6)
  electron_density_maps.map.calc_factor (file "refine2.params", line 7)
  electron_density_maps.map.kicked (file "refine2.params", line 8)
  electron_density_maps.map.fill_missing_f_obs_with_weighted_f_model 
(file "refine2.params", line 9)
  electron_density_maps.map.mtz_label_amplitudes (file "refine2.params", 
line 12)
  electron_density_maps.map.mtz_label_phases (file "refine2.params", 
line 13)
  electron_density_maps.map.likelihood_weighted (file "refine2.params", 
line 14)
  electron_density_maps.map.obs_factor (file "refine2.params", line 15)
  electron_density_maps.map.calc_factor (file "refine2.params", line 16)
  electron_density_maps.map.kicked (file "refine2.params", line 17)
  electron_density_maps.map.fill_missing_f_obs_with_weighted_f_model 
(file "refine2.params", line 18)
*******************************************************************************
Sorry: Unused parameter definitions:
  Please check the input file(s) for spelling errors and obsolete
  parameter definitions.
  To disable this error message, add
    --unused_ok
  to the command line arguments.
I also tested the input file using :  libtbx.phil refine2.params and it 
seems OK?
Would be great if you could tell me where I am going wrong! Thanks a lot 
for your help in advance!
Sabine

Re: [phenixbb] problems with kicked maps in phenix version 1.4-162

Pavel Afonine