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

Pavel Afonine PAfonine at lbl.gov
Tue Sep 15 08:10:52 PDT 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
>
>
>   



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