[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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