[phenixbb] problems with kicked maps in phenix version 1.4-162
Sabine Schneider
sabine.schneider at cup.uni-muenchen.de
Tue Sep 15 08:04:50 PDT 2009
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
--
------------------------------------------
Dr. Sabine Schneider
Ludwig-Maximilians-University
Department of Chemistry and Biochemistry
Butenandtstrasse 5-13, Building F
81377 Munich
Germany
Phone: +49 (0)89 2180 77752
Fax: +49 (0)89 2180 77756
http://www.carellgroup.de/
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