problems with kicked maps in phenix version 1.4-162
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/
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
participants (2)
-
Pavel Afonine -
Sabine Schneider