Hi Pavel, sorry to send you this letter again, as I did not get the answer. I ran phenix.refine to produce a kicked map after deleting my ligand (to get an omit map). I could not make the Average Kick mFo-DFc Map using phenix.refine or phenix.maps. I got an error message. Sorry: Duplicate mtz_label_amplitudes:2FOFCWT Here is part of my .def file: How should I change it? map { mtz_label_amplitudes = None mtz_label_phases = None likelihood_weighted = None obs_factor = None calc_factor = None kicked = False fill_missing_f_obs_with_weighted_f_model = True } map { mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" 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" mtz_label_phases = "PHFOFCWT" likelihood_weighted = True obs_factor = 1 calc_factor = 1 kicked = True fill_missing_f_obs_with_weighted_f_model = False } map { mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" likelihood_weighted = True obs_factor = 2 calc_factor = 1 kicked = False fill_missing_f_obs_with_weighted_f_model = False } Pavel Afonine wrote:
Hi Maia,
just a remark: probably the quickest and simplest option to see if your ligand is there is to do these two steps:
1) physically remove the ligand from PDB file; 2) compute Average Kick mFo-DFc Map using phenix.refine or phenix.maps.
Pavel.
I am wondering what is the difference between an omit map that is produced by the refinement without a ligand and an omit map produced by autobuild.
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