ample.util.cphasematch module¶

calc_phase_error_mtz(native_mtz_phased, mr_mtz, f_label=None, sigf_label=None, native_phase_labels=['FC', 'PHIC'], mr_phase_labels=['FC', 'PHIC'], cleanup=True, origin=None)[source]¶

Phase error between native_pdb+native_mtz and mr_mtz

calc_phase_error_pdb(native_pdb, native_mtz, mr_mtz, f_label, sigf_label, native_phase_labels=['FC', 'PHIC'], mr_phase_labels=['FC', 'PHIC'], cleanup=True, origin=None)[source]¶

Phase error between native_pdb+native_mtz and mr_mtz

merge_mtz(mtz1_path, mtz1_labels, mtz2_path, mtz2_labels)[source]¶

Create MTZ file with columns from the given mtz files and mtz labels in each file

merge_mtz_cctbx(mtz1_path, mtz1_labels, mtz2_path, mtz2_labels)[source]¶

TODO! Create MTZ file with F from native_mtz and calculated phases from native_mtz and mr_mtz to enable phaser error calc by cphasematch

parse_cphasematch_log(logfile)[source]¶

Return phase error before_origin& after_origin from cphasematch logfile

place_native_pdb(native_pdb, native_mtz, f_label, sigf_label, cleanup=True)[source]¶

Place native_pdb into data from native_mtz using phaser with f_label and sigf_label

run_cphasematch(merged_mtz, f_sigf_labels, native_phase_labels, mr_phase_labels, resolution_bins=12, cleanup=True)[source]¶

run cphasematch to get phase error