How to run the command line version:
- Run phenix.maps without any arguments: just type phenix.maps in the command line and hit Enter. This will creare a parameter file called maps.params, which can be renamed if desired.
- Edit maps.params file to specify input/output file names, data labels and the desired maps. It is possible to request as many maps as desired. By default, the file maps.params specifies 5 maps to be created: 2mFo-DFc, 2mFo-DFc with missing Fobs filled with DFcalc, mFo-DFc and anomalous difference maps will be output in MTZ format, and one 2mFo-DFc map will be output in CCP4 format. NOTE: the anomalous difference map will only be created if the input reflection data file contains Bijvoet maps (F+/F- or I+/I-).
- Run this command to compute requested maps: phenix.maps maps.params
Alternately, you may specify input files (and additional parameters) directly on the command line:
% phenix.maps model.pdb data.mtz
and it will automatically generate the default maps as described above.
Important Facts:
- phenix.maps is available in PHENIX GUI.
- The scope of parameters 'map_coefficients' defines the map that will be output as Fourier map coefficients. The scope of parameters 'map' defines the maps that will be output as CCP4 or X-plor format.
- To create several maps: duplicate either 'map_coefficients' or 'map' or both scopes of parameters as many times as many maps is desired. Then edit each of them to define the maps.
- A map is defined by specifying a map type using 'map_type' keyword available within each scope of parameters: 'map_coefficients' or 'map'. The general supported format for 'map_type' is: [p][m]Fo+[q][D]Fc[_filled]. For example: 2Fo-Fc, 2mFobs-DFcalc, 3Fobs-2Fmodel, Fo-Fc, mfobs-Dfcalc, anom, llg. The 'map_type' parser will automatically recognize which map is requested.
- The program creates as many files with CCP4 or X-plor formatted maps as is requested, and it creates only one MTZ formatted file with all Fourier map coefficients in it.
- The CCP4 or X-plor formatted maps can be computed in the entire unit cell or around selected atoms only.
- Twinning (if detected) will be accounted for automatically. This can be disabled by using "skip_twin_detection=True" keyword.
- All arrays used in map calculation, for example: Fobs, Fmodel, Fcalc, Fmask, m, D, etc., can be output into a CNS or MTZ formatted reflection file.
- For those who likes to experiment: bulk solvent correction and anisotropic scaling can be turned off, the data can be filtered by sigma and resolution.
- For some map types certain 'map_coefficients' or 'map' scope parameters may not be applicable. For example, for "map_type=anomalous" the keywords "fill_missing_f_obs" and some other are not applicable.
- For LLG map calculation, if you specify the wavelength any existing heavy atoms (P or heavier) will be modeled as anomalous scatterers using the theoretical values of f' and f''.
All phenix.maps parameters:
maps { input { pdb_file_name = None reflection_data { file_name = None labels = None high_resolution = None low_resolution = None outliers_rejection = True french_wilson_scale = True french_wilson { max_bins = 60 min_bin_size = 40 } sigma_fobs_rejection_criterion = None sigma_iobs_rejection_criterion = None r_free_flags { file_name = None label = None test_flag_value = None ignore_r_free_flags = False } } } output { directory = None prefix = None title = None fmodel_data_file_format = mtz include_r_free_flags = False } scattering_table = wk1995 it1992 *n_gaussian neutron electron wavelength = None bulk_solvent_correction = True anisotropic_scaling = True skip_twin_detection = False omit { method = *simple selection = None } map_coefficients { map_type = 2mFo-DFc format = *mtz phs mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = False sharpening = False sharpening_b_factor = None exclude_free_r_reflections = False isotropize = True } map_coefficients { map_type = 2mFo-DFc format = *mtz phs mtz_label_amplitudes = 2FOFCWT_fill mtz_label_phases = PH2FOFCWT_fill fill_missing_f_obs = True sharpening = False sharpening_b_factor = None exclude_free_r_reflections = False isotropize = True } map_coefficients { map_type = mFo-DFc format = *mtz phs mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT fill_missing_f_obs = False sharpening = False sharpening_b_factor = None exclude_free_r_reflections = False isotropize = True } map_coefficients { map_type = anomalous format = *mtz phs mtz_label_amplitudes = ANOM mtz_label_phases = PHANOM fill_missing_f_obs = False sharpening = False sharpening_b_factor = None exclude_free_r_reflections = False isotropize = True } map { map_type = 2mFo-DFc format = xplor *ccp4 file_name = None fill_missing_f_obs = False grid_resolution_factor = 1/4. region = *selection cell atom_selection = None atom_selection_buffer = 3 sharpening = False sharpening_b_factor = None exclude_free_r_reflections = False isotropize = True } }