phenix.reciprocal_space_arrays:
compute various arrays such as Fcalc, Fmask, Fmodel, Fbulk, and more.
 Inputs:
 File with reflection data (Fobs or Iobs), Rfree flags, and optionally HL
coefficients. It can be in most of known formats and spread across
multiple files;
 label(s) selecting which reflection data arrays should be used (in case
there are multiple choices in input file, there is no need to provide labels
otherwise);
 PDB file with input model.
 Usage examples:
 phenix.reciprocal_space_arrays model.pdb data.hkl f_obs_label="IOBS"
 phenix.reciprocal_space_arrays model.pdb data.hkl r_free_flags_label="FREE"
 Output:
MTZ file with data arrays. Depending on the input data, the following arrays
may be present:
 FOBS : data from input reflection file
 SIGFOBS : corresponding sigmas
 R_FREE_FLAGS : Rfree flags (0  work, 1  test)
 FMODEL : total model structure factor. See phenix.fmodel for details
 PHIFMODEL : corresponding phases
 FCALC : Fcalc from atomic model
 PHIFCALC : corresponding phases
 FMASK : Fmask from bulksolvent mask. See phenix.fmodel for details
 PHIFMASK : corresponding phases
 FBULK : bulksolvent contribution. See phenix.fmodel for details
 PHIFBULK : corresponding phases
 FB_CART : overall anisotropic scale factor
 FOM : figures of merit
 ALPHA : ML parameter used in m&D calculation for 2mFoDFc maps
 BETA : ML parameter used in m&D calculation for 2mFoDFc maps
 HLA : HL coefficients from from input reflection file
 HLB : HL coefficients from from input reflection file
 HLC : HL coefficients from from input reflection file
 HLD : HL coefficients from from input reflection file
 HLmodelA : HL coefficients from the model (C=D=0)
 HLmodelB : HL coefficients from the model (C=D=0)
 HLmodelC : HL coefficients from the model (C=D=0)
 HLmodelD : HL coefficients from the model (C=D=0)
 HLcombA : combined HL: model + input
 HLcombB : combined HL: model + input
 HLcombC : combined HL: model + input
 HLcombD : combined HL: model + input
 RESOLUTION : resolution per reflection
Default params:
hkl_file = None
pdb_file = None
f_obs_label = None
r_free_flags_label = None
remove_f_obs_outliers = True
bulk_solvent_and_scaling = True
hendrickson_lattman_coefficients_label = None
output_file_name = None
space_group = None
unit_cell = None
job_title = None
