phenix.reciprocal_space_arrays: compute various arrays such as Fcalc, Fmask, Fmodel, Fbulk, and more.

Inputs:

• File with reflection data (Fobs or Iobs), R-free 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:

1. phenix.reciprocal_space_arrays model.pdb data.hkl f_obs_label="IOBS"
2. 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 : R-free 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 bulk-solvent mask. See phenix.fmodel for details
• PHIFMASK : corresponding phases
• FBULK : bulk-solvent 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 2mFo-DFc maps
• BETA : ML parameter used in m&D calculation for 2mFo-DFc 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

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