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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);
  • Model file (PDB or mmCIF) 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
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