Examples

• running the program:

  /path/to/redchi file_containing_commands.inp > output.log 

• sample 1 - simple, high resolution dataset:

  # this is a comment
  debug fileio fit parser
  
  # I/SIGI/FP/SIGFP
  read mtz "data/input_file.mtz"
  
  # calculate Fc and Fs from PDB file
  read pdb fc "data/model_highres.pdb"
  
  # set up labels (only input labels are necessary,
  # but this also sets up the output MTZ labels)
  fsigf "F,SIGF" flag "FreeR_flag"
  
  # crystal settings
  bins 10
  cvflag 0
  
  # select all atoms
  select "group1" "*"
  # refine xyz per-atom
  xyz_refine individual "group1"
  # could also be done this way:
  # xyz_refine individual
  
  # refine individual istropic thermal displacements
  adp_refine individual isotropic "group1"
  
  # figure out occupancy refinement automatically
  # (atoms with alternate conformers will be refined, etc.)
  occ_refine auto "group1"
  
  # add hydrogens to the input file
  set add_h on
  
  # carry out refinement and calculate the reduced chi
  refine mlf 10
  
  # graph the scaled Fo's, sigFo's and Fc's values as a function of
  # resolution (this requires that Grace be installed) for all the
  # possible default symbols, see the input file commands list
  graph "F,SIGF" "FC,PHIC"
  
  # write out the new data
  write pdb "output.pdb"
  write mtz "output.mtz"
  
       

• sample 2 - a minimized version of the above:

  
  fsigf "F,SIGF"
  cvflag 0
  
  xyz_refine individual
  adp_refine individual isotropic
  occ_refine auto
  
  set add_h on
  
  graph "F,SIGF" "FC,PHIC"
  
  # write out the new data
  write pdb "output.pdb"
  write mtz "output.mtz"
  
       

  • since no mtz or pdb input file is given in this example, the program will search the current working directory for files that it can use.
  • or, mtz/pdb files can be read in from the command line (see the command line options), like so:

    /path/to/redchi -m input.mtz -p input.pdb file_containing_commands.inp > output.log 

• sample 3 - simulated annealing

  
  read mtz "input.mtz"
  read pdb fc "input.pdb"
  
  fsigf "F,SIGF" flag "FreeR_flag"
  
  bins 10
  cvflag 0
  
  # selects all atoms
  select "group1" "*"
  
  # only selects chain A
  select "group2" "A/*"
  
  # only selects chain B
  select "group3" "B/*"
  
  # selects everything *except* chain Z
  select "group4" "*" xor "Z/*"
  
  ncs_restrain "ncs1" "group2" "group3" weight 0.2
  # don't refine the waters during simulated annealing
  xyz_refine individual "group4"
  
  weight xray 1.0
  set add_h on
  
  # simulated annealing
  refine mlf anneal 5
  
  # turn off xray component to regularize geometry
  set include_xray off
  # and refine for 10 rounds
  refine mlf bfgs2 10
  
  # now refine ADPs
  adp_refine individual isotropic "group1"
  # turn X-ray term back on
  set include_xray on
  # refine 10 more rounds
  refine mlf bfgs2 10
  
  # output
  write pdb "output.pdb"
  write mtz "output.mtz"