phenix_logo
Python-based Hierarchical ENvironment for Integrated Xtallography
Documentation Home
 

Building starting with a very poor map with parallel_autobuild

Authors
Purpose
How parallel autobuild works
Inputs for parallel autobuild
Possible Problems
Specific limitations:
References:
Keywords:
List of all parallel_autobuild keywords

Authors

parallel_autobuild: Tom Terwilliger

Purpose

The goal of parallel_autobuild is to build models starting from very poor maps. In this situation most of the models created by autobuild are not very good, but some will be a little better than others. The strategy is to find these slightly-better models and iterate model-building based on them. The working hypothesis for parallel_autobuild is that the quality of the starting map is a key determinant of how good the final model will be. The strategy is then to take a starting map and data, get the best model from this starting point, and use it to calculate a new starting map that is hopefully a little better than the first one. Iterating this process may finally lead to a starting map that is good enough to yield a complete model.

How parallel autobuild works

parallel_autobuild is a tool to carry out the process of picking good models from many autobuild runs automatically. It will run parallel jobs of phenix.autobuild, identify the best model and the corresponding map, then take the best map as the starting point for another cycle of building. The choice of what is the best model is not always obvious. Parallel_autobuild uses the R-values of the models to make this choice if the R is less than 0.50 (by default), and if all R-values are higher, the map correlation of each model to its corresponding density-modified map is used to make the choice.

Inputs for parallel autobuild

The inputs for parallel autobuild are the same as for autobuild, with the addition of a few control parameters. Also parallel autobuild requires you to specify what each input file is (it won't guess). The main parameters are the number of processors to use, the number of overall cycles, and the number of parallel autobuild jobs to be run in each cycle. The number of processors available for each autobuild job then determines how many models are built in each autobuild cycle.

You can also specify whether the model obtained on each cycle is to be used in the next cycle (by default, if you supply a starting model the model obtained each cycle is used, and if you do not, it is tossed and only the new map is used.)

A run_command keyword allows you to specify how jobs are to be run. Parallel autobuild can be run on a queueing system (with a command such as qsub) or on a multiprocessor machine (e.g., with sh).

Possible Problems

Specific limitations:

Parallel_autobuild does not recombine models from different parallel runs. It is possible that the use of phenix.combine_models with parallel_autobuild could further improve its performance.

References:

  • Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard. T.C. Terwilliger, R.W. Grosse-Kunstleve, P.V. Afonine, N.W. Moriarty, P.H. Zwart, L.-W. Hung, R.J. Read, and P.D. Adams. Acta Cryst. D64, 61-69 (2008).

Keywords:

List of all parallel_autobuild keywords

------------------------------------------------------------------------------- 
Legend: black bold - scope names
        black - parameter names
        red - parameter values
        blue - parameter help
        blue bold - scope help
        Parameter values:
          * means selected parameter (where multiple choices are available)
          False is No
          True is Yes
          None means not provided, not predefined, or left up to the program
          "%3d" is a Python style formatting descriptor
------------------------------------------------------------------------------- 
parallel_autobuild
   iterations= 1 Total number of iterations of autobuilding
   n_parallel= 1 Total number of autobuild runs in each iteration
   parallel_r_switch= 0.5 If R is less than parallel_r_switch, use R to choose
                      best model; otherwise use map correlation
   nproc= 1 Number of processors to use
   background= True run jobs in background or not (if nproc is greater than 1)
   run_command= "sh " Command for running jobs (e.g., sh or qsub )
   verbose= False verbose output
   raise_sorry= False Raise sorry if problems
   debug= False debugging output
   temp_dir= Auto Optional temporary work directory
   work_dir= "" Work directory (by default, PARALLEL_AUTOBUILD_RUN_xxxx/)
   output_dir= "" Output directory where files are to be written
   dry_run= False Just read in and check parameter names
   check_wait_time= 10.0 You can specify the length of time (seconds) to wait
                    between checking for subprocesses to end
   wait_between_submit_time= 1.0 You can specify the length of time (seconds)
                             to wait between each job that is submitted when
                             running sub-processes. This can be helpful on
                             NFS-mounted systems when running with multiple
                             processors to avoid file conflicts. The symptom
                             of too short a wait_between_submit_time is File
                             exists:....
   update_model_each_cycle= None You can specify whether the model obtained
                            each cycle is to be used in the next cycle.
                            Default is True if a model is supplied at the
                            beginning and False otherwise.
autobuild
   data= None Datafile. This file can be a .sca or mtz or other standard file.
         The Wizard will guess the column identification. You can specify the
         column labels to use with: input_labels='FP SIGFP PHIB FOM HLA HLB
         HLC HLD FreeR_flag' Substitute any labels you do not have with None.
         If you only have myFP and mysigFP you can just say input_labels='myFP
         mysigFP'. If you have free R flags, phase information or HL
         coefficients that you want to use then an mtz file is required. If
         this file contains phase information, this phase information should
         be experimental (i.e., MAD/SAD/MIR etc), and should not be
         density-modified phases (enter any files with density-modified phases
         as input_map_file instead). NOTE: If you supply HL coefficients they
         will be used in phase recombination. If you supply PHIB or PHIB and
         FOM and not HL coefficients, then HL coefficients will be derived
         from your PHIB and FOM and used in phase recombination. If you also
         specify a hires data file, then FP and SIGFP will come from that data
         file (and not this one) If an input_refinement_file is specified,
         then F, Sigma, FreeR_flag (if present) from that file will be used
         for refinement instead of this one.
   model= None PDB file with starting model. NOTE: If your PDB file has been
          previously refined, then please make sure that you provide the free
          R flags that were used in that refinement. These can come from the
          data file or from the refinement_file.
   seq_file= Auto Text file with 1-letter code of protein sequence. Separate
             chains with a blank line or line starting with >. Normally you
             should include one copy of each unique chain. NOTE: if 1 copy of
             each unique chain is provided it is assumed that there are
             ncs_copies (could be 1) of each unique chain. If more than one
             copy of any chain is provided it is assumed that the asymmetric
             unit contains the number of copies of each chain that are given,
             multiplied by ncs_copies. So if the sequence file has two copies
             of the sequence for chain A and one of chain B, the cell contents
             are assumed to be ncs_copies*2 of chain A and ncs_copies of chain
             B. ADDITIONAL NOTES: 1. lines starting with > are ignored and
             separate chains 2. FASTA format is fine 3. If you enter a PDB
             file for rebuilding and it has the sequence you want, then the
             sequence file is not necessary. NOTE: You can also enter the name
             of a PDB file that contains SEQRES records, and the sequence from
             the SEQRES records will be read, written to
             seq_from_seqres_records.dat, and used as your input sequence. If
             you have a duplex DNA, enter each strand as a separate chain.
             NOTE: for AutoBuild you can specify start_chains_list on the
             first line of your sequence file: >> start_chains_list 23
             11 5
   map_file= Auto MTZ file containing starting map. This file must be a mtz
             file. The Wizard will guess the column identification. You can
             specify the column labels to use with: input_map_labels='FP PHIB
             FOM' Substitute any labels you do not have with None. If you only
             have myFP and myPHIB you can just say input_map_labels='myFP
             myPHIB'. This map will be used in the first cycle of
             model-building. NOTE 1: If use_map_file_as_hklstart=True then
             this file will be used instead to start density modification.
             NOTE 2: default for this keyword is Auto, which means "carry
             out normal process to guess this keyword". This means if you
             specify "after_autosol" in AutoBuild, AutoBuild will
             automatically take the value from AutoSol. If you do not want
             this to happen, you can specify None which means "No
             file"
   refinement_file= Auto File for refinement. This file can be a .sca or mtz
                    or other standard file. This file will be merged with your
                    data file, with any phase information coming from your
                    data file. If this file has free R flags, they will be
                    used, otherwise if the data file has them, those will be
                    used, otherwise they will be generated. The Wizard will
                    guess the column identification. You can specify the
                    column labels to use with: input_refinement_labels='FP
                    SIGFP FreeR_flag' Substitute any labels you do not have
                    with None. If you only have myFP and mysigFP you can just
                    say input_refinement_labels='myFP mysigFP'. Data file to
                    use for refinement. The data in this file should not be
                    corrected for anisotropy. It will be combined with
                    experimental phase information (if any) from
                    input_data_file for refinement. If you leave this blank,
                    then the data in the input_data_file will be used in
                    refinement. If no anisotropy correction is applied to the
                    data you do not need to specify a datafile for refinement.
                    If an anisotropy correction is applied to the data files,
                    then you should enter an uncorrected datafile for
                    refinement. Any standard format is fine; normally only F
                    and sigF will be used. Bijvoet pairs and duplicates will
                    be averaged. If an mtz file is provided then a free R flag
                    can be read in as well. Any HL coeffs and phase
                    information in this file is ignored. NOTE: default for
                    this keyword is Auto, which means "carry out normal
                    process to guess this keyword". This means if you
                    specify "after_autosol" in AutoBuild, AutoBuild
                    will automatically take the value from AutoSol. If you do
                    not want this to happen, you can specify None which means
                    "No file"
   hires_file= Auto File with high-resolution data. This file can be a .sca or
               mtz or other standard file. The Wizard will guess the column
               identification. You can specify the column labels to use with:
               input_hires_labels='FP SIGFP'.
   crystal_info
      unit_cell= None Enter cell parameter (a b c alpha beta gamma)
      space_group= None Space Group symbol (i.e., C2221 or C 2 2 21)
      solvent_fraction= None Solvent fraction in crystals (0 to 1). This is
                        normally set automatically from the number of NCS
                        copies and the sequence.
      chain_type= *Auto PROTEIN DNA RNA You can specify whether to build
                  protein, DNA, or RNA chains. At present you can only build
                  one of these in a single run. If you have both DNA and
                  protein, build one first, then run AutoBuild again,
                  supplying the prebuilt model in the
                  "input_lig_file_list" and build the other. NOTE:
                  default for this keyword is Auto, which means "carry
                  out normal process to guess this keyword". The process
                  is to look at the sequence file and/or input pdb file to see
                  what the chain type is. If there are more than one type, the
                  type with the larger number of residues is guessed. If you
                  want to force the chain_type, then set it to PROTEIN RNA or
                  DNA.
      resolution= 0 High-resolution limit. Used as resolution limit for
                  density modification and as general default high-resolution
                  limit. If resolution_build or refinement_resolution are set
                  then they override this for model-building or refinement. If
                  overall_resolution is set then data beyond that resolution
                  is ignored completely. Zero means keep everything.
      dmax= 500 Low-resolution limit
      overall_resolution= 0 If overall_resolution is set, then all data beyond
                          this is ignored. NOTE: this is only suggested if you
                          have a very big cell and need to truncate the data
                          to allow the wizard to run at all. Normally you
                          should use 'resolution' and 'resolution_build' and
                          'refinement_resolution' to set the high-resolution
                          limit
      sequence= None Plain text containing 1-letter code of protein sequence
                Same as seq_file except the sequence is read directly, not
                from a file. If both are given, seq_file is ignored.
   input_files
      input_labels= None Labels for input data columns
      input_hires_labels= None Labels for input hires file (FP SIGFP
                          FreeR_flag)
      input_map_labels= None Labels for input map coefficient columns (FP PHIB
                        FOM) NOTE: FOM is optional (set to None if you wish)
      input_refinement_labels= None Labels for input refinement file columns
                               (FP SIGFP FreeR_flag)
      input_ha_file= None If the flag "truncate_ha_sites_in_resolve"
                     is set then density at sites specified with input_ha_file
                     is truncated to improve the density modification
                     procedure. Additionally these sites are added to
                     input_lig_file_list.
      include_ha_in_model= True Add contents of input_ha_file to the working
                           model just before refinement (by adding it to
                           input_lig_file_list).
      cif_def_file_list= None You can enter any number of CIF definition
                         files. These are normally used to tell phenix.refine
                         about the geometry of a ligand or unusual residue.
                         You usually will use these in combination with
                         "PDB file with metals/ligands" (keyword
                         "input_lig_file_list" ) which allows you to
                         attach the contents of any PDB file you like to your
                         model just before it gets refined. You can use
                         phenix.elbow to generate these if you do not have a
                         CIF file and one is requested by phenix.refine
      input_lig_file_list= None This script adds the contents of these PDB
                           files to each model just prior to refinement.
                           Normally you might use this to put in any
                           heavy-atoms that are in the refined structure (for
                           example the heavy atoms that were used in phasing),
                           or to add a ligand to your model. (By default if
                           you supply input_ha_file this will be added to your
                           input_lig_file_list.) If the atoms in this PDB file
                           are not recognized by phenix.refine, then you can
                           specify their geometries with a cif definitions
                           file using the keyword
                           "cif_def_files_list". You can easily
                           generate cif definitions for many ligands using
                           phenix.elbow in PHENIX. You can put anything you
                           like in the files in input_lig_file_list, but any
                           atoms that fall within 1.5 A of any atom in the
                           current model will be tossed (not written to the
                           model).
      keep_input_ligands= True You can choose whether to (by default) let the
                          wizard keep ligands by separating them out from the
                          rest of your model and adding them back to your
                          rebuilt model, or alternatively to remove all
                          ligands from your input pdb file before
                          rebuild_in_place.
      keep_input_waters= False You can choose whether to keep input waters
                         (solvent) when using rebuild_in_place. If you keep
                         them, then you should specify either
                         "place_waters=No" or
                         "keep_pdb_atoms=No" because if
                         place_waters=True and keep_pdb_atoms=True then
                         phenix.refine will add waters and then the wizard
                         will keep the new waters from the new PDB file
                         created by phenix.refine preferentially over the ones
                         in your input file.
      keep_pdb_atoms= True If true, keep the model coordinates when model and
                      ligand coordinates are within dist_close_overlap and
                      ligands in input_lig_file_list are being added to the
                      current model. If false, keep instead the ligand
                      coordinates.
      refine_eff_file_list= None You can enter any number of refinement
                            parameter files. These are normally used to tell
                            phenix.refine defaults to apply, as well as
                            creating specialized definitions such as unusual
                            amino acid residues and linkages. These parameters
                            override the normal phenix.refine defaults. They
                            themselves can be overridden by parameters set by
                            the Wizard and by you, controlling the Wizard.
                            NOTE: Any parameters set by AutoBuild directly
                            (such as number_of_macro_cycles, high_resolution,
                            etc...) will not be taken from this parameters
                            file. This is useful only for adding extra
                            parameters not normally set by AutoBuild.
      map_file_is_density_modified= False You can specify that the
                                    input_map_file has been density modified.
                                    (This changes the assumptions on
                                    statistics of the map.)
      map_file_fom= None You can specify the FOM of the input map file (useful
                    in cases where the map file has only FWT PHFWT and no FOM
                    column). This FOM is used to set the default smoothing
                    radius for the density modification solvent boundary and
                    also to decide whether extreme density modification is to
                    be applied
      use_map_file_as_hklstart= False You can specify that the file named as
                                input_map_file will be used as starting
                                coefficients for density modification in the
                                first cycle. NOTE: if maps_only=True and
                                input_map_file is set, then
                                use_map_file_as_hklstart will be set to True
      use_map_in_resolve_with_model= False You can specify that the current
                                     map file be used as hklstart in density
                                     modification with a model.
      identity_from_remark= True You can use sequence identity from remark
                            like this one: REMARK PHASER ENSEMBLE MODEL 0 ID
                            100.0 Here the identity is 100 percent. Ignored if
                            there is no remark of this kind in the input
                            model.
   aniso
      remove_aniso= True Remove anisotropy from data files before use Note:
                    map files are assumed to be already corrected and are not
                    affected by this. Also the input refinement file is not
                    affected by this.
      b_iso= None Target overall B value for anisotropy correction. Ignored if
             remove_aniso = False. If None, default is minimum of (max_b_iso,
             lowest B of datasets, target_b_ratio*resolution)
      max_b_iso= 40. Default maximum overall B value for anisotropy
                 correction. Ignored if remove_aniso = False. Ignored if b_iso
                 is set. If used, default is minimum of (max_b_iso, lowest B
                 of datasets, target_b_ratio*resolution)
      target_b_ratio= 10. Default ratio of target B value to resolution for
                      anisotropy correction. Ignored if remove_aniso = False.
                      Ignored if b_iso is set. If used, default is minimum of
                      (max_b_iso, lowest B of datasets,
                      target_b_ratio*resolution)
   decision_making
      acceptable_r= 0.25 Used to decide whether the model is acceptable enough
                    to quit if it is not improving much. A good value is 0.25
      r_switch= 0.4 R-value criteria for deciding whether to use R-value or
                map correlation as a criteria for model quality. A good value
                is 0.40
      semi_acceptable_r= 0.3 Used to decide whether the model is acceptable
                         enough to skip rebuilding the model from scratch and
                         focus on adding loops and extending it. A good value
                         is 0.3
      reject_weak= False You can rebuild or remove just the residues in weak
                   density This will reject residues with density < 0.5 * mean
                   - SD where the density, mean and SD are for either
                   main-chain or all atoms in residues. If set, overrides
                   min_cc_res_rebuild and worst_percent_res_rebuild.
      min_weak_z= 0.2 Minimum number of sd of rho above 0.5*mean of all
                  residues for keeping weak residues if reject_weak=True
      min_cc_res_rebuild= 0.4 You can rebuild just the worst parts of your
                          model by setting touch_up=True. You can decide what
                          parts to rebuild based on a minimum model-map
                          correlation (by residue). You can decide how much to
                          rebuild using worst_percent_res_rebuild or with
                          min_cc_res_rebuild, or both.
      min_seq_identity_percent= 50 The sequence in your input PDB file will be
                                adjusted to match the sequence in your
                                sequence file (if any). If there are
                                insertions/deletions in your model and the
                                wizard does not seem to identify them, you can
                                split up your PDB file by adding records like
                                this: BREAK You can specify the minimum
                                sequence identity between your sequence file
                                and a segment from your input PDB file to
                                consider the sequences to be matched. Default
                                is 50.0%. You might want a higher number to
                                make sure that deletions in the sequence are
                                noticed.
      dist_close= None If main-chain atom rmsd is less than dist_close then
                  crossover between chains in different models is allowed at
                  this point. If you input a negative number the defaults will
                  be used
      dist_close_overlap= 1.5 Model or ligand coordinates but not both are
                          kept when model and ligand coordinates are within
                          dist_close_overlap and ligands in
                          input_lig_file_list are being added to the current
                          model. NOTE: you might want to decrease this if your
                          ligand atoms get removed by the wizard. Default=1.5
                          A
      loop_cc_min= 0.4 You can specify the minimum correlation of density from
                   a loop with the map.
      group_ca_length= 4 In resolve building you can specify how short a
                       fragment to keep. Normally 4 or 5 residues should be
                       the minimum.
      group_length= 2 In resolve building you can specify how many fragments
                    must be joined to make a connected group that is kept.
                    Normally 2 fragments should be the minimum.
      include_molprobity= False This command is currently disabled. You can
                          choose to include the clash score from MolProbity as
                          one of the scoring criteria in comparing and merging
                          models. The score is combined with the model-map
                          correlation CC by summing in a weighted clashscore.
                          If clashscore for a residue has a value <
                          ok_molp_score then its value is
                          (clashscore-ok_molp_score)*scale_molp_score,
                          otherwise its value is zero.
      ok_molp_score= None You can choose to include the clash score from
                     MolProbity as one of the scoring criteria in comparing
                     and merging models. The score is combined with the
                     model-map correlation CC by summing in a weighted
                     clashscore. If clashscore for a residue has a value <
                     ok_molp_score (the threshold defined by ok_molp_score)
                     then its value is
                     (clashscore-ok_molp_score)*scale_molp_score, otherwise
                     its value is zero.
      scale_molp_score= None You can choose to include the clash score from
                        MolProbity as one of the scoring criteria in comparing
                        and merging models. The score is combined with the
                        model-map correlation CC by summing in a weighted
                        clashscore. If clashscore for a residue has a value <
                        ok_molp_score then its value is
                        (clashscore-ok_molp_score)*scale_molp_score, otherwise
                        its value is zero.
   density_modification
      thorough_denmod= *Auto True False Choose whether you want to go for
                       thorough density modification when no model is used
                       ("False" speeds it up and for a terrible map
                       is sometimes better)
      hl= False You can choose whether to calculate hl coeffs when doing
          density modification (True) or not to do so (False). Default is No.
      mask_type= *histograms probability wang classic Choose method for
                 obtaining probability that a point is in the protein vs
                 solvent region. Default is "histograms". If you
                 have a SAD dataset with a heavy atom such as Pt or Au then
                 you may wish to choose "wang" because the histogram
                 method is sensitive to very high peaks. Options are:
                 histograms: compare local rms of map and local skew of map to
                 values from a model map and estimate probabilities. This one
                 is usually the best. probability: compare local rms of map to
                 distribution for all points in this map and estimate
                 probabilities. In a few cases this one is much better than
                 histograms. wang: take points with highest local rms and
                 define as protein. Classic runs classical density
                 modification with solvent flipping.
      mask_from_pdb= None You can specify a PDB file to define a mask for the
                     macromolecule in density modification (i.e., the solvent
                     boundary). All points within rad_mask_from_pdb of an atom
                     in the PDB file defined by mask_from_pdb will be
                     considered to be within the macromolecule
      mask_type_extreme_dm= histograms probability *wang classic If FOM of
                            phasing is less up to fom_for_extreme_dm_rebuild
                            then defaults for density modification become:
                            mask_type=wang wang_radius=20 mask_cycles=1
                            minor_cycles=4. Applies to rebuild stages of
                            autobuild. For build use instead
                            fom_for_extreme_dm
      mask_cycles_extreme_dm= 1 Mask cycles in extreme density modification
      minor_cycles_extreme_dm= 4 Minor cycles in extreme density modification
      wang_radius_extreme_dm= 20. Wang radius in extreme density modification
      precondition= False Precondition density before modification
      minimum_ncs_cc= 0.30 Minimum NCS correlation to keep, except in case of
                      extreme_dm
      extreme_dm= False Turns on extreme density modification if FOM is up to
                  fom_for_extreme_dm
      fom_for_extreme_dm_rebuild= 0.10 If extreme_dm is true and FOM of
                                  phasing is up to fom_for_extreme_dm_rebuild
                                  then defaults for density modification
                                  become: mask_type=mask_type_extreme_dm
                                  wang_radius=wang_radius_extreme_dm
                                  mask_cycles=mask_cycles_extreme_dm
                                  minor_cycles=minor_cycles_extreme_dm Applies
                                  to rebuild stages of autobuild. For build
                                  use instead fom_for_extreme_dm
      fom_for_extreme_dm= 0.35 If extreme_dm is true and FOM of phasing is up
                          to fom_for_extreme_dm then defaults for density
                          modification become: mask_type=wang wang_radius=20
                          mask_cycles=1 minor_cycles=4. Applies to build
                          stages of autobuild. For rebuild use instead
                          fom_for_extreme_dm_rebuild
      rad_mask_from_pdb= 2 You can define the radius for calculation of the
                         protein mask Applies only to mask_from_pdb
      modify_outside_delta_solvent= 0.05 You can set the initial solvent
                                    content to be a little lower than
                                    calculated when you are running
                                    modify_outside_model Usually 0.05 is fine.
      modify_outside_model= False You can choose whether to modify the density
                            in the "protein" region outside the
                            region specified in your current model by matching
                            histograms with the region that is specified by
                            that model. This can help by raising the density
                            in this protein region up to a value similar to
                            that where atoms are already placed.
      truncate_ha_sites_in_resolve= *Auto True False You can choose to
                                    truncate the density near heavy-atom sites
                                    at a maximum of 2.5 sigma. This is useful
                                    in cases where the heavy-atom sites are
                                    very strong, and rarely hurts in cases
                                    where they are not. The heavy-atom sites
                                    are specified with
                                    "input_ha_file" and the radius
                                    is rad_mask
      rad_mask= None You can define the radius for calculation of the protein
                mask Applies only to truncate_ha_sites_in_resolve. Default is
                resolution of data.
      use_resolve_fragments= True This script normally uses information from
                             fragment identification as part of density
                             modification for the first few cycles of
                             model-building. Fragments are identified during
                             model-building. The fragments are used, with
                             weighting according to the confidence in their
                             placement, in density modification as targets for
                             density values.
      use_resolve_pattern= True Local pattern identification is normally used
                           as part of density modification during the first
                           few cycles of model building.
      use_hl_anom_in_denmod= False Default is False (use HL coefficients in
                             density modification) NOTE: if True, you must
                             supply HLanom coefficients Allows you to specify
                             that HL coefficients including only the phase
                             information from the imaginary (anomalous
                             difference) contribution from the anomalous
                             scatterers are to be used in density
                             modification. Two sets of HL coefficients are
                             produced by Phaser. HLA HLB etc are HL
                             coefficients including the contribution of both
                             the real scattering and the anomalous
                             differences. HLanomA HLanomB etc are HL
                             coefficients including the contribution of the
                             anomalous differences alone. These HL
                             coefficients for anomalous differences alone are
                             the ones that you will want to use in cases where
                             you are bringing in model information that
                             includes the real scattering from the model used
                             in Phaser, such as when you are carrying out
                             density modification with a model or refinement
                             of a model If use_hl_anom_in_denmod=True then the
                             HLanom HL coefficients from Phaser are used in
                             density modification
      use_hl_anom_in_denmod_with_model= False See use_hl_anom_in_denmod If
                                        use_hl_anom_in_denmod=True then the
                                        HLanom HL coefficients from Phaser are
                                        used in density modification with a
                                        model
      mask_as_mtz= False Defines how omit_output_mask_file
                   ncs_output_mask_file and protein_output_mask_file are
                   written out. If mask_as_mtz=False it will be a ccp4 map. If
                   mask_as_mtz=True it will be an mtz file with map
                   coefficients FP PHIM FOMM (all three required)
      protein_output_mask_file= None Name of map to be written out
                                representing your protein (non-solvent)
                                region. If mask_as_mtz=False the map will be a
                                ccp4 map. If mask_as_mtz=True it will be an
                                mtz file with map coefficients FP PHIM FOMM
                                (all three required)
      ncs_output_mask_file= None Name of map to be written out representing
                            your ncs asymmetric unit. If mask_as_mtz=False the
                            map will be a ccp4 map. If mask_as_mtz=True it
                            will be an mtz file with map coefficients FP PHIM
                            FOMM (all three required)
      omit_output_mask_file= None Name of map to be written out representing
                             your omit region. If mask_as_mtz=False the map
                             will be a ccp4 map. If mask_as_mtz=True it will
                             be an mtz file with map coefficients FP PHIM FOMM
                             (all three required)
   maps
      maps_only= False You can choose whether to skip all model-building and
                 just calculate maps and write out the results. This also runs
                 just 1 cycle and turns on HL coefficients.
      n_xyz_list= None You can specify the grid to use for map calculations.
   model_building
      build_type= *RESOLVE RESOLVE_AND_BUCCANEER You can choose to build
                  models with RESOLVE or with RESOLVE and BUCCANEER #and
                  TEXTAL and how many different models to build with RESOLVE.
                  The more you build, the more likely to get a complete model.
                  Note that rebuild_in_place can only be carried out with
                  RESOLVE model-building. For BUCCANEER model building you
                  need CCP4 version 6.1.2 or higher and BUCCANEER version
                  1.3.0 or higher
      allow_negative_residues= False Normally the wizard does not allow
                               negative residue numbers, and all residues with
                               negative numbers are rejected when they are
                               read in. You can allow them if you wish.
      highest_resno= None Highest residue number to be considered
                     "placed" in sequence for rebuild_in_place
      semet= False You can specify that the dataset that is used for
             refinement is a selenomethionine dataset, and that the model
             should be the SeMet version of the protein, with all SD of MET
             replaced with Se of MSE.
      use_met_in_align= *Auto True False You can use the heavy-atom positions
                        in input_ha_file as markers for Met SD positions.
      base_model= None You can enter a PDB file with coordinates to be used as
                  a starting point for model-building. These coordinates will
                  be included in the same way as fragments placed by searching
                  for helices and strand in initial model-building. Note the
                  difference from the use of models in
                  consider_main_chain_list, which are merged with models after
                  they are built. NOTE: Only use this if you want to keep the
                  input model and just add to it.
      consider_main_chain_list= None This keyword lets you name any number of
                                PDB files to consider as templates for
                                model-building. Every time models are built,
                                the contents of these files will be merged
                                with them and the best parts will be kept.
                                NOTE: this only uses the main-chain atoms of
                                your PDB files.
      dist_connect_max_helices= None Set maximum distance between ends of
                                helices and other ends to try and connect them
                                in insert_helices.
      edit_pdb= True You can choose to edit the input PDB file in
                rebuild_in_place to match the input sequence (default=True).
                NOTE: residues with residue numbers higher than
                'highest_resno' are assumed to not have a known sequence and
                will not be edited. By default the value of 'highest_resno' is
                the highest residue number from the sequence file, after
                adding it to the starting residue number from
                start_chains_list. You can also set it directly
      helices_strands_only= False You can choose to use a quick model-building
                            method that only builds secondary structure. At
                            low resolution this may be both quicker and more
                            accurate than trying to build the entire structure
                            If you are running the AutoSol Wizard, normally
                            you should choose 'False' as standard building is
                            quick. When your structure is solved by AutoSol,
                            go on to AutoBuild and build a more complete model
                            (still using helices_strands_only=False). NOTE:
                            helices_strands_only does not apply in AutoSol if
                            phase_improve_and_build=True
      helices_strands_start= False You can choose to use a quick
                             model-building method that builds secondary
                             structure as a way to get started...then model
                             completion is done as usual. (Contrast with
                             helices_strands_only which only does secondary
                             structure)
      cc_helix_min= None Minimum CC of helical density to map at low
                    resolution when using helices_strands_only
      cc_strand_min= None Minimum CC of strand density to map when using
                     helices_strands_only
      loop_lib= False Use loop library to fit loops Only applicable for
                chain_type=PROTEIN
      standard_loops= True Use standard loop fitting
      trace_loops= False Use loop tracing to fit loops Only applicable for
                   chain_type=PROTEIN
      refine_trace_loops= True Refine loops (real-space) after trace_loops
      density_of_points= None Packing density of points to consider as as
                         possible CA atoms in trace_loops. Try 1.0 for a quick
                         run, up to 5 for much more thorough run If None, try
                         value depending on value of quick.
      max_density_of_points= None Maximum packing density of points to
                             consider as as possible CA atoms in trace_loops.
      cutout_model_radius= None Radius to cut out density for trace_loops If
                           None, guess based on length of loop
      max_cutout_model_radius= 20. Maximum value of cutout_model_radius to try
      padding= 1. Padding for cut out density in trace_loops
      max_span= 30 Maximum length of a gap to try to fill
      max_overlap= None Maximum number of residues from ends to start with.
                   (1=use existing ends, 2=one in from ends etc) If None, set
                   based on value of quick.
      min_overlap= None Minimum number of residues from ends to start with.
                   (1=use existing ends, 2=one in from ends etc)
      include_input_model= True The keyword include_input_model defines
                           whether the input model (if any) is to be crossed
                           with models that are derived from it, and the best
                           parts of each kept. It also defines whether the
                           input model is to be included in combination steps
                           during initial model-building. Note that if
                           multiple_models=True and include_input_model=True
                           then no initial cycle of randomization will be
                           carried out and the keyword
                           multiple_models_starting_resolution is ignored. In
                           most cases you should use include_input_model=True
                           If you want to generate maximum diversity with
                           multiple-models then you may wish to use
                           include_input_model=False. Also if you want to
                           decrease the amount of bias from your starting
                           model you may wish to use
                           include_input_model=False.
      input_compare_file= None If you are rebuilding a model or already think
                          you know what the model should be, you can include a
                          comparison file in rebuilding. The model is not used
                          for anything except to write out information on
                          coordinate differences in the output log files.
                          NOTE: this feature does not always work correctly.
      merge_models= False You can choose to only merge any input models and
                    write out the resulting model. The best parts of each
                    model will be kept based on model-map correlation.
                    Normally used along with number_of_parallel_models=1
      morph= False You can choose whether to distort your input model in order
             to match the current working map. This may be useful for MR
             models that are quite distant from the correct structure.
      morph_main= False You can choose whether to use only main-chain atoms
                  plus c-beta atoms in calculation of shifts in morphing.
                  Default is morph_main=False; use all atoms including
                  side-chain atoms.
      dist_cut_base= 3.0 Tolerance for base pairing (A) for RNA/DNA)
      morph_cycles= 2 Number of iterations of morphing each time it is run.
      morph_rad= 7 Smoothing radius for morphing. The density from your model
                 and from the map are calculated with the radius rad_morph,
                 then they are adjusted to overlap optimally
      n_ca_enough_helices= None Set maximum number of CA to add to ends of
                           helices and other ends to try and connect them in
                           insert_helices.
      delta_phi= 20 Approximate angular sampling for search for regular
                 secondary structure in building
      offsets_list= 53 7 23 You can specify an offset for the orientation of
                    the helix and strand templates in building. This is used
                    in generating different starting models.
      all_maps_in_rebuild= False If two_fofc_in_rebuild or
                           two_fofc_denmod_in_rebuild are set you can choose
                           to try both density-modified and two_fofc-based
                           maps in building. Note: Set to True if you specify
                           rebuild_from_fragments=True. Note: not compatible
                           with map_phasing=True.
      ps_in_rebuild= False You can choose to use a prime-and-switch resolve
                     map in all cycles of rebuilding instead of a
                     density-modified map. This is normally used in
                     combination with maps_only to generate a prime-and-switch
                     map. The map coeffs will be in prime_and_switch.mtz
      use_ncs_in_ps= False You can choose to use NCS in prime-and-switch
      remove_outlier_segments_z_cut= 3.0 You can remove any segments that are
                                     not assigned to sequence during
                                     model-building if the mean density at
                                     atomic positions are more than
                                     remove_outlier_segments_z_cut sd lower
                                     than the mean for the structure.
      refine= True This script normally refines the model during building. Say
              False to skip refinement
      refine_final_model_vs_orig_data= True This script normally refines the
                                       model at the end against the original
                                       (non-aniso-corrected) data and writes
                                       out a CIF version of the model as well
      reference_model= None You can specify a reference model for refinement
      resolution_build= 0 Enter the high-resolution limit for model-building.
                        If 0.0, the value of resolution is used as a default.
      restart_cycle_after_morph= 5 Morphing (if morph=True) will go only up to
                                 this cycle, and then the morphed PDB file
                                 will be used as a starting PDB file from then
                                 on, removing all previous models. If
                                 restart_cycle_after_morph=0 then the model
                                 will be morphed and not rebuilt
      retrace_before_build= False You can choose to retrace your model n_mini
                            times and use a map based on these retraced models
                            to start off model-building. This is the default
                            for rebuilding models if you are not using
                            rebuild_in_place. You can also specify
                            n_iter_rebuild, the number of cycles of
                            retrace-density-modify-build before starting the
                            main build.
      reuse_chain_prev_cycle= True You can choose to allow model-building to
                              include atoms from each cycle in the model the
                              next cycle or not This must be true if you use
                              retrace_before_build
      richardson_rotamers= *Auto True False You can choose to use the rotamer
                           library from SC Lovell, JM Word, JS Richardson and
                           DC Richardson (2000) " The Penultimate Rotamer
                           Library" Proteins: Structure Function and
                           Genetics 40 389-408. if you wish. Typically this
                           works well in RESOLVE model-building for
                           nearly-final models but not as well earlier in the
                           process . Default (Auto) is to use these rotamers
                           for rebuild_in_place but not otherwise.
      rms_random_frag= None Rms random position change added to residues on
                       ends of fragments when extending them If you enter a
                       negative number, defaults will be used.
      rms_random_loop= None Rms random position change added to residues on
                       ends of loops in tries for building loops If you enter
                       a negative number, defaults will be used.
      start_chains_list= None You can specify the starting residue number for
                         each of the unique chains in your structure. If you
                         use a sequence file then the unique chains are
                         extracted and the order must match the order of your
                         starting residue numbers. For example, if your
                         sequence file has chains A and B (identical) and
                         chains C and D (identical to each other, but
                         different than A and B) then you can enter 2 numbers,
                         the starting residues for chains A and C. NOTE: you
                         need to specify an input sequence file for
                         start_chains_list to be applied.
      trace_as_lig= False You can specify that in building steps the ends of
                    chains are to be extended using the LigandFit algorithm.
                    This is default for nucleic acid model-building.
      track_libs= False You can keep track of what libraries each atom in a
                  built structure comes from.
      two_fofc_denmod_in_rebuild= False You can choose to use a
                                  density-modified sigmaa-weighted 2Fo-Fc map
                                  in all cycles of rebuilding instead of a
                                  density-modified map. In density
                                  modification the density in the region
                                  defined by the current model will be
                                  truncated at +2sigma to reduce the dominance
                                  of parts of the map with model defined.
                                  Additionaly only 2 mask cycles of 3 minor
                                  cycles will be done. Additionally
                                  place_waters will be turned off. If the
                                  model is highly incomplete this can
                                  sometimes allow model-building to work even
                                  when it will not for density-modified maps.
                                  The map coeffs will be in
                                  two_fofc_denmod_map.mtz. You might consider
                                  turning on all_maps_in_rebuild as well.
                                  Note: Setting
                                  two_fofc_denmod_in_rebuild=True will by
                                  default set place_waters=False. Set to True
                                  if you specify rebuild_from_fragments=True.
      rebuild_from_fragments= False You can use rebuild_from_fragments=True as
                              a shortcut to turn on two_fofc_denmod_in_rebuild
                              and all_maps_in_rebuild and to use your model in
                              each cycle with consider_main_chain_list. If you
                              use rebuild_from_fragments=True you might also
                              want to set i_ran_seed=xxxxx for some integer
                              xxxxx and run the job 10 or 20 times to have a
                              higher chance of success. This approach is
                              designed for cases where you have a small part
                              of your model very accurately placed and want to
                              build the rest of the model.
      two_fofc_in_rebuild= False You can choose to use a sigmaa-weighted
                           2Fo-Fc map in all cycles of rebuilding instead of a
                           density-modified map. If the model is poor this can
                           sometimes allow model-building in place to work
                           even when it will not for density-modified maps.
      refine_map_coeff_labels= "2FOFCWT PH2FOFCWT" You can pick which map
                               coefficients from phenix.refine to use if
                               two_fofc_in_rebuild=True
      filled_2fofc_maps= True You can choose to use filled 2Fo-Fc maps when
                         two_fofc_in_rebuild is used. Default is True
      map_phasing= False You can choose to use statistical density
                   modification starting with a 2mFo-DFc map, including model
                   information instead of a standard density-modified map with
                   model information. This density modification will include
                   NCS if present. Note: not compatible with
                   all_maps_in_rebuild=True
      use_any_side= True You can choose to have resolve model-building place
                    the best-fitting side chain at each position, even if the
                    sequence is not matched to the map.
      use_cc_in_combine_extend= False You can choose to use the correlation of
                                density rather than density at atomic
                                positions to score models in combine_extend
      sort_hetatms= False Waters are automatically named with the chain of the
                    closest macromolecule if you set sort_hetatms=True This is
                    for the final model only.
      map_to_object= None you can supply a target position for your model with
                     map_to_object=my_target.pdb. Then at the very end your
                     molecule will be placed as close to this as possible. The
                     center of mass of the autobuild model will be
                     superimposed on the center of mass of my_target.pdb using
                     space group symmetry, taking any match closer than 15 A
                     within 3 unit cells of the original position. The new
                     file will be overall_best_mapped.pdb
   multiple_models
      combine_only= False Once you have created a set of initial models you
                    can merge them together into a final set. This option is
                    useful if you have split up the creation of multiple
                    models into different directories, and then you have
                    copied all the initial models to one directory for
                    combining.
      multiple_models= False You can build a set of models, all compatible
                       with your data. You can specify how many models with
                       multiple_models_number. If you are using
                       rebuild_in_place you can specify whether to generate
                       starting models or not with multiple_models_starting.
      multiple_models_first= 1 Specify which model to build first
      multiple_models_group_number= 5 You can build several initial models and
                                    merge them. Normally 5 initial models is
                                    fine.
      multiple_models_last= 20 Specify which model to end with
      multiple_models_number= 20 Specify how many models to build.
      multiple_models_starting= True You can specify how to generate starting
                                models for multiple models. If you are using
                                rebuild_in_place and you specify
                                "True" then the Wizard will rebuild
                                your starting model at the resolution
                                specified in
                                multiple_models_starting_resolution. If you
                                are not using rebuild_in_place the Wizard will
                                always build a starting model at the current
                                resolution.
      multiple_models_starting_resolution= 4 You can set the resolution for
                                           rebuilding an initial model. A
                                           value of 0.0 will use the
                                           resolution of the dataset.
      place_waters_in_combine= None You can choose whether phenix.refine
                               automatically places ordered solvent (waters)
                               during the last cycle of multiple-model
                               generation. This is separate from place_waters,
                               which applies to all other cycles. If None,
                               then value of place_waters will be used.
   ncs
      find_ncs= *Auto True False This script normally deduces ncs information
                from the NCS in chains of models that are built during
                iterative model-building. The update is done each cycle in
                which an improved model is obtained. Say False to skip this.
                See also "input_ncs_file" which can be used to
                specify NCS at the start of the process. If
                find_ncs="No" then only this starting NCS will be
                used and it will not be updated. You can use find_ncs
                "No" to specify exactly what residues will be used
                in NCS refinement and exactly what NCS operators to use in
                density modification. You can use the function
                $PHENIX/phenix/phenix/command_line/simple_ncs_from_pdb.py to
                help you set up an input_ncs_file that has your specifications
                in it. NOTE: if an input map_file is provided then if no ncs
                is found from a model, ncs will be searched for in the density
                of that map.
      input_ncs_file= None You can enter NCS information in 3 ways: (1) an
                      ncs_spec file produced by AutoSol or AutoBuild with NCS
                      information (2) a heavy-atom PDB file that contains ncs
                      in the heavy-atom sites (3) a PDB file with a model that
                      contains chains with NCS The wizard will derive NCS
                      information from any of these if specified. See also
                      "find_ncs" which determines whether the wizard
                      will update NCS from models that are built during
                      iterative building.
      ncs_copies= None Number of copies of the molecule in the au (note: only
                  one type of molecule allowed at present)
      ncs_refine_coord_sigma_from_rmsd= False You can choose to use the
                                        current NCS rmsd as the value of the
                                        sigma for NCS restraints. See also
                                        ncs_refine_coord_sigma_from_rmsd_ratio
      ncs_refine_coord_sigma_from_rmsd_ratio= 1 You can choose to multiply the
                                              current NCS rmsd by this value
                                              before using it as the sigma for
                                              NCS restraints See also
                                              ncs_refine_coord_sigma_from_rmsd
      no_merge_ncs_copies= False Normally False (do merge NCS copies). If
                           True, then do not use each NCS copy to try to build
                           the others.
      optimize_ncs= True This script normally deduces ncs information from the
                    NCS in chains of models that are built during iterative
                    model-building. Optimize NCS adds a step to try and make
                    the molecule formed by NCS as compact as possible, without
                    losing any point-group symmetry.
      use_ncs_in_build= True Use NCS information in the model assembly stage
                        of model-building. Also if no_merge_ncs_copies is not
                        set, then use each NCS copy to try to build the
                        others.
      ncs_in_refinement= *torsion cartesian None Use torsion_angle refinement
                         of NCS. Alternative is cartesian or None (None will
                         use phenix.refine default)
   omit
      composite_omit_type= *None simple_omit refine_omit sa_omit
                           iterative_build_omit Your choices of types of OMIT
                           maps are: None - normal operation, no omit
                           simple_omit - omit the atoms in OMIT region in
                           calculating a sigmaA-weighted 2mFo-DFc map with no
                           refinement. refine_omit - as simple_omit, but
                           refine with standard refinement. sa_omit - omit the
                           atoms in OMIT region, carry out simulated-annealing
                           refinement, then calculate a sigmaA-weighted
                           2mFo-DFc map. iterative_build_omit - set occupancy
                           of atoms in OMIT region to 0 throughout an entire
                           iterative model-building, density modification and
                           refinement process (takes a long time). All these
                           omit map types are available as composite omit maps
                           (default) or as omit maps around a region defined
                           by a PDB file (using omit_box_pdb_list) The
                           resulting OMIT map will be in the directory OMIT
                           with file name resolve_composite_map.mtz . This mtz
                           file contains the map coefficients to create the
                           OMIT map. The file "omit_region.mtz"
                           contains the coefficients for a map showing the
                           boundaries of the OMIT region.
      n_box_target= None You can tell the Wizard how many omit boxes to try
                    and set up (but it will not necessarily choose your number
                    because it has to be nicely divisible into boxes that fit
                    your asymmetric unit). A suitable number is 24. The larger
                    the number of boxes, the better the map will be, but the
                    longer it will take to calculate the map.
      n_cycle_image_min= 3 Pattern recognition (resolve_pattern) and fragment
                         identification ("image based density
                         modification") are used as part of the density
                         modification process. These are normally only useful
                         in the first few cycles of iterative model-building.
                         This script tries model-building both with and
                         without including image information, and proceeds
                         with the most complete model. Once at least
                         n_cycle_image_min cycles have been carried out with
                         image information, if the image-based map results in
                         a less-complete model than the one without image
                         information, image information is no longer included.
      n_cycle_rebuild_omit= 10 Model-building is normally carried out using
                            the "best" available map. If
                            omit_on_rebuild is True, then every
                            n_cycle_rebuild_omit cycle of model rebuilding, a
                            composite omit map is used instead. If you specify
                            0 and omit_on_rebuild is True, omit maps will be
                            used every cycle. Normally every 10th cycle is
                            optimal.
      offset_boundary= 2. Specify the boundary in A around atoms in
                       omit_box_pdb for definition of omit region. Contrast
                       with omit_boundary which applies for composite omit
      omit_boundary= 2. Specify the boundary in A around atoms in omit_boxes
                     for definition of omit region. Contrast with
                     offset_boundary which applies for omit_box_pdb
      omit_box_start= 0 To only carry out omit in some of the omit boxes, use
                      omit_box_start and omit_box_end
      omit_box_end= 0 To only carry out omit in some of the omit boxes, use
                    omit_box_start and omit_box_end
      omit_box_pdb_list= None This keyword applies if you have set OMIT region
                         specification to "omit_around_pdb". To
                         automatically set an OMIT region specify a PDB
                         file(s) with omit_box_pdb_list. The omit region
                         boundaries will be the limits in x y z of the atoms
                         in this file, plus a border of offset_boundary. To
                         use only some of the atoms in the file, specify
                         values for starting, ending and chain to omit
                         (omit_res_start_list and omit_res_end_list and
                         omit_chain_list) If you specify more than one file
                         (or if you specify more than one segment of a file
                         with omit_chain_list or omit_res_start_list and
                         omit_res_end_list) then a set of omit runs will be
                         carried out and combined into one composite omit.
      omit_chain_list= None You can choose to omit just a portion of your
                       model keywords omit_res_start_list 3 omit_res_end_list
                       4 omit_chain_list chain1 (use "" to select
                       all chains) The residues from 3 to 4 of chain1 will be
                       omitted. You can specify more than one region by
                       listing them separated by spaces If you specify more
                       than one region, a separate omit run will be carried
                       out for each one and then the maps will be put together
                       afterwards. If there are more than one chains in the
                       input PDB file then only the chain defined by
                       omit_chain will be omitted NOTE: Zero for start and end
                       and "" for chain is the same as choosing
                       everything
      omit_offset_list= 0 0 0 0 0 0 To carry out one iterative build omit,
                        with a region defined in grid units, enter
                        nxs,nxe,nys,nye,nzs,nze in omit_offset_list.
      omit_on_rebuild= False You can specify whether to use an omit map for
                       building the model on rebuild cycles. Default is True
                       if you start with a model, False if you are building a
                       model from scratch. The omit map is calculated every
                       n_cycle_rebuild_omit cycles
      omit_selection= None Selection string defining atoms in input pdb to be
                      used to define the OMIT region. For use with
                      omit_region_specification=omit_selection
      omit_region_specification= *composite_omit omit_around_pdb
                                 omit_selection You can specify what region an
                                 omit (simple/sa-omit/iterative-build-omit)
                                 map is to be calculated for. Composite omit
                                 will create a map over the entire asymmetric
                                 unit by dividing the asymmetric unit into
                                 overlapping boxes, calculating omit maps for
                                 each, and splicing all the results together
                                 into a single composite omit map. You can
                                 tell the Wizard how many omit boxes to try
                                 and set up with the keyword
                                 "n_box_target" (but it will not
                                 necessarily choose your number because it has
                                 to be nicely divisible into boxes that fit
                                 your asymmetric unit). Omit around PDB will
                                 omit around the region defined by the PDB
                                 file(s) you enter for omit_box_pdb (or around
                                 the residues in that PDB file that you
                                 specify). If you specify omit_around_pdb then
                                 you must enter a pdb file to omit around. If
                                 you specify omit_selection you must enter a
                                 selection string in omit_selection
      omit_res_start_list= None You can choose to omit just a portion of your
                           model keywords omit_res_start_list 3
                           omit_res_end_list 4 omit_chain_list chain1 (use
                           " " for blank). The residues from 3 to 4
                           of chain1 will be omitted. You can specify more
                           more than one region by listing them separated by
                           spaces If you specify more than one region, a
                           separate omit run will be carried out for each one
                           and then the maps will be put together afterwards.
                           If there are more than one chains in the input PDB
                           file then only the chain defined by omit_chain will
                           be rebuilt. NOTE: Zero for start and end and
                           "" for chain is the same as choosing
                           everything
      omit_res_end_list= None You can choose to omit just a portion of your
                         model keywords omit_res_start_list 3
                         omit_res_end_list 4 omit_chain_list chain1 (use
                         " " for blank). The residues from 3 to 4 of
                         chain1 will be omitted. You can specify more more
                         than one region by listing them separated by spaces
                         If you specify more than one region, a separate omit
                         run will be carried out for each one and then the
                         maps will be put together afterwards. If there are
                         more than one chains in the input PDB file then only
                         the chain defined by omit_chain will be omitted NOTE:
                         Zero for start and end and "" for chain is
                         the same as choosing everything
   rebuild_in_place
      min_seq_identity_percent_rebuild_in_place= 95 Minimum sequence identity
                                                 to use rebuild_in_place by
                                                 default
      n_cycle_rebuild_in_place= None Number of cycles for rebuild_in_place for
                                multiple models only
      n_rebuild_in_place= 1 You can choose how many times to rebuild your
                          model in place with rebuild_in_place
      rebuild_chain_list= None You can choose to rebuild just a portion of
                          your model keywords rebuild_res_start_list 3
                          rebuild_res_end_list 4 rebuild_chain_list chain1
                          (use " " for blank). The residues from 3
                          to 4 of chain1 will be rebuilt. You can specify more
                          than one region by using the Parameter Group Options
                          button to add lines. If there are more than one
                          chains in the input PDB file then only the chain
                          defined by rebuild_chain will be rebuilt. The
                          smallest region that can be rebuilt is 4 residues.
      rebuild_in_place= *Auto True False You can choose to rebuild your model
                        while fixing the sequence alignment by iteratively
                        rebuilding segments within the model. This is done
                        n_rebuild_in_place times, then the models are
                        recombined, taking the best-fitting parts of each.
                        Crossovers allowed where main-chain atom rmsd is less
                        than dist_close. Note that the sequence of the input
                        model must match the supplied sequence closely enough
                        to allow a clear alignment. Also this method does not
                        build any new chain, it just moves the existing model
                        around. Normally this procedure is useful if the model
                        is greater than 95% identical with the target
                        sequence. You can include information directly from
                        the starting model if you want with the keyword
                        include_input_model. Then this model will be
                        recombined with the models that are built based on it.
                        Note that this requires that the input model have a
                        sequence that is identical to the model to be rebuilt.
                        You can also rebuild just a portion of the model with
                        the keywords keywords rebuild_res_start_list 3
                        rebuild_res_end_list 4 rebuild_chain_list chain1 (use
                        " " for blank) The residues from 3 to 4 of
                        chain1 will be rebuilt. You can specify more than one
                        region by using the Parameter Group Options button to
                        add lines NOTE: if a region cannot be rebuilt the
                        original coordinates will be preserved for that
                        region.
      rebuild_near_chain= None You can specify where to rebuild either with
                          rebuild_res_start_list rebuild_res_end_list
                          rebuild_chain_list or with rebuild_near_res and
                          rebuild_near_chain and rebuild_near_dist.
      rebuild_near_dist= 7.5 You can specify where to rebuild either with
                         rebuild_res_start_list rebuild_res_end_list
                         rebuild_chain_list or with rebuild_near_res and
                         rebuild_near_chain and rebuild_near_dist.
      rebuild_near_res= None You can specify where to rebuild either with
                        rebuild_res_start_list rebuild_res_end_list
                        rebuild_chain_list or with rebuild_near_res and
                        rebuild_near_chain and rebuild_near_dist.
      rebuild_res_end_list= None You can choose to rebuild just a portion of
                            your model keywords rebuild_res_start_list 3
                            rebuild_res_end_list 4 rebuild_chain_list chain1
                            (use " " for blank). The residues from 3
                            to 4 of chain1 will be rebuilt. You can specify
                            more than one region by using the Parameter Group
                            Options button to add lines. If there are more
                            than one chains in the input PDB file then only
                            the chain defined by rebuild_chain will be
                            rebuilt. The smallest region that can be rebuilt
                            is 4 residues.
      rebuild_res_start_list= None You can choose to rebuild just a portion of
                              your model keywords rebuild_res_start_list 3
                              rebuild_res_end_list 4 rebuild_chain_list chain1
                              (use " " for blank). The residues from
                              3 to 4 of chain1 will be rebuilt. You can
                              specify more than one region by using the
                              Parameter Group Options button to add lines. If
                              there are more than one chains in the input PDB
                              file then only the chain defined by
                              rebuild_chain will be rebuilt. The smallest
                              region that can be rebuilt is 4 residues.
      rebuild_side_chains= False You can choose to replace side chains (with
                           extend_only) before rebuilding the model (not
                           normally used)
      redo_side_chains= True You can chooses to have AutoBuild choose whether
                        to replace all your side chains in rebuild_in_place,
                        taking new ones if they fit the density better. If
                        True, this is applied to all side chains, not only
                        those that are rebuilt.
      replace_existing= True In rebuild_in_place the usual default is to force
                        the replacement of all residues, even if the rebuilt
                        ones are not as good a fit as the original. The
                        rebuilt model is then crossed with the original model
                        (if include_input_model=True) and the better parts of
                        each are then kept. You can override the replacement
                        of all residues in the initial model-building by
                        saying "False" (do not force replacement of
                        residues, keep whatever is better). Additionally if
                        you set the "touch_up" flag then the default
                        is "True": keep whatever is better.
      delete_bad_residues_only= False You can simply delete the worst parts of
                                your model and write out the resulting model
                                with delete_bad_residues_only=True The
                                criteria used are the ones set with touch_up.
                                Any residues that would be rebuild by
                                touch_up=True will be deleted by
                                delete_bad_residues_only. NOTE:
                                delete_bad_residues_only ignores ligands,
                                waters etc. so you may need to put them back
                                in afterwards.
      touch_up= False You can rebuild just the worst parts of your model by
                setting touch_up=True. You can decide what parts to rebuild
                based on an minimum model-map correlation (by residue). This
                is set with min_cc_residue_rebuild=0.82 Alternatively you can
                rebuild the worst percentage of these:
                worst_percent_res_rebuild=6. If a value is set for both of
                these then residues qualifying in either way are rebuilt.
                NOTE: touch_up is only available with rebuild_in_place.
      touch_up_extra_residues= None Number of residues on each side of the
                               residues identified in touch_up that you want
                               to rebuild. Normally you will want to rebuild
                               one or more on each side.
      worst_percent_res_rebuild= 2 You can rebuild just the worst parts of
                                 your model by setting touch_up=True. You can
                                 decide how much to rebuild using
                                 worst_percent_res_rebuild or with
                                 min_cc_res_rebuild, or both.
      smooth_range= None You can specify what number of residues to smooth in
                    making choices for touch_up and delete_bad_residues_only
                    Typically use 3 or 5.
      smooth_minimum_length= None If specified, then any segments remaining
                             after smoothing that are shorter than
                             smooth_mininum_length will be removed.
   refinement
      refine_b= True You can choose whether phenix.refine is to refine
                individual atomic displacement parameters (B values)
      refine_se_occ= True You can choose to refine the occupancy of SE atoms
                     in a SEMET structure (default=True). This only applies if
                     semet=true
      skip_clash_guard= True Skip refinement check for atoms that clash
      correct_special_position_tolerance= None Adjust tolerance for special
                                          position check. If 0., then check
                                          for clashes near special positions
                                          is not carried out. This sometimes
                                          allows phenix.refine to continue
                                          even if an atom is near a special
                                          position. If 1., then checks within
                                          1 A of special positions. If None,
                                          then uses phenix.refine default. (1)
      use_mlhl= True This script normally uses information from the input file
                (HLA HLB HLC HLD) in refinement. Say No to only refine on Fobs
      generate_hl_if_missing= False This script normally uses information from
                              the input file (HLA HLB HLC HLD) in refinement.
                              Say No to not generate HL coeffs from input
                              phases.
      place_waters= True You can choose whether phenix.refine automatically
                    places ordered solvent (waters) during the refinement
                    process.
      refinement_resolution= 0 Enter the high-resolution limit for refinement
                             only. This high-resolution limit can be different
                             than the high-resolution limit for other steps.
                             The default ("None" or 0.0) is to use
                             the overall high-resolution limit for this run
                             (as set by resolution)
      ordered_solvent_low_resolution= None You can choose what resolution
                                      cutoff to use fo placing ordered solvent
                                      in phenix.refine. If the resolution of
                                      refinement is greater than this cutoff,
                                      then no ordered solvent will be placed,
                                      even if
                                      refinement.main.ordered_solvent=True.
      link_distance_cutoff= 3 You can specify the maximum bond distance for
                            linking residues in phenix.refine called from the
                            wizards.
      r_free_flags_fraction= 0.1 Maximum fraction of reflections in the free R
                             set. You can choose the maximum fraction of
                             reflections in the free R set and the maximum
                             number of reflections in the free R set. The
                             number of reflections in the free R set will be
                             up the lower of the values defined by these two
                             parameters.
      r_free_flags_max_free= 2000 Maximum number of reflections in the free R
                             set. You can choose the maximum fraction of
                             reflections in the free R set and the maximum
                             number of reflections in the free R set. The
                             number of reflections in the free R set will be
                             up the lower of the values defined by these two
                             parameters.
      r_free_flags_use_lattice_symmetry= True When generating r_free_flags you
                                         can decide whether to include lattice
                                         symmetry (good in general, necessary
                                         if there is twinning).
      r_free_flags_lattice_symmetry_max_delta= 5 You can set the maximum
                                               deviation of distances in the
                                               lattice that are to be
                                               considered the same for
                                               purposes of generating a
                                               lattice-symmetry-unique set of
                                               free R flags.
      allow_overlapping= None Default is None (set automatically, normally
                         False unless S or Se atoms are the
                         anomalously-scattering atoms). You can allow atoms in
                         your ligand files to overlap atoms in your
                         protein/nucleic acid model. This overrides
                         'keep_pdb_atoms' Useful in early stages of
                         model-building and refinement The ligand atoms get
                         the altloc indicator 'L' NOTE: The ligand occupancy
                         will be refined by default if you set
                         allow_overlapping=True (because of the altloc
                         indicator) You can turn this off with
                         fix_ligand_occupancy=True
      fix_ligand_occupancy= None If allow_overlapping=True then ligand
                            occupancies are refined as a group. You can turn
                            this off with fix_ligand_occupancy=true NOTE: has
                            no effect if allow_overlapping=False
      remove_outlier_segments= True You can remove any segments that are not
                               assigned to sequence if their mean B values are
                               more than remove_outlier_segments_z_cut sd
                               higher than the mean for the structure. NOTE:
                               this is done after refinement, so the R/Rfree
                               are no longer applicable; the remarks in the
                               PDB file are removed
      twin_law= None You can specify a twin law for refinement like this:
                twin_law='-h,k,-l'
      max_occ= None You can choose to set the maximum value of occupancy for
               atoms that have their occupancies refined. Default is None (use
               default value of 1.0 from phenix.refine)
      refine_before_rebuild= True You can choose to refine the input model
                             before rebuilding it
      refine_with_ncs= True This script can allow phenix.refine to
                       automatically identify NCS and use it in refinement.
                       NOTE: ncs refinement and placing waters automatically
                       are mutually exclusive at present.
      refine_xyz= True You can choose whether phenix.refine is to refine
                  coordinates
      s_annealing= False You can choose to carry out simulated annealing
                   during the first refinement after initial model-building
      skip_hexdigest= False You may wish to ignore the hexdigest of the free R
                      flags in your input PDB file if (1) the dataset you
                      provide is not identical to the one that you refined
                      with (but has the same free R flags), or (2) you are
                      providing both an input_data_file and an
                      input_refinement_file or input_hires_file and. In the
                      second case, the resulting composite file may not have
                      the same hexdigest even though the free R flags are
                      copied over. The default is to set skip_hexdigest=True
                      for case #2. For case #1 you have to tell the Wizard to
                      skip the hexdigest (because it cannot know about this).
      use_hl_anom_in_refinement= False See use_hl_anom_in_denmod. If
                                 use_hl_anom_in_refinement=True then the
                                 HLanom HL coefficients from Phaser are used
                                 in refinement
   thoroughness
      build_outside= True Define whether to use the BuildOutside module in
                     model_building
      connect= True Define whether to use the connect module in
               model_building. This module tries to connect nearby chains with
               loops, without using the sequence. This is different than
               fit_loops (which uses the sequence to identify the exact number
               of residues in the loop).
      extensive_build= False You can choose whether to build a new model on
                       every cycle and carry out extra model-building steps
                       every cycle. Default is False (build a new model on
                       first cycle, after that carry out extra steps).
      fit_loops= True You can fit loops automatically if sequence alignment
                 has been done.
      insert_helices= True Define whether to use the insert_helices module in
                      model_building. This module tries to insert helices
                      identified with find_helices_strands into the current
                      working model. This can be useful as the standard build
                      sometimes builds strands into helical density at low
                      resolution.
      n_cycle_build= None Choose number of cycles of building and chain
                     extension during each cycle of model-building. (default
                     of 1 ).
      n_cycle_build_max= 6 Maximum number of cycles for iterative
                         model-building, starting from experimental phases
                         without a model. Even if a satisfactory model is not
                         found, a maximum of n_cycle_build_max cycles will be
                         carried out.
      n_cycle_build_min= 1 Minimum number of cycles for iterative
                         model-building, starting from experimental phases
                         without a model. Even if a satisfactory model is
                         found, n_cycle_build_min cycles will be carried out.
      n_cycle_rebuild_max= 15 Maximum number of cycles for iterative
                           model-rebuilding, starting from a model. Even if a
                           satisfactory model is not found, a maximum of
                           n_cycle_rebuild_max cycles will be carried out.
      n_cycle_rebuild_min= 1 Mininum number of cycles for iterative
                           model-rebuilding, starting from a model. Even if a
                           satisfactory model is found, n_cycle_rebuild_min
                           cycles will be carried out.
      n_mini= 10 You can choose how many times to retrace your model in
              "retrace_before_build"
      n_random_frag= 0 In resolve building you can randomize each fragment
                     slightly so as to generate more possibilities for tracing
                     based on extending it.
      n_random_loop= 3 Number of randomized tries from each end for building
                     loops If 0, then one try. If N, then N additional tries
                     with randomization based on rms_random_loop.
      n_try_rebuild= 2 Number of attempts to build each segment of chain
      ncycle_refine= 3 Choose number of refinement cycles (3)
      number_of_models= None This parameter lets you choose how many initial
                        models to build with RESOLVE within a single build
                        cycle. This parameter is now superseded by
                        number_of_parallel_models, which sets the number of
                        models (but now entire build cycles) to carry out in
                        parallel. None or zero means set it automatically.
                        That is what you normally should use. The
                        number_of_models is by default set to 1 and
                        number_of_parallel_models is set to the value of
                        nbatch (typically 4).
      number_of_parallel_models= 0 This parameter lets you choose how many
                                 models to build in parallel. None or 0 means
                                 set it automatically. That is what you
                                 normally should use. You can set this to 1 to
                                 prevent the wizard from running multiple jobs
                                 in parallel
      skip_combine_extend= False You can choose whether to skip the
                           combine-extend step in model-building if only one
                           model is available
      fully_skip_combine_extend= False You can choose whether to skip the
                                 combine-extend step in model-building in all
                                 cases
      thorough_loop_fit= True Try many conformations and accept them even if
                         the fit is not perfect? If you say True the
                         parameters for thorough loop fitting are:
                         n_random_loop=100 rms_random_loop=0.3
                         rho_min_main=0.5 while if you say False those for
                         quick loop fitting are: n_random_loop=20
                         rms_random_loop=0.3 rho_min_main=1.0
   general
      coot_name= "coot" If your version of coot is called something else, then
                 you can specify that here.
      i_ran_seed= 72432 Random seed (positive integer) for model-building and
                  simulated annealing refinement
      raise_sorry= False You can have any failure end with a Sorry instead of
                   simply printout to the screen
      background= True When you specify nproc=nn, you can run the jobs in
                  background (default if nproc is greater than 1) or
                  foreground (default if nproc=1). If you set run_command=qsub
                  (or otherwise submit to a batch queue), then you should set
                  background=False, so that the batch queue can keep track of
                  your runs. There is no need to use background=True in this
                  case because all the runs go as controlled by your batch
                  system. If you use run_command='sh ' (or similar, sh is
                  default) then normally you will use background=True so that
                  all the jobs run simultaneously.
      check_wait_time= 1.0 You can specify the length of time (seconds) to
                       wait between checking for subprocesses to end
      max_wait_time= 1.0 You can specify the length of time (seconds) to wait
                     when looking for a file. If you have a cluster where jobs
                     do not start right away you may need a longer time to
                     wait. The symptom of too short a wait time is 'File not
                     found'
      wait_between_submit_time= 1.0 You can specify the length of time
                                (seconds) to wait between each job that is
                                submitted when running sub-processes. This can
                                be helpful on NFS-mounted systems when running
                                with multiple processors to avoid file
                                conflicts. The symptom of too short a
                                wait_between_submit_time is File exists:....
      cache_resolve_libs= True Use caching of resolve libraries to speed up
                          resolve
      resolve_size= 12 Size for solve/resolve
                    ("","_giant",
                    "_huge","_extra_huge" or a number
                    where 12=giant 18=huge
      check_run_command= False You can have the wizard check your run command
                         at startup
      run_command= "sh " When you specify nproc=nn, you can run the
                   subprocesses as jobs in background with sh (default) or
                   submit them to a queue with the command of your choice
                   (i.e., qsub ). If you have a multi-processor machine, use
                   sh. If you have a cluster, use qsub or the equivalent
                   command for your system. NOTE: If you set run_command=qsub
                   (or otherwise submit to a batch queue), then you should set
                   background=False, so that the batch queue can keep track of
                   your runs. There is no need to use background=True in this
                   case because all the runs go as controlled by your batch
                   system. If nproc is greater than 1 and you use
                   run_command='sh '(or similar, sh is default) then normally
                   you will use background=True so that all the jobs run
                   simultaneously.
      queue_commands= None You can add any commands that need to be run for
                      your queueing system. These are written before any other
                      commands in the file that is submitted to your queueing
                      system. For example on a PBS system you might say:
                      queue_commands='#PBS -N mr_rosetta' queue_commands='#PBS
                      -j oe' queue_commands='#PBS -l walltime=03:00:00'
                      queue_commands='#PBS -l nodes=1:ppn=1' NOTE: you can put
                      in the characters '' in any queue_commands line and this
                      will be replaced by a string of characters based on the
                      path to the run directory. The first character and last
                      two characters of each part of the path will be
                      included, separated by '_',up to 15 characters. For
                      example
                      'test_autobuild/WORK_5/AutoBuild_run_1_/TEMP0/RUN_1'
                      would be represented by: 'tld_W_5_A1__TP0_1'
      condor_universe= vanilla The universe for condor is usually vanilla.
                       However you might need to set it to local for your
                       cluster
      add_double_quotes_in_condor= True You might need to turn on or off
                                   double quotes in condor job submission
                                   scripts. These are already default
                                   elsewhere but may interfere with condor
                                   paths.
      condor= None Specifies if the group_run_command is submitting a job to a
              condor cluster. Set by default to True if
              group_run_command=condor_submit, otherwise False. For condor job
              submission mr_rosetta uses a customized script with condor
              commands. Also uses one_subprocess_level=True
      last_process_is_local= True If true, run the last process in a group in
                             background with sh as part of the job that is
                             submitting jobs. This prevents having the job
                             that is submitting jobs sit and wait for all the
                             others while doing nothing
      skip_r_factor= False You can skip R-factor calculation if refinement is
                     not done and maps_only=True
      skip_xtriage= False You can bypass xtriage if you want. This will
                    prevent you from applying anisotropy corrections, however.
      base_path= None You can specify the base path for files (default is
                 current working directory)
      temp_dir= None Define a temporary directory (it must exist)
      clean_up= None At the end of the entire run the TEMP directories will be
                removed if clean_up is True. Files listed in keep_files will
                not be deleted. If you want to remove files after your run is
                finished use a command like "phenix.autobuild run=1
                clean_up=True"
      print_citations= True Print citations at end of run
      solution_output_pickle_file= None At end of run, write solutions to this
                                   file in output directory if defined
      title= None Enter any text you like to help identify what you did in
             this run
      top_output_dir= None This is used in subprocess calls of wizards and to
                      tell the Wizard where to look for the STOPWIZARD file.
      wizard_directory_number= None This is used by the GUI to define the run
                               number for Wizards. It is the same as
                               desired_run_number NOTE: this value can only be
                               specified on the command line, as the directory
                               number is set before parameters files are read.
      verbose= False Command files and other verbose output will be printed
      extra_verbose= False Facts and possible commands will be printed every
                     cycle if True
      debug= False You can have the wizard stop with error messages about the
             code if you use debug. Additionally the output goes to the
             terminal if you specify "debug=True"
      require_nonzero= True Require non-zero values in data columns to
                       consider reading in.
      remove_path_word_list= None List of words identifying paths to remove
                             from PATH These can be used to shorten your PATH.
                             For example... cns ccp4 coot would remove all
                             paths containing these words except those also
                             containing phenix. Capitalization is ignored.
      fill= False Fill in all missing reflections to resolution res_fill.
            Applies to density modified maps. See also filled_2fofc_maps in
            autobuild.
      res_fill= None Resolution for filling in missing data (default = highest
                resolution of any datafile). Only applies to density modified
                maps. Default is fill to high resolution of data. Ignored if
                fill=False
      check_only= False Just read in and check initial parameters. Not for
                  general use
      keep_files= overall_best* AutoBuild_run_*.log List of files that are not
                  to be cleaned up. wildcards permitted
      after_autosol= False You can specify that you want to continue on
                     starting with the highest-scoring run of AutoSol in your
                     working directory.
      nbatch= 3 You can specify the number of processors to use (nproc) and
              the number of batches to divide the data into for parallel jobs.
              Normally you will set nproc to the number of processors
              available and leave nbatch alone. If you leave nbatch as None it
              will be set automatically, with a value depending on the Wizard.
              This is recommended. The value of nbatch can affect the results
              that you get, as the jobs are not split into exact replicates,
              but are rather run with different random numbers. If you want to
              get the same results, keep the same value of nbatch.
      nproc= 1 You can specify the number of processors to use (nproc) and the
             number of batches to divide the data into for parallel jobs.
             Normally you will set nproc to the number of processors available
             and leave nbatch alone. If you leave nbatch as None it will be
             set automatically, with a value depending on the Wizard. This is
             recommended. The value of nbatch can affect the results that you
             get, as the jobs are not split into exact replicates, but are
             rather run with different random numbers. If you want to get the
             same results, keep the same value of nbatch. If you set
             nproc=Auto and your machine has n processors, then it will use
             n-1 processors, or 1 if only 1 is available
      quick= False Run everything quickly (number_of_parallel_models=1
             n_cycle_build_max=1 n_cycle_rebuild_max=1)
      resolve_command_list= None Commands for resolve. One per line in the
                            form: keyword value value can be optional
                            Examples: coarse_grid resolution 200 2.0 hklin
                            test.mtz NOTE: for command-line usage you need to
                            enclose the whole set of commands in double quotes
                            (") and each individual command in single
                            quotes (') like this:
                            resolve_command_list="'no_build' 'b_overall
                            23' "
      resolve_pattern_command_list= None Commands for resolve_pattern. One per
                                    line in the form: keyword value value can
                                    be optional Examples: resolution 200 2.0
                                    hklin test.mtz NOTE: for command-line
                                    usage you need to enclose the whole set of
                                    commands in double quotes (") and
                                    each individual command in single quotes
                                    (') like this:
                                    resolve_pattern_command_list="'resolut
                                   ion 200 20' 'hklin test.mtz' "
      ignore_errors_in_subprocess= False Try to ignore errors in sub-processes
                                   This is useful in cases where a very rare
                                   crash occurs and you want to just ignore
                                   that step and go on.
      send_notification= False
      notify_email= None
   special_keywords
      write_run_directory_to_file= None Writes the full name of a run
                                   directory to the specified file. This can
                                   be used as a call-back to tell a script
                                   where the output is going to go.
   run_control
      coot= None Set coot to True and optionally run=[run-number] to run Coot
            with the current model and map for run run-number. In some wizards
            (AutoBuild) you can edit the model and give it back to PHENIX to
            use as part of the model-building process. If you just say coot
            then the facts for the highest-numbered existing run will be
            shown.
      ignore_blanks= None ignore_blanks allows you to have a command-line
                     keyword with a blank value like
                     "input_lig_file_list="
      stop= None You can stop the current wizard with "stopwizard"
            or "stop". If you type "phenix.autobuild run=3
            stop" then this will stop run 3 of autobuild.
      display_facts= None Set display_facts to True and optionally
                     run=[run-number] to display the facts for run run-number.
                     If you just say display_facts then the facts for the
                     highest-numbered existing run will be shown.
      display_summary= None Set display_summary to True and optionally
                       run=[run-number] to show the summary for run
                       run-number. If you just say display_summary then the
                       summary for the highest-numbered existing run will be
                       shown.
      carry_on= None Set carry_on to True to carry on with highest-numbered
                run from where you left off.
      run= None Set run to n to continue with run n where you left off.
      copy_run= None Set copy_run to n to copy run n to a new run and continue
                where you left off.
      display_runs= None List all runs for this wizard.
      delete_runs= None List runs to delete: 1 2 3-5 9:12
      display_labels= None display_labels=test.mtz will list all the labels
                      that identify data in test.mtz. You can use the label
                      strings that are produced in AutoSol to identify which
                      data to use from a datafile like this:
                      peak.data="F+ SIGF+ F- SIGF-". The entire
                      string in quotes counts here You can use the individual
                      labels from these strings as identifiers for data
                      columns in AutoSol or AutoBuild like this:
                      input_refinement_labels="FP SIGFP FreeR_flags"
                      # each individual label counts
      dry_run= False Just read in and check parameter names
      params_only= False Just read in and return parameter defaults. Not for
                   general use
      display_all= False Just read in and display parameter defaults
   non_user_parameters These are obsolete parameters and parameters that the
                       wizards use to communicate among themselves. Not
                       normally for general use.
      gui_output_dir= None Used only by the GUI
      background_map= None You can supply an mtz file (REQUIRED LABELS: FP
                      PHIM FOMM) to use as map coefficients to calculate the
                      electron density in all points in an omit map that are
                      not part of any omitted region. (Default="")
      boundary_background_map= None You can supply an mtz file (REQUIRED
                               LABELS: FP PHIM FOMM) to use as map
                               coefficients to calculate the electron density
                               in all points in the boundary map that are not
                               part of any omitted region.
                               (Default="")
      extend_try_list= True You can fill out the list of parallel jobs to
                       match the number of jobs you want to run at one time,
                       as specified with nbatch.
      force_combine_extend= False You can choose whether to force the
                            combine-extend step in model-building
      model_list= None This keyword lets you name any number of PDB files to
                  consider as starting models for model-building. NOTE: This
                  differs from consider_main_chain_list which will try to add
                  your PDB files EVERY cycle of merging models. In contrast
                  model_list will only do it on the first cycle. NOTE: this
                  only uses the main-chain atoms of your PDB files.
      oasis_cnos= None Enter number of C N O and S atoms here if you have
                  OASIS and want to run it before resolve density modification
                  like this: "C 250 N 121 O 85 S 3"
      offset_boundary_background_map= None You can set the offset of the
                                      boundary_background_map.
      skip_refine= False Skip refinement (used in
                   get_connections/assign_sequence)
      sg= None Obsolete. Use space_group instead
      input_data_file= None Not normally used (same as "data=").
      input_map_file= Auto Not normally used. (Same as map_file).
      input_refinement_file= Auto Not normally used. Same as refinement_file
      input_pdb_file= None Not normally used. Same as "model="
      input_seq_file= Auto Not normally used. Same as seq_file
      super_quick= None Shortcut for very quick run of autobuild. Same as :
                   number_of_parallel_models=1 refine=false
                   n_cycle_rebuild_max=1 remove_aniso=False skip_xtriage=True
                   ncs_copies=1 find_ncs=false fully_skip_combine_extend=True
                   fit_loops=False redo_side_chains=False insert_helices=False
                   build_outside=False connect=False
      require_test_set= False Require that input data file have a test set