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Quick model-building of a single model with resolve using build_one_model

Author(s)
Purpose
Usage
How build_one_model works:
Output files from build_one_model
Examples
Standard run of build_one_model:
Possible Problems
Specific limitations and problems:
Literature
Additional information
List of all build_one_model keywords

Author(s)

  • build_one_model: Tom Terwilliger

Purpose

If you have an mtz map coefficients file and a sequence file, you can use build_one_model to just build a single model with resolve. You can also extend an existing model.

Usage

How build_one_model works:

build_one_model runs resolve model-building, by default in superquick_build mode. If you supply a model, then resolve will try to extend the ends of each chain in your model.




Output files from build_one_model

build_one_model.pdb: A PDB file with the resulting model

Examples

Standard run of build_one_model:

Running build_one_model is easy. From the command-line you can type:

phenix.build_one_model  map_coeffs.mtz \
   sequence.dat free_in=exptl_fobs_phases_freeR_flags.mtz
where exptl_fobs_phases_freeR_flags.mtz has your free R flags for refinement. If you want to supply a PDB file to extend instead you can do that:
phenix.build_one_model map_coeffs.mtz \
  sequence.dat free_in=exptl_fobs_phases_freeR_flags.mtz \
  model.pdb

Possible Problems

Specific limitations and problems:

Literature

Additional information

List of all build_one_model 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
------------------------------------------------------------------------------- 
build_one_model
   input_files
      seq_file= None File with 1-letter code sequence of molecule. Chains
                separated by blank line or greater-than sign
      pdb_in= None Optional starting PDB file (ends will be extended if
              present)
      map_coeffs= None MTZ file with coefficients for a map
      labin_map_coeffs= None Labin line for MTZ file with map coefficients.
                        This is optional if build_one_model can guess the
                        correct coefficients for FP PHI and FOM. Otherwise
                        specify: LABIN FP=myFP PHIB=myPHI FOM=myFOM where myFP
                        is your column label for FP
      ncs_info_file= None ncs_spec file with NCS information (written by
                     simple_ncs_from_pdb or find_ncs)
      remove_free
         free_in= None MTZ file containing FreeR_flags NOTE free_in only used
                  in build_one_model. Ignored by phase_and_build Used as
                  source of freeR information for real_space refinement. Note
                  other columns of data may be present and can be used in
                  reciprocal-space refinement. A suitable file is
                  exptf_fobs_phases_freeR_flags.mtz from autosol/autobuild or
                  my_model_refine_data.mtz from phenix.refine
         labin_free= None Labin line for MTZ file with FreeR_flags. This is
                     optional if build_one_model can guess the correct
                     coefficients for FreeR_flags.Otherwise specify:
                     FreeR_flags==myFreeR_flags
         map_coeffs_no_free= None Optional MTZ file with coefficients for a
                             map with freeR set removed. Use instead of
                             free_in. This map will be used for real-space
                             refinement
         labin_no_free= None Labin line for MTZ file with map coefficients and
                        freeR set removed. This is optional if build_one_model
                        can guess the correct coefficients for FP PHI and FOM.
                        Otherwise specify: LABIN FP=myFP PHIB=myPHI FOM=myFOM
                        where myFP is your column label for FP
   output_files
      pdb_out= build_one_model.pdb Output PDB file
      log= build_one_model.log Output log file
      params_out= build_one_model_params.eff Parameters file to rerun
                  build_one_model
      model_building_log= model_building.log Log file for model-building
   refinement
      rs_refine= True You can run real-space refinement after model-building
                 NOTE: real_space refinement requires a source of FreeR_flag
                 and standard requires Fobs SigFobs and a source of FreeR_flag
                 For real-space refinement you can supply either an mtz file
                 with a FreeR_flag column or an mtz map file that has all the
                 FreeR reflections removed
   model_building
      quick= False You can run quickly (superquick_build/delta_phi=30.) or
             more thoroughly (default, thorough_build/delta_phi=20.)
      insert_helices= False You can find helices and use them as a starting
                      point for model-building. This is useful if your
                      resolution is worse than 3 A.
      i_ran_seed= 712341 Random seed for model-building
   directories
      temp_dir= "temp_dir" Optional temporary work directory
      output_dir= "" Output directory where files are to be written
      top_output_dir= "" Top output directory for control files
   crystal_info
      resolution= 0. high-resolution limit for map calculation
      solvent_fraction= None You can specify the solvent fraction Normally it
                        is set automatically
      chain_type= *PROTEIN DNA RNA Chain type (for identifying main-chain and
                  side-chain atoms)
      semet= False You can specify that your protein contains selenomethionine
   control
      verbose= False Verbose output
      raise_sorry= False Raise sorry if problems
      debug= False Debugging output
      dry_run= False Just read in and check parameter names
      write_run_directory_to_file= None The working directory name is written
                                   to this file
      resolve_command_list= None You can supply any resolve command here 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' "