Author(s)

• rebuild_model: Tom Terwilliger

Purpose

Rebuild a model, keeping all connectivity the same but allowing insertions and deletions.

How rebuild_model works:

Rebuild model rebuilds each chain in your model (optionally in segments of about 15-20 residues) and reassembles these into a new model with the same connectivity as the original.

Each segment is rebuilt with several different base methods (default base methods are refinement, fixing insertions and deletions, and rebuilding from CA positions).

For each base method, a sequence of optimization steps is carried out (typically refinement, the base method, replacement of side chains, regularization, and another replacement of side chains).

Rebuilt segments are scored based on map correlation. The highest-scoring segments are used to replace the corresponding segment in the original model.

If there are multiple chains in your model, each is rebuilt separately.

The quick option can be used to speed up the process. It sets the number of refinement cycles to 1 (otherwise there are 3 carried out) and skips all the optimization steps except the base method.

Examples

Standard run of rebuild_model:

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

phenix.rebuild_model my_model.pdb my_map.mrc resolution=3 nproc=8

This will rebuild my_model.pdb based on the map my_map.mrc at a resolution of 3 A using 8 processors.

Possible Problems

Specific limitations and problems:

Literature

Additional information

List of all available keywords

• job_title = None Job title in PHENIX GUI, not used on command line
• input_files
  • seq_file = None Sequence file. Used to guess sequence if insertions and deletions are allowed.
  • selection = None If specified, use selected part of model (discard remainder)
  • chain_id = None Rebuild first_resno to last_resno of chain chain_id
  • first_resno = None Rebuild first_resno to last_resno of chain chain_id
  • last_resno = None Rebuild first_resno to last_resno of chain chain_id
  • map_model
    • full_map = None Input full map file
    • half_map = None Input half map files
    • model = None Input model file
• output
  • rebuilt_model = None Output file name
  • overwrite = True Overwrite files with same names
• rebuild_model
  • fix_insertions_deletions = True Fix insertions/deletions
  • refine_cycles = None Refinement cycles (set to zero to not refine). Default is 3 for standard run and 1 for quick
  • macro_cycles = 1 Overall macro-cycles carrying out all steps
  • base_methods = *None fix_insertions_deletions ca_to_model refine Base methods to run. None will run all applicable methods
  • optimization_sequence = *None refine base replace_side regularize_model replace_side Optimization sequence to run. None will run all applicable methods
  • take_anything_over_original = None True to not use original model
  • segment_length = None If set, break chains up into pieces about this size
• crystal_info
  • resolution = None Nominal resolution of map
  • minimum_resolution = 2.5 If resolution is finer than minimum_resolution, use minimum_resolution. This speeds up model-building.
  • scattering_table = n_gaussian wk1995 it1992 *electron neutron Choice of scattering table for structure factor calculations. Standard for X-ray is n_gaussian, for cryoEM is electron.
  • wrapping = None You can specify whether the map is wrapped (can map values outside bounds to inside with cell translations).
  • sequence = None Sequences
• control
  • nproc = 1 Number of processors (if None, use all available)
  • ignore_symmetry_conflicts = False You can ignore the symmetry information (CRYST1) from coordinate files. This may be necessary if your model has been placed in a box with box_map for example.
  • verbose = False Verbose output
  • quick = False Run quickly. Sets refinement_cycles to 1 and optimization_sequence to base_method
• guiGUI-specific parameter required for output directory
  • output_dir = None