Author(s)

• refine_ca_model: Tom Terwilliger

Purpose

The routine refine_ca_model is a tool for adjusting CA/CB positions in a preliminary model to increase its suitability for generating an all-atom model.

Usage

How refine_ca_model works:

The refine_ca_model tool takes a set of CA positions, and optionally, a set of CB positions. It adjusts the CA/CB positions to put the atoms in density (if possible) and also to place the CB atoms in plausible positions relative to the CA positions and also to make the CA-CA distances as close to 3.8 A as possible.

Using refine_ca_model:

The tool refine_ca_model is usually run automatically as part of trace_and_build. However you can run it yourself with a CA/CB model, a map, and a resolution.

Input map file: The map file should cover the model you supply.

Resolution: Specify the resolution of your map (usually the resolution defined by your half-dataset Fourier shell correlation

CA/CB model: Supply a model that at least has CA positions. If you supply CB positions the new CB positions will be restrained towards the ones you supply.

Examples

Standard run of refine_ca_model:

You can use refine_ca_model to adjust a CA/CB model based on a cryo-EM map:

phenix.refine_ca_model my_map.mrc resolution=2.8 ca_cb_model.pdb

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
  • map_file = None File with CCP4-style map. May have origin in any location.
  • model_file = None Input PDB file with CA positions to be adjusted. Other atoms ignored
• output_files
  • target_output_format = *None pdb mmcif Desired output format (if possible). Choices are None ( try to use input format), pdb, mmcif. If output model does not fit in pdb format, mmcif will be used. Default is pdb.
  • pdb_out = refined_model.pdb Model with refined CA and CB positions (and optional full model)
  • temp_dir = None Temporary directory
• crystal_info
  • resolution = None High-resolution limit for map analysis.
  • 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.
  • chain_type = *PROTEIN Chain type. Must be PROTEIN
  • ca_ca_distance = 3.8 CA-CA distance
  • solvent_content = None Solvent fraction of the cell. If this is density cut out from a bigger cell, you can specify the fraction of the volume of this cell that is taken up by the macromolecule. Normally set automatically. Values go from 0 to 1. Used to scale density.
  • solvent_content_iterations = 3 Iterations of solvent fraction estimation
  • cb_up_from_ca = 1.36 CB atom is cb_up_from_ca in direction of CA atom from mid-point between previous and next CA atoms.
  • cb_right_from_ca = 0.68 CB atom is cb_right_from_ca in direction of (CA atom from mid-point between previous and next CA atoms) cross direction of (previous CA atom to next CA atom).
  • cb_scale = 0.80 Scale on distance for CA-CB. Use 1/cb_scale for density
  • origin_cart = None Origin (cartesian coordinates, overrides value based on map)
• refine
  • refine_group_length = 10 Length of segments to refine
  • refine_in_groups = False Refine in groups, not all at once
  • refine_start = None first residue to refine
  • refine_end = None Last residue to refine
  • residual_start = None first residue to include in residual
  • residual_end = None Last residue to include in residual
  • max_iterations = 10 Iterations in refinement
• weights
  • weight_ca_ca_dist = 1. weight on CA-CA distance
  • weight_cb = 5. weight on CB initial positions
  • weight_proximity_to_initial_position = 0.5 weight on proximity to input CA position
  • weight_density = -1.0 weight on density at CA atoms, between CA atoms, and CB positions
  • weight_cb_density = -5. weight on density at CA atoms, between CA atoms, and CB positions
• control
  • nproc = 1 Number of processors to use
  • random_seed = 171731 Random seed
  • resolve_size = None Size of resolve to use.
  • 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
  • skip_optimization = False Skip optimization
  • max_dirs = 1000 Maximum number of directories (refine_ca_model_xxx)
• guiGUI-specific parameter required for output directory
  • output_dir = None