Replace side chains in a model to match the sequence with replace_side_chains

Author(s)

Purpose

Usage

How replace_side_chains works:

Output files from replace_side_chains

Examples

Standard run of replace_side_chains:

Possible Problems

Specific limitations and problems:

Literature

Additional information

List of all replace_side_chains keywords

Author(s)

• replace_side_chains: Tom Terwilliger

Purpose

replace_side_chains is a tool to take a main-chain model and to add side-chains from a rotamer library based on an electron density map.

NOTE: Normally this method is called from phenix.phase_and_build but you can use it interactively if you want.

Usage

How replace_side_chains works:

replace_side_chains uses resolve to replace the side chains in a model. You can choose to use the default resolve rotamer library or the Lovell et al penultimate rotamer library.

Output files from replace_side_chains

replace_side_chains.pdb: A PDB file with side chains replaced.

Examples

Standard run of replace_side_chains:

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

phenix.replace_side_chains  model.pdb map_coeffs.mtz sequence.dat

Possible Problems

Specific limitations and problems:

Literature

Additional information

List of all replace_side_chains 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
------------------------------------------------------------------------------- 
replace_side_chains
   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 PDB file with coordinates to evaluate
      mtz_in= None MTZ file with coefficients for a map
      labin= "" Labin line for MTZ file with map coefficients. This is
             optional if replace_side_chains 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= replace_side_chains.pdb Output PDB file
      log= None Output log file
      params_out= replace_side_chains_params.eff Parameters file to rerun
                  replace_side_chains
   crystal_info
      resolution= 0. high-resolution limit for map calculation
      chain_type= *PROTEIN DNA RNA Chain type (for identifying main-chain and
                  side-chain atoms)
   side_chains
      richardson_rotamers= False Use rotamers from Lovell et al., 2000 library
      force_replace= True Replace all side chains, whether better or not if
                     False, then only replace if it improves fit
   directories
      temp_dir= "temp_dir" Optional temporary work directory
   control
      verbose= True Verbose output
      raise_sorry= False Raise sorry if problems
      debug= False Debugging output
      dry_run= False Just read in and check parameter names