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
      map_coeff_labels= None If map coefficients cannot be identified
                        automatically from your MTZ file, you can specify the
                        label or labels for them. (Please separate labels with
                        blank space, MTZ columns grouped together separated by
                        commas with no blanks.) You can specify:
                        map_coeff_labels (e.g., FWT,PHIFWT) amplitudes and
                        phases (e.g., FP,SIGFP PHIB) or amplitudes, phases,
                        weights (e.g., FP,SIGFP PHIB FOM)
      labin= "" For backward compatibility only. 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) NOTE: residues that are not this type will
                  be ignored and not written out.
   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= False Verbose output
      raise_sorry= False Raise sorry if problems
      debug= False Debugging output
      dry_run= False Just read in and check parameter names