make_template_pdb.py

This script adds constraint flags to a modified PDB file. Main use is after the initial model has been capped as PyMOL removes the non-standard constraint column.

The template PDB is designed to simplify the computational workflow by taking constraint application/management off the user’s hands.

Help message 

usage: make_template_pdb.py [-h] [-model MODNAME] [-noh NO_H_PDB] [-addh H_ADD_PDB]

Prepare template PDB files

options:
  -h, --help       show this help message and exit
  -model MODNAME   model number
  -noh NO_H_PDB    trimmed_pdb_file
  -addh H_ADD_PDB  hadded_pdb_file

Inputs

Inputs are an initial model PDB file containing constraint flags and a subsequently modified model PDB file without constraint flags. These can be specified in one of two ways.

Specifiying by model:

  • -model: model number to make template PDB for
    • Given as integer
    • Will define the initial PDB and modified PDB as res_N.pdb and res_N_h.pdb for given model label N
    • Example: -model 10

Specifying the two PDBs separately:

  • -noh: initial PDB with constraints
    • Given as filename
    • Example: -noh res_N.pdb
  • -addh: modified PDB without constraints
    • Given as filename
    • Example: -addh res_N_h.pdb

Outputs

  • model_N_template.pdb, a constraint-encoded model PDB file