pymol_protonate.py

Help message 

usage: pymol_protonate.py [-h] [-pdb PDB [PDB ...]] [-ignore_ids IGNORE_IDS] [-ignore_atoms IGNORE_ATOMS] [-ignore_atnames IGNORE_ATNAMES]

options:
  -h, --help            show this help message and exit
  -pdb PDB [PDB ...]
  -ignore_ids IGNORE_IDS
  -ignore_atoms IGNORE_ATOMS
  -ignore_atnames IGNORE_ATNAMES

Inputs

  • -pdb: Trimmed PDB to be protonated (required)
    • Given as filename (res_N.pdb)
    • Example: -pdb res_10.pdb
  • -ignore_ids: fragment(s) to exclude from protonation
    • Given as ch:ID pairs
    • We recommend excluding the seed/anything that has manually been protonated in a specific way
    • Examples: -ignore_ids A:203 or -ignore_ids A:301,A:302
  • -ignore_atoms: specific atom(s) to exclude from protonation
    • Given as ch:ID:atom[+atom[+atom…]]
    • More specific control for protecting manually protonated stuff, e.g. keeping one atom of a side chain unprotonated when you still need CA to be capped
    • Examples: -ignore_atoms A:203:C1 or -ignore_ids A:203:C5+O5 etc
  • -ignore_atnames: specific atom type(s) to exclude from protonation
    • Given as atom names, e.g. “ND1,NE2” to avoid PyMOL changing any histidine protonation states
    • Be careful with this!!
    • Example: -ignore_atnames ND1,NE2

Outputs

  • res_N_h.pdb for input res_N.pdb: capped PDB file, will not have the frozen atom column from res_N.pdb
  • log.pml: pymol script used to run the protonation. If pymol_protonate.py can’t run pymol for whatever reason, the user can run this in pymol manually