Generate a PyMOL visualization from a .tbl file

haddock-restraints can generate a PyMOL (.pml) visualization directly from an existing .tbl restraints file and the PDB(s) it refers to — without needing a config.json.

This is the standalone equivalent of the --pml option available on tbl, ti, unambig-ti, and restraint, for when you already have a .tbl file (handed to you, or from a previous run) instead of the inputs that generated it.

Usage

haddock-restraints tbl2pml restraints.tbl complex.pdb --output network.pml

Multiple PDBs can be passed if the restraints span more than one structure file; each gets its own load line in the generated script:

haddock-restraints tbl2pml restraints.tbl chainA.pdb chainB.pdb --output network.pml

pymol network.pml

Like the rest of --pml, active residues are colored red, passive residues green, with dashed lines drawn between restrained residue pairs.

Note: tbl2pml checks that the PDB(s) you pass exist, but does not validate that the segid values in the .tbl match chain IDs present in them — a mismatch simply renders nothing for that residue in PyMOL, the same way an unresolved selection would in any other .pml script.