Visualizing restraints with PyMOL (--pml)

The tbl, ti, unambig-ti, and restraint subcommands all accept a --pml option that, in addition to generating the restraints file, writes out a PyMOL script (.pml) to visualize the restraints network.

The script colors active residues red, passive residues green, and draws dashed lines between the residues involved in each restraint, making it easy to inspect whether the network makes sense before starting a docking run.

Usage

Pass --pml with an output filename to any of the supported subcommands. For example:

haddock-restraints tbl path/to/config.json --pml network.pml > restraints.tbl

The generated script includes a load command for the structure it was built from, so it's self-contained — just open it directly in PyMOL:

Note (tbl subcommand only): --pml needs to know which PDB the restraints refer to. For ti, unambig-ti, and restraint this is just the PDB argument you already pass on the command line. For tbl, it's read from the structure field in your configuration file, at least one interactor must set it, and if more than one interactor sets it, they must all point to the same file. Otherwise haddock-restraints exits with an error rather than emitting a .pml with no visible network.

pymol network.pml

or, from within an already open PyMOL session:

@network.pml