How to delete everything but a specific ligand from a PDB file using Linux-compatible free software? I would like to delete everything from a PDB file except a specific ligand that I know the PDB code for. Is there a simple way to using free Linux-compatible software? If you want a specific example for your answer 1YAT and its ligand FK5 (tacrolimus) is an example I'm presently working on. I think PyMOL might have this capability using the delete command but running:

delete /1YAT/A


which should delete the macromolecule (chain A) at least but I saw no visually-obvious change. I have viewed the PyMOL Wiki article on the delete command but it was not helpful as what name meant was not obvious to me. 

By free software I mean free of charge not free as in freedom. One piece of software that I used to do this with on Windows was Accelrys (or BIOVIA) Discovery Studio Visualizer, tried to run it on Arch Linux, however, as it has a Linux binary, but it failed to run. This is presumably because it is for Red Hat Enterprise Linux/SUSE Linux Enterprise which has too old of system libraries for Arch Linux compatibility.
What about a straightforward

grep -w " AAA " file.pdb &gt; ligand.pdb


? Where you substitute AAA with the name of the residue you want.