Back to Filters page.

RepackWithoutLigand

Calculates delta_energy or RMSD of protein residues in a protein-ligand interface when the ligand is removed and the interface repacked.

Access delta_energy by using energy_threshold option.

Access RMSD by using rms_threshold and target_res options.

<RepackWithoutLigand name="(&string)"  scorefxn="(&string, score12)" target_res="(&string)" target_cstids="(&string)" energy_threshold="(0.0 &float)" rms_threshold="(0.5 &float)"/>
  • target_cstids: comma-separated list corresponding to cstids (see EnzScore for cstid format)
  • target_res: comma-separated list corresponding to res_nums/pdb_nums (following usual convention: RosettaScripts#rosettascripts-conventions_specifying-residues ) OR "all_repacked" which will include all repacked neighbors of the ligand (the repack shell).
  • rms_threshold: maximum allowed RMS of repacked region; (i.e. RMSD<rms_threshold filter passes, else fails)
  • energy_threshold: delta_Energy allowed (i.e. if E(with_ligand)-E(no_ligand) < threshold, filter passes else fails)

Known issues: Use command line flag -detect_design_interface to speed up the filter. This filter is very slow without this flag.

See also: