On 03/26/2010 09:07 PM, Thomas Evangelidis wrote: > Thanks, I did what you said and the ligand fits beautifully into the > cavity. Just out of curiosity, does automodel.nonstd_restraints() apply > only to BLK residues? I tried to override this function to build models > with ATP but Modeller always seems to define its own restraints. Do I > always have to do that trick with moving the ligand far from the > protein, as described in the advanced tutorial?
nonstd_restraints() builds restraints on all HETATM residues: http://salilab.org/modeller/9v7/manual/node65.html
If you simply override it to do nothing (e.g. define the method to simply return, or 'pass') then Modeller will not build any of those restraints.
Note that if you do the "move the ligand far away" trick then Modeller will not build any protein-ligand restraints, but it will still build intra- and inter-residue ligand restraints.
Ben Webb, Modeller Caretaker