FAQ: rhofit has found the correct site to fit but the ligand has not been fitted correctly

Things to check:

  1. is the cluster file used in the fit sensible? Does it cover all the difference density? These easiest way to check this is to use the visualise-rhofit-coot visualiser and click on the "Cluster visible" tick box. If the cluster does not cover all the difference density then it might be worthwhile manually producing cluster files.
  2. could the bad fit be caused by a poor ligand dictionary?
    • rhofit uses refinement restraints to work out how it can adjust a ligand's conformation to fit the density.
    • The misidentification of planes is probably the biggest problem in restraint dictionary generation. Plane problems are often behind rhofit failures.
    • To quickly visualize what plane restraints are being used for the ligand in rhofit, you can use the EditTNT program
    • simply cd to rhofit results directory and issue the command:
EditTNT best.dic best.pdb
    • for instance, using rhofit to fit the "880" ligand to 1pmq using libcheck to generate a cif dictionary from SMILES results in a poor fit.
    • EditTNT shows that the three unsaturated rings are held in a single plane so cannot rotate relative to one another.
    • 1pmq_ligand_editnt_plane.png (click on image to zoom in)
    • the density clearly shows this is incorrect.
    • If the input cif dictionary is edited splitting the plane into 3 separate planes the fit works.
  1. If it still doesn't work, please let us know, giving all the details you're allowed of the input PDB, MTZ file, and ligand.

Page by Oliver Smart original version 1 April 2010. Address problems, corrections and clarifications to buster-develop@globalphasing.com