FAQ: I have a ligand that binds covalently: how should I use rhofit?

This current version of rhofit (March 2010) does not explicitly treat covalently bound ligands. But if your density is good enough you can still may a good prediction of the binding position without using the information about the bond to restrict the fit. When doing this it is important to turn off the protein-ligand contacts between the atom in the ligand that is in reality bonded to the protein. There are two ways to do this:

  1. the simple way turn off ALL protein ligand contacts by using rhofit argument -clashweight 0
  2. The more complex way. Leave protein ligand contacts on but delete the atom in the protein to which the ligand binds, and any atoms bonded to it, from the protein file that you give to rhofit, so that the contact term doesn't distort the ligand. An example where such an approach works 1b0f/SEI from Wlodek et al. (2006) test set.

Once rhofit has fit the ligand you should only take solutions seriously if they position the bonded atom in the ligand next to the protein side chain it joins to.

It is planned to improve rhofit to treat covalently bound ligands for a future release.

Page by Oliver Smart original version 5 November 2009, Updated 1 April 2010. Address problems, corrections and clarifications to buster-develop@globalphasing.com