We use a similar work flow to that described by Scott Pegan, except we use the Dundee PROGDR server to generate the ligand PDB and cif file. I would add that you should double check your cif file and make sure it has all the proper restraints, and also double check your stereochemistry. If you are not used to this, it could take some time, but it is easy to make mistakes here (at least for me).
If the ligand density in not clear, try to finish as much of the structure as possible before adding ligand, but beware amino acid side chains drifting into ligand density. We sometimes see more than one possible orientation of the ligand, or parts of it. Most of the time this can be resolved by docking both ligand binding orientations and doing a round of refinement. Best, Kendall Nettles The Scripps Research Institute On 2/5/09 10:27 AM, "ANDY DODDS" <[email protected]> wrote: > Hello, > > does anyone know of a tutorial which lays out some sort of pipeline, > hopefully using CCP4 packages, to fit and refine a small molecule > ligand please? > > cheers > > andy
