Andy, We do a lot of liganding fitting with CCP4. This is the general order of steps we take (post initial solution of the protein itself):
1) Build the potential ligand in CCP4 Sketcher a) Rename all the Hydrogens to H#, CCP4 Refmac has some issues with Hydrogens marked OH1, NH1, etc. To simplify things I normally just renumber all the Hydrogens starting from 1. Also makes for less hassle when using the definition file, as the labels in the definition file has to match the pdb of the ligand (this will be more important below). b) Use the regularize function with Refmac 2) Using Coot, load the protein and maps 3) Load the ligand and definition file (####_mon_lib.cif) 4) Use the find ligand function in Coot (find it under other modeling tools) a) select the protein, map you want to search 5) If you find results you desire, merge those ligands with the main pdb 6) Run Refmac on the merged PDB with the library for the ligand in the library input space. Hope this helps, Scott On Thu, Feb 5, 2009 at 9:27 AM, ANDY DODDS <andy.dod...@googlemail.com>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 > > -- Scott D. Pegan, Ph.D. Senior Research Specialist Center for Pharmaceutical Biotechnology University of Illinois at Chicago
