Hello Sam, if the ligand dictionary file is not available from the CCP4 monomer library (refmac would stop when it recognized an unknown ligand), you have to generate it from either the PRODRG server ( http://davapc1.bioch.dundee.ac.uk/prodrg/) or PHENIX eLBOW ( http://www.phenix-online.org/documentation/elbow.htm). Use it as LIBIN for refmac to define the restraints. Coot will also need it (File --> Import CIF dictionary) for real space refinement.
Wei-Chun On Thu, Sep 29, 2011 at 11:12 PM, Sam Arnosti <meisam.nosr...@gmail.com>wrote: > Hi every one > > I have a problem with docking my ligand into the electron density map and > make the connections ( bonds ) with the protein. > > It is a Lysine residue that makes a Schiff Base with a long chain aldehyde. > > I do not know how to make the bonds and control the torsion angles of the > ligand. > > I am using the CCP4 and Coot program for refining. > > Thanks > > Sam > -- Wei-Chun Kao, MSc. TEL: +49-761-203-5277 Institute for Biochemistry and Molecular Biology Albert-Ludwigs-Universitaet Freiburg im Breisgau Stefan-Meier-Str. 17 D-79104 Freiburg im Breisgau Germany
