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Hi Paul, the command phenix.ready_set model_with_unknown_ligand.pdb will create a CIF file for all novel ligands in your input PDB files. You can do it from the command line or using the main GUI. phenix.elbow will do this too. Pavel. On 6/21/10 3:40 AM, Paul Lindblom wrote: > Hi all, > > I need to create a cif file for a new ligand that does not exist in > the pdb, so far. Normally refmac created such a cif file when I merged > the ligand to the structure, but this time it stops with a "fatal > error". I think the alternatives are "sketcher" and the prodrg server. > Can anybody tell me if I have to define the geometric restraints by > myself, or is it possible to take just the output files and put them > into refmac.? And if I have to define the geometric restraints, how to > do this? > > Thanks, > > Paul