Hi Christine, I think you need to do this (Ralf please correct me if I'm wrong): 1) Run phenix.elbow to create a cif file for your ligand (if you don't have one): % phenix.elbow model.pdb --do-all elbow will go though your pdb file and create a dictionary file for whatever is not present in the standard library. One of the output cif files with "all" (xxx_all.cif) in its name is the file that you need to use. 2) Now you need to tell phenix.refine that your ligand is covalently bonded to the macromolecule: % phenix.refine model.pdb data.mtz xxx_all.cif may_params.par where may_params.par defines the bond and contains these lines, for example: refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = chain X and resname HIS and resid 117 and name NE2 atom_selection_2 = resname LIG and resid 98 and name C distance_ideal = 1.45 sigma = 0.02 } } You can also define an angle. Look "Definition of custom bonds and angles" in phenix.refine manual for more information: http://www.phenix-online.org/documentation/refinement.htm Please let us know if you have any questions. Pavel. On 2/21/2008 5:52 PM, Christine Gee wrote:

Dear Phenix developers I have a covalently bound ligand in my structure and I would like to use phenix to refine the structure. The ligand is bound to the sulfur of a cysteine. What is the best method for defining the ligand. Should I generate a cif file for the whole amino acid and the ligand, or can I make one for just the ligand and add in some restraint somewhere which tells phenix to make a bond between the ligand atom and a nearby sulfur in a cysteine. If I generate a cif file with the whole amino acid and ligand, I assume I will I have to follow some convention in atom naming so that the main chain bonds and angles will form and refine OK? Regards Christine

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