Where does PHENIX find the monomer libraries? Here's why I ask: I submit a refinement job for a peptide containing a mix of D- and L-amino acids. The program seems to have no problem with D-versions of Glu, Asn, or Phe (DGL, DAS, or DPN), but it flags the atoms in a D-ornithine (ORD) residue as having unknown nonbonded energy type symbols. Curiously, when I look in the relevant directories in ...Contents/phenix-1.8.1-1168/chem_data/chemical_components I can find cif files corresponding to ALL of these D-amino acids, including ORD (...chemical_components/o/data_ORD.cif). Files are also present for DGL, DAS, and DPN. However, these files don't contain all of the information I'm accustomed to seeing in monomer libraries (e.g., explicit bond lengths & angles), so I'm not sure if the same information is somehow encoded differently (via the idealized coordinates, perhaps?), or if I'm barking up the wrong tree. So: Are these the actual monomer libraries that phenix.refine consults? And in this case why doesn't phenix.refine recognize ORD? Or are the true monomer libraries hiding elsewhere? As always, thanks, Pat ps the directory structure I'm describing is under OS X 10.7.5 --------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 [email protected] [email protected] [email protected]