On Wed, Oct 24, 2012 at 8:07 AM, Patrick Loll
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?
No. The chemical components CIFs are basic descriptions of molecules in the PDB, with accurate topology and some geometry information, but they do not include restraint targets. eLBOW can generate the restraints for you given a 3-character residue ID if it's in that directory, however. The actual built-in restraints live either in chem_data/mon_lib (the CCP4 monomer library), or chem_data/geostd (a manually curated set, some modified from the monomer library, some created entirely with eLBOW). -Nat