Re: [phenixbb] question du jour: monomer libs where?

On 24 Oct 2012, at 11:15 AM, Nathaniel Echols wrote:

On Wed, Oct 24, 2012 at 8:07 AM, Patrick Loll wrote:

...

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).

Sorry to be thick, but how then can I run a refinement job using an input PDB that contains DGL, DAS, and DPN, when files corresponding to these monomers are not found in either chem_data/mon_lib/d or chem_data/geostd/d? I see that these residues are listed in mon_lib_list.cif, but I can't find the actual restraints files. I'm hoping to use one or more such files to help inform my efforts to create a modified restraints file, so my questions, albeit annoying, reflect more than mere idle curiosity... Pat --------------------------------------------------------------------------------------- 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]