[phenixbb] question du jour: monomer libs where?

Nathaniel Echols nechols at lbl.gov
Wed Oct 24 08:15:24 PDT 2012

On Wed, Oct 24, 2012 at 8:07 AM, Patrick Loll <pat.loll at drexel.edu> 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).


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