[phenixbb] question du jour: monomer libs where?

Patrick Loll pat.loll at drexel.edu
Wed Oct 24 09:40:48 PDT 2012

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

> 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).

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...


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
pat.loll at drexelmed.edu

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