[phenixbb] question du jour: monomer libs where?

Patrick Loll pat.loll at drexel.edu
Wed Oct 24 08:07:14 PDT 2012

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


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,


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
pjloll at gmail.com
pat.loll at drexelmed.edu
pat.loll at drexel.edu

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