Do you need to define links to define the bonds?

From: [email protected] [mailto:[email protected]] On Behalf Of Daniel Keedy
Sent: Tuesday, 2 December 2014 8:10 a.m.
To: [email protected]
Subject: [phenixbb] norleucine (NLE) restraints

Hi everybody,

First-time poster!  I'm trying to re-refine 2f4k.pdb, but phenix.refine chokes on the non-standard norleucine (NLE) amino acid.  I've tried phenix.elbow and phenix.ready_set using different version of PHENIX, with the NLE cards as either HETATM or ATOM, all to no avail.  SHELX was used to refine the structure originally, but I'd like to use PHENIX to re-refine it.  Any ideas on how to define these restraints?

Daniel Keedy

James Fraser Lab

UCSF