On Mon Dec 01 2014 at 1:54:12 PM Nigel Moriarty <nwmoriarty@lbl.gov> wrote:

Dan

The problem is that NLE restraints file is a legacy from the v2 PDB atom names. I have attached a restraints file that I created using

phenix.elbow --chemical_component=NLE

I will update the restraints library in Phenix.

Cheers

Nigel

---
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : NWMoriarty@LBL.gov
Fax : 510-486-5909 Web : CCI.LBL.gov

On Mon, Dec 1, 2014 at 1:19 PM, Joel Tyndall <joel.tyndall@otago.ac.nz> wrote:

Do you need to define links to define the bonds?

From: phenixbb-bounces@phenix-online.org [mailto:phenixbb-bounces@phenix-online.org] On Behalf Of Daniel Keedy
Sent: Tuesday, 2 December 2014 8:10 a.m.
To: phenixbb@phenix-online.org
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

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