Hi Nigel, Beautiful -- those new restraints did the trick. Thank you! ~Daniel On Mon Dec 01 2014 at 1:54:12 PM Nigel Moriarty 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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov

On Mon, Dec 1, 2014 at 1:19 PM, Joel Tyndall wrote:

...

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

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