[phenixbb] norleucine (NLE) restraints

[Daniel Keedy]

Hi Nigel,

Beautiful -- those new restraints did the trick.  Thank you!

~Daniel

On Mon Dec 01 2014 at 1:54:12 PM Nigel Moriarty <nwmoriarty at 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 at LBL.gov
> Fax   : 510-486-5909       Web  : CCI.LBL.gov
>
> On Mon, Dec 1, 2014 at 1:19 PM, Joel Tyndall <joel.tyndall at otago.ac.nz>
> wrote:
>
>>  Do you need to define links to define the bonds?
>>
>>
>>
>> *From:* phenixbb-bounces at phenix-online.org [mailto:
>> phenixbb-bounces at phenix-online.org] *On Behalf Of *Daniel Keedy
>> *Sent:* Tuesday, 2 December 2014 8:10 a.m.
>> *To:* phenixbb at 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
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>>
>>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20141201/1a360906/attachment.htm>