[phenixbb] refinement of peptide with non-standard aminocids

[Nigel Moriarty]

This may solve your problems. I used

phenix.ligand_linking 3dw8.pdb

in a recent version. You should read the article, however, as it will
allow you to troubleshoot and obtain proof of linkage.

Cheers

Nigel

On Sun, May 13, 2012 at 10:39 AM, Ralf Grosse-Kunstleve
<rwgrosse-kunstleve at lbl.gov> wrote:
> See this newsletter:
>
> http://www.phenix-online.org/newsletter/CCN_2011_01.pdf
>
> pages 3-5: FAQ
> There are two methods to add links between atoms in Phenix. Which one should
> I use?
>
> Let us know if this doesn't fully answer your question.
>
> Ralf
>
>
> On Sat, May 12, 2012 at 6:58 PM, Vitali Stanevich <stanevich at wisc.edu>
> wrote:
>>
>> Hi,
>>
>> I am trying to refine protein structure with MCLR ligand - this is cyclic
>> hepta-peptide which has some non-standard amino acids. Sequence is
>> DAL-LEU-ACB-ARG-1ZN-FGA-DAM. It's exactly the same compound as chain G at
>> 3dw8 PDB entry.
>>
>> I could successfully import amino acids in coot through "get monomer"
>> option, renumber and combine in one chain. Problem is that whenever I use
>> phenix.refine it returns all residues nonbonded. Corresponding carboxyl and
>> amino groups are in close proximity to make a bond. I tried to write LINKR
>> record in .pdb - with no success:
>> ...
>> LINKR             1ZN G   5                     FGA G   6
>> trans
>> LINKR             FGA G   6                     DAM G   7
>> trans
>> ...
>>
>> Is there a way to create peptide bonds in this inhibitor chain? I'm using
>> phenix Version: 1.7.3.
>>
>> Thanks in advance,
>> Vitali
>>
>>
>> _______________________________________________
>> 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
>



-- 
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
-------------- next part --------------
A non-text attachment was scrubbed...
Name: data_link.cif
Type: application/octet-stream
Size: 3091 bytes
Desc: not available
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20120513/01ad5b82/attachment.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: apply_link.def
Type: application/octet-stream
Size: 1599 bytes
Desc: not available
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20120513/01ad5b82/attachment-0001.obj>