[phenixbb] Restraints file for a new amino acid residue

Nigel Moriarty nwmoriarty at lbl.gov
Fri Aug 13 10:02:10 PDT 2010


The only things you need for phenix.refine to link a non-standard
amino acid into the peptide chain is

a) The backbone atoms must be named according to the convention - CA, C, N, O
b) The cartesian coordinates need to be reasonable so a bond can be
formed between residues
c) In older versions, the restraints file needs to have a double bond
between C and O.

To get a restraints file, if you have the non-standard amino acid in
the model PDB, you can do several different things depending on you
needs.  Using eLBOW directly

phenix.elbow --residue NSA model.pdb


phenix.elbow --do-all model.pdb

You can also get a similar results from ReadySet!

phenix.ready_set model.pdb

ReadySet! does some more correcting of atom names.  If you have any
trouble let me know and I'll take a look at you specified situation.


On Fri, Aug 13, 2010 at 9:38 AM, Joseph Noel <noel at salk.edu> wrote:
> Hi All,
> How does one create a new CIF file using Elbow for a non-natural amino acid
> not found yet in the PDB? I know how to carry it out for the isolated
> residue readily (but of course thinks it is isolated and doesn't include the
> necessary peptide bonding) but how does one ensure the correct backbone
> restraints for it are included since it is not isolated but part of the
> chain?
> Joe
> ___________________________________________________________
> Joseph P. Noel, Ph.D.
> Investigator, Howard Hughes Medical Institute
> Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics
> The Salk Institute for Biological Studies
> 10010 North Torrey Pines Road
> La Jolla, CA  92037 USA
> Phone: (858) 453-4100 extension 1442
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> Web Site (HHMI): http://hhmi.org/research/investigators/noel.html
> ___________________________________________________________
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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

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