[phenixbb] Best practices for modified aminoacids

Nigel Moriarty nwmoriarty at lbl.gov
Fri Jul 27 12:54:50 PDT 2012


phenix.refine will automatically link a non-standard aminoacid into
the chain if the main chain atoms are named in the same fashion as the
standard, i.e. C, CA, N, O. Unfortunately, the PDB decided to name the
N7D in a "non-compliant" fashion. You have choices.

1. Use the cif link facility to link them.

phenix.ligand_linking model.pdb

may provide this for you but I'd appreciate the copy of the three
residues involved to double check the validity of the links.

2. Rename the atoms in your model to the standard names for the main
chain (and ideally change the residue to something else) and run

phenix.elbow model.pdb --residue=NWM

to get a new cif file for the new residue. eLBOW attempts to match the
main chain restraints in the other restraints files if it detects that
the residue is an aminoacid.



On Fri, Jul 27, 2012 at 10:43 AM, Schubert, Carsten [JRDUS]
<CSCHUBER at its.jnj.com> wrote:
> What are the current best practices for modified aminoacids? I have a
> peptide with and N-terminal Acetyl-proline which I am trying to model. The
> initial approach was to locate the aminoacid in the chemical components
> dictionary (N7P) and replace the residue in coot. Unfortunately the link to
> the next residue is not recognized, so the residue is just floating about.
> Next I just added an acetyl next to the proline and added some restraints in
> the .def file. That sort of works, but looks a bit cludgy. Is there a way to
> do this more cleanly?
> Cheers,
>                 Carsten
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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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