[phenixbb] refinement of peptide with non-standard aminocids

[Vitali Stanevich]

Hi again,

Thanks to your advices, I was able create bonds of desired length for
phenix.refine. But I have 2 more questions:

1) Perhaps naive, but how do I define dihedral angle? I tried:

dihedral {
     atom_selection_1 = name C18 and chain G and resname 1ZN and resseq 5
     atom_selection_2 = name C20 and chain G and resname 1ZN and resseq 5
     atom_selection_3 = name N4 and chain G and resname FGA and resseq 6
     atom_selection_4 = name C4 and chain G and resname FGA and resseq 6
     dihedral_ideal = 180
     sigma = 5
    }
And it was ignored by phenix.refine. Or dihedral is somehow defined just
through the angles?

2) After I try to apply "real_space_refine" in coot to the ligand molecule
- bonds which I defined in "edits" file break and my polymer again becomes
several monomers. Is that normal?

Thanks again,
Vitali

On Sun, May 13, 2012 at 6:42 PM, Nigel Moriarty <nwmoriarty at lbl.gov> wrote:

> 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
> >>
> >
> >
> > _______________________________________________
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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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>
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