[phenixbb] refinement of peptide with non-standard aminocids

[Ralf Grosse-Kunstleve]

phenix.refine doesn't support custom dihedrals. Sorry. For this you need to
work with CIF links.

Coot ignores our edits. I'm not sure how it deals with CIF links. I hope
someone else can help.

Ralf

On Mon, May 14, 2012 at 8:05 PM, Vitali Stanevich <stanevich at wisc.edu>wrote:

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