Ralf

On Mon, May 14, 2012 at 8:05 PM, Vitali Stanevich <stanevich@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@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@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@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@LBL.gov
Fax   : 510-486-5909    Web : CCI.LBL.gov

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