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 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 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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-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709     Email : [email protected] Fax   : 510-486-5909       Web  : CCI.LBL.gov

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 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 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 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 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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_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov

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