[phenixbb] define acetyl-methionine for coot and phenix
Paul Emsley
pemsley at mrc-lmb.cam.ac.uk
Mon Sep 23 03:27:12 PDT 2013
You will need to make sure that the group of the AME is "peptide" (or
"L-peptide"). If you tell Coot that it's a non-polymer, it will believe
you.
I guess this should be added to the FAQ. Thanks.
Paul.
On 20/09/13 23:22, Ursula Schulze-Gahmen wrote:
> Thanks Nigel,
>
> All I need now is a cif file for acetyl-methionine. How do I get to
> this? And should the cif file be for the free amino acid or for the
> residue in the peptide chain?
>
> Ursula
>
>
> On Fri, Sep 20, 2013 at 1:15 PM, Nigel Moriarty <nwmoriarty at lbl.gov
> <mailto:nwmoriarty at lbl.gov>> wrote:
>
> To have the refinement link the residues you should use the
> parameter intra_chain=True and check the bonds in the .geo file.
>
> Paul Emsley will likely answer that Coot question.
>
> Nigel
>
>
> On Fri, Sep 20, 2013 at 12:06 PM, Ursula Schulze-Gahmen
> <uschulze-gahmen at lbl.gov <mailto:uschulze-gahmen at lbl.gov>> wrote:
>
> I am trying to include a N-terminal acetylated methionine in
> my model.
> I replaced my methionine with a AME residue from the pdb data
> bank and
> included a link command to connect the C from AME with the N
> of the
> second residue. The AME is defined as HETATM. When I try to
> regularize
> this structure in Coot it doesn't recognize that the 1. and 2.
> residue
> should stay connected. What or how do I need to define this
> residue or
> the connection so that I can model in Coot and refine in Phenix?
>
> Ursula
> --
> Ursula Schulze-Gahmen, Ph.D.
> Assistant Researcher
> UC Berkeley, QB3
> 356 Stanley Hall #3220
> Berkeley, CA 94720-3220
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>
>
>
>
> --
> Nigel W. Moriarty
> Building 64R0246B, Physical Biosciences Division
> Lawrence Berkeley National Laboratory
> Berkeley, CA 94720-8235
> Phone : 510-486-5709 <tel:510-486-5709> Email : NWMoriarty at LBL.gov
> Fax : 510-486-5909 <tel:510-486-5909> Web : CCI.LBL.gov
> <http://CCI.LBL.gov>
>
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>
>
>
> --
> Ursula Schulze-Gahmen, Ph.D.
> Assistant Researcher
> UC Berkeley, QB3
> 356 Stanley Hall #3220
> Berkeley, CA 94720-3220
>
>
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