[phenixbb] define acetyl-methionine for coot and phenix

[Paul Emsley]

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
>         _______________________________________________
>         phenixbb mailing list
>         phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
>         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 <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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