On Fri, Sep 20, 2013 at 1:15 PM, Nigel Moriarty <[email protected]> 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 <[email protected]> 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
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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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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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Ursula Schulze-Gahmen, Ph.D.
Assistant Researcher
UC Berkeley, QB3
356 Stanley Hall #3220
Berkeley, CA 94720-3220