UrsulaI actually got a decent structure out of Phenix with AME connected to the next residue. AME is composed of heteroatoms at this point. When I read this into coot, it looks alright, but I am not able to manipulate any conformations for the AME because it is not defined. What do I need to define, or is it perhaps a better approach to just define an acetylgroup and link this to the N-terminal normal methionine?Hi Paul,I am sorry I did not understand that advice. What is the group definition for a residues or compound? And I do want AME connected to the polypeptide.
On Mon, Sep 23, 2013 at 3:27 AM, Paul Emsley <pemsley@mrc-lmb.cam.ac.uk> wrote:
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:
UrsulaThanks 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?
On Fri, Sep 20, 2013 at 1:15 PM, Nigel Moriarty <nwmoriarty@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@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?
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UC Berkeley, QB3
356 Stanley Hall #3220
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Assistant Researcher
UC Berkeley, QB3
356 Stanley Hall #3220
Berkeley, CA 94720-3220
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