Re: [phenixbb] define acetyl-methionine for coot and phenix

Ursula Use this file, it has peptide in the right place. You do have to "import" it into Coot. Nigel On Mon, Sep 23, 2013 at 10:13 AM, Ursula Schulze-Gahmen < [email protected]> wrote:

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.

I 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?

Ursula

On Mon, Sep 23, 2013 at 3:27 AM, Paul Emsley 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:

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 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 -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220 _______________________________________________ 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

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

-- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

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

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

-- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

_______________________________________________ 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