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 mailto:[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 mailto:[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] mailto:[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 tel:510-486-5709 Email : [email protected] Fax : 510-486-5909 tel:510-486-5909 Web : CCI.LBL.gov http://CCI.LBL.gov

_______________________________________________ phenixbb mailing list [email protected] mailto:[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

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