[phenixbb] define acetyl-methionine for coot and phenix

Ursula Schulze-Gahmen uschulze-gahmen at lbl.gov
Fri Sep 20 15:22:05 PDT 2013


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> 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> 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
>> 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 : NWMoriarty at LBL.gov
> Fax   : 510-486-5909       Web  : CCI.LBL.gov
>
> _______________________________________________
> phenixbb mailing list
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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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