[phenixbb] define acetyl-methionine for coot and phenix
uschulze-gahmen at lbl.gov
Mon Sep 23 10:13:22 PDT 2013
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?
On Mon, Sep 23, 2013 at 3:27 AM, Paul Emsley <pemsley at 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
> I guess this should be added to the FAQ. Thanks.
> 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?
> 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.
>> 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 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
>> 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
>> phenixbb at phenix-online.org
> Ursula Schulze-Gahmen, Ph.D.
> Assistant Researcher
> UC Berkeley, QB3
> 356 Stanley Hall #3220
> Berkeley, CA 94720-3220
> phenixbb mailing listphenixbb at phenix-online.orghttp://phenix-online.org/mailman/listinfo/phenixbb
> phenixbb mailing list
> phenixbb at phenix-online.org
Ursula Schulze-Gahmen, Ph.D.
UC Berkeley, QB3
356 Stanley Hall #3220
Berkeley, CA 94720-3220
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