[phenixbb] define acetyl-methionine for coot and phenix

[Nigel Moriarty]

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 <
uschulze-gahmen at lbl.gov> 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 <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
>> 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 <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
>>> phenixbb at phenix-online.org
>>> 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 listphenixbb at phenix-online.orghttp://phenix-online.org/mailman/listinfo/phenixbb
>>
>>
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> 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
> 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
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