[phenixbb] C-ter amidation of peptide
May Marsh
may at cryst.bioc.cam.ac.uk
Tue Nov 10 14:08:32 PST 2009
Hi Nate,
I had a very similar problem which I solved by first manually adding a link
record to the pdb.
e.g
LINK N NH2 C 6 C ALA C 5
Then running phenix.link_edits to create a restraints file.
I hope that helps,
May
On Nov 9 2009, Nate Nicely wrote:
>Dear all,
>
> How best to handle a C-terminally amidated peptide in phenix? I defined
> the atom as 'N' and the resname as 'NH2' following a structure I found
> that also bears a C-terminally amidated peptide. However phenix.refine
> seems not to be making the linkage between the amide and the preceding
> residue. Putting the structure into phenix.elbow returns, "No unknown
> residues."
>
>Thanks,
>
>Nate N.
>
>
>
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--
Dr. May Marsh
Department of Biochemistry, University of Cambridge
may at cryst.bioc.cam.ac.uk
tel: +44-(0)1223 760 468
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