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.
Hi Nate, NH2 is something different in the monomer library, which phenix.refine will pick up. Could you try with a different residue name that's not already in the monomer library? Use the command phenix.where_mon_lib_list_cif to find the location of the monomer library. Then look in e.g. mon_lib/n/NH2.cif what's there and pick a name that doesn't exist. phenix.refine uses the presence of N-CA-C-O atoms with a double-bond for C-O to decide "this is a peptide and I should link it." With a different residue name, hopefully elbow will give you a working file straight away. Let me know if it doesn't work out; if you send me the last two residues of the chain I'll take a closer look. Ralf
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.
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
-- Dr. May Marsh Department of Biochemistry, University of Cambridge [email protected] tel: +44-(0)1223 760 468
participants (3)
-
May Marsh -
Nate Nicely -
Ralf W. Grosse-Kunstleve