Since no one has answered the SHELX part of this question I'll
jump in. The PRODRG restraints should work as is, assuming you've
named the peptide atoms correctly (C, O, CA, N). But just in case
they don't you can explicitly attach it to the main chain with the
addition of a couple of spare restraints. The ones I've listed
below are for a protein I work on whose numbering convention lacks
residue 126 for some unfathomable reason. You'd need a set of
these for both the preceding and following residues.
DFIX C_125 N_127 1.329
DANG O_125 N_127 2.250
DANG CA_125 N_127 2.425
DANG C_125 CA_127 2.435
FLAT 0.3 O_125 CA_125 N_127 C_125 CA_127
RTAB Omeg CA_125 C_125 N_127 CA_127
RTAB Phi C_125 N_127 CA_127 C_127
RTAB Psi N_125 CA_125 C_125 N_127
Hope this helps,
Katherine
On Wed Jun 23 12:10:33 EDT 2010, Paul Emsley
<paul.ems...@bioch.ox.ac.uk> wrote:
On 23/06/10 14:40, Fatima wrote:
Dear all,
I'm finishing a refinement using SHELX and Coot (1.3A) and I
have a modified Arginine. There???s a blob of positive density
(9.04 and 7.01 sigma) binding NH2 in the 2 conformations. I
think it could be a hydroxyl there.
1) How can I add that in Coot?
Centre on the residue you want to replace, then,
Extensions -> Modelling -> Replace Residue -> HAR -> Mutate
(that presumes that you have want an N-omega-hydroxyl-arginine)
2) Does SHELXL recognise modified residues?
Hmm... pass.
How can I get restraints then, by using PRODRG?
Libcheck (in this case). Coot runs libcheck for you.
Paul.
--
SIPPEL,KATHERINE H
Ph. D. candidate
McKenna Lab
Department of Biochemistry and Molecular Biology
College of Medicine
University of Florida
