[phenixbb] ligand refinement - elbow
Christine Gee
chrgee at gmail.com
Fri Feb 29 16:27:46 PST 2008
Hi
Its taken me a while to get around to it, but I just ran elbow to
create a cif file etc for my inhibitor, but the bond lengths are
quite different from what I got from the PRODRUG server, and it seems
that the pdb file I got out of elbow has a few problems (COOT doesn't
join up the aromatic ring for example because the carbons are now too
far away on one part of the ring). I was wondering how the bond
lengths are selected? It seems it is giving the aromatic carbons a
bond length of 1.5, when my previous file (and phenylalanine for
example have 1.3). Also, I still am not 100% sure how to add the
CONNECT information to make the ligand able to covalently bind to the
protein.
Regards
Christine
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