[phenixbb] refinement with a covalent inhibitor.
sabine.schneider at cup.uni-muenchen.de
Tue Mar 17 00:54:25 PDT 2009
Have you checked, if there are any wrong/weird hydrogens defined at your
ligand? That can screw up your defined geometry. I usually use refmac to
check my cifs, by running it using "structure idealisation" and
"generate all hydrogens and output to coordinate file", putting in the
coordinates of the ligand and the respect cif file. Than you will see,
what is actually in your cif file.
Maybe that helps
Maia Cherney wrote:
> Hi all,
> I am trying to refine a complex with a covalent inhibitor (E-64) that
> has a carboxylate group. My model has it planar, but after refinement
> the two oxygens of the carboxyl group get out of the plane. In the cif
> file generated by elbow this plane description is missing, I added it
> manually, but the result is the same.
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> phenixbb at phenix-online.org
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