[phenixbb] refinement with a covalent inhibitor.

Sabine Schneider sabine.schneider at cup.uni-muenchen.de
Tue Mar 17 00:54:25 PDT 2009

Hello Maia,

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.
> Maia
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