[phenixbb] refinement with a covalent inhibitor.
chern at ualberta.ca
Tue Mar 17 10:04:55 PDT 2009
I have checked all hydrogens that are produced by elbow in the
elbow.ligand.pdb and they look fine. The carboxyl group has a hydrogen
that has to be dissociated in a carboxylate. May be this is causing the
problem. The best geometry I got for this ligand i got in CNS. HIC-Up
server says 5 flat planes, but elbow finds only 2.
Hopefully, Ralf will figure out the problem.
Sabine Schneider wrote:
> 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.
>> phenixbb mailing list
>> phenixbb at phenix-online.org
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