Hi Sabine, 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
Sabine
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 _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
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