[phenixbb] Ensemble refinement with covalent ligands - bond length > 5Å

Wed Nov 18 03:10:55 PST 2020

Dear all,

I am running phenix.ensemble_refinement on a covalent protein-ligand complex providing the same parameter-files used for phenix.refine. I also included the .def and .cif files generated by phenix.ligand_linking.

However, in quite a few of the ensemble structures, the covalent link exceeds 5Å, which is obviously wrong. How can I obtain ensemble structures with reasonable covalent bond length?

Best,

Eike

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Dr. Eike C. Schulz
Max Planck Institute for the Structure and Dynamics of Matter
Luruper Chaussee 149 | 22761 Hamburg | Germany
Building 99 (CFEL) | Office O2.101
Phone +49 (0)40 8998-6264<tel:%2B49%20%280%2940%208998-6264> | Fax +49 (0)40 8994-6264<tel:%2B49%20%280%2940%208994-6264> | Website www.mpsd.mpg.de<http://www.mpsd.mpg.de/>

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