Elke Can you send the files so I can check? Also what version are you using? And are you using the GUI? Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov On Wed, Nov 18, 2020 at 3:14 AM Schulz, Eike-Christian < [email protected]> wrote:

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

————————————————————————————

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 <%2B49%20%280%2940%208998-6264> | Fax +49 (0)40 8994-6264 <%2B49%20%280%2940%208994-6264> | Website www.mpsd.mpg.de

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]