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

[Nigel Moriarty]

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 : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov


On Wed, Nov 18, 2020 at 3:14 AM Schulz, Eike-Christian <
eike.schulz at mpsd.mpg.de> 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
>
>
>
>
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