[phenixbb] Re: CSD changes conformation to planar during phenix.refine

hello On Thu, Mar 20, 2025, 6:52 PM Nigel Moriarty wrote:

Andrea

Can you send me the files directly?

Cheers

Nigel

--- Nigel W. Moriarty Building 91, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email : [email protected] Web : CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464

On Thu, Mar 20, 2025 at 7:49 AM Andrea Smith wrote:

...

Hi all,

I have a structure where I clearly see that one of the cysteines is oxidised. I have modelled CSD instead of CYS and when I do real space refine in Coot, the CSD sits nicely in the density. When I submit the phenix.refine job, I can see that the geometry changes and now the SOOH is planar. I tried to add the CSD.cif from PDB into phenix.refine as restraints, but it doesn't help and during the automatic refinement the geometry is changed to planar again.

Anyone experienced same thing? What do I do?

Thank you,

Andrea _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s

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