[phenixbb] Phenix.refine question

Boniecki, Michal michal.boniecki at usask.ca
Fri Mar 18 13:09:55 PDT 2022

I had similar problem and updating phenix to latest version helped

> On Mar 18, 2022, at 12:52 PM, lbetts0508 <laurie.betts0508 at gmail.com> wrote:
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> I am refining a small protein crystal model with 1.3 A data, there is a Tyrosine that won't stay put where it looks to me it should go (see below in it's original position, in the negative density; I moved the ring into the positive Fo-Fc density).  After I move it into the positive density, save the coordinates, and do another refinement with the new coordinates, I find it right back in the negative density, even if I only refine ADP or OCC.  Is there some trivial reason this is happening, or can I tell it to not refine that residue?
> https://docs.google.com/document/d/1RkZSH312q2Pimxb9gKLjibm1XbpsVpyzmrX4wGxrNDg/edit?usp=sharing
> THanks
> Laurie Betts
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