[phenixbb] an atom moves away during model refinement

[Nigel Moriarty]

Dmitry

I suspect you will need to add some restraints but if you send me the
model, I can take a look.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Email : NWMoriarty at LBL.gov
Web  : CCI.LBL.gov
ORCID : orcid.org/0000-0001-8857-9464


On Sat, Nov 4, 2023 at 1:16 PM Dmitry Semchonok <semchonok at gmail.com> wrote:

> Dear colleagues,
>
>
>
> While refining my model, the Mg atom for some of the margin units moves
> far away from them. I am also using the ELBOW files of Mg during the
> refinement.
>
>
>
> What is the way to restrict the movement of atoms during refinement?
>
> I found that this behaviour can be observed after simulated annealing is
> on. And the harmonic_restraints may be acquired to restrict atom movement.
>
>
> Is that right?
>
> I am using the GUI version of Phenix, and I cannot see those parameters.
>
>
>
> Thank you.
>
>
>
> Sincerely,
>
> Dmitry
>
>
>
>
>
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