Thank you everyone for suggestions.
As it turns out, there is a problem in the 1.20 phenix version that I was using. I updated to 1.21 as suggested by Dorothee, repeated one refinement job and had no more C-beta outliers, so I am guessing I will not have them in other models either.
Best,
Andrea
On Friday, June 14, 2024 21:16 CEST, Nigel Moriarty wrote:
Andrea Can you send me files off-line?
Cheers
Nigel
---Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated BioimagingLawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Email : [email protected] : CCI.LBL.govORCID : orcid.org/0000-0001-8857-9464
On Thu, Jun 13, 2024 at 9:59 AM Andrea Smith wrote:
Hi all,
I am running Phenix v. 1.20.1-4487 on Windows and I keep on getting C-beta outliers of methionine residues after phenix.refine (happened in different data from two different proteins). Even if I correct the methionines in Coot (and they fit perfectly in the density), I get the outliers at the end of refinement again (while these outliers don't fit the density and I can see a green difference map where the C-beta is).
Why is this? Is there a way to tell phenix.refine not to move a specific amino acid during refinement?
Thanks,
Andrea
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