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 <nwmoriarty@lbl.gov> wrote:

 

Andrea

 
Can you send me files off-line?


 

Cheers


 

Nigel


 
---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Email : NWMoriarty@LBL.gov
Web  : CCI.LBL.gov


 


 

On Thu, Jun 13, 2024 at 9:59 AM Andrea Smith <andrea.smith@uochb.cas.cz> 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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