Hi,
Since your protein is small and at low resolution,
CTF refinement is difficult, and can make defocus values worse.
You can try (1) reducing the defocus search range
and/or (2) refine only the beam tilt.
If it still makes the resolution worse, give up using CtfRefine.
At such low resolution, per-particle defocus variations within
a micrograph do not really matter.
By the way, for difficult cases like this, saying No to
"mask individual particles with zeros" in Refine3D
sometimes (but not always) gives you a better map.
Best regards,
Takanori Nakane
> Dear Community,
>
> For one of my projects , about a small protein complex ( 150kDa ) with a
> membrane protein component, I face an unexpected behavior of my CTF
> refinement in Relion3 . Indeed, when I proceed to a 3DRefinement , I got a
> postprocessed density map with an average resolution of 4.8 A and the
> following CTF curve.
>
> Then I tried to apply the ctfrefinement and I refined again, after
> postprocessing, I get a map with an average resolution of 5.4A after
> Postprocessing and the following CTF profile:
>
> Regarding to this results and to my limited experience with the CTF
> refinement I would like to know if someone can supply me an explanation
> about it. I also noticed the bumps in the first FSC curve which make
> myself wondering if there is not an over-fitting issue for the first
> refinement. I did the ctf estimation on the non dose weighted motion
> corrected pictures.
> Thank you very much for your interest,
>
> Cheers,
>
> Julien
>
> *************************************************
> Bous Julien
> PhD student
> Biochemistry structural center
> Montpellier
>
>
>
>
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