Local resolution: FSC default threshold - justification

Post Processing
1

Dear colleagues,

I would like to draw your attention to the default parameters of the local resolution estimation protocol. More in detail, the FSC default threshold. In the In the CryoSPARC, it is set as 0.5 by default.
Is keeping the FSC 0.5 for the local resolution common practice in the articles?
In which cases the FSC threshold shall be changed to 0.143?

I understand that both FSC threshold criteria are shown in the PDB deposition server, but I am concerned about the figure representation used in the article.

Many thanks for your opinion.

Kind regards,
Dmitry

2

For local resolution, 0.5 is pretty standard. Because in local resolution only a sub-region of the map (a sphere or cube) is used for the local FSC calculation, this FSC is pretty noisy, and 0.143 can be pretty close to the noise. Look up the reference for bsoft/blocres, which uses a similar algorithm, for further details.

EDIT: see here, Fig 2 & associated discussion.

3 Likes
3

Dear Oli @olibclarke ,

Thanks a lot!

Kind regards,
Dmitry