Hi,

> micrographs were not entirely gain corrected and
> I had to subtract a reference image using -Dark in MotionCor2

You are applying bias (i.e. additive systematic bias) correction,
not gain (i.e. multiplicative systematic bias) correction.
Is this what you really want to do?

If the problem is in the gain reference, not dark reference,
you can re-estimate the gain from frames (see CCPEM archive).

> My question is: does Relion recognize this additional argument when doing
> Bayesian Polishing

Unfortunately no.

> does it look at the raw movies which are not corrected?

Yes.

> Would it be better for Relion to gain correct the single frames first and
> then start MotionCor2 inside Relion?

Yes, although this takes large disk space...

Best regards,

Takanori Nakane

> Dear all,
>
> I’ve got a dataset where 80 % of the micrographs were not entirely gain cor
> rected and I had to subtract a reference image using -Dark in MotionCor2
(ad
> ditional argument in Relion).
> The remaining 20 % are fine.
>
> My question is: does Relion recognize this additional argument when doing
> Bayesian Polishing or does it look at the raw movies which are not
> corrected?
> I guess in the latter case it would create shiny particles from the non
> gain corrected movies.
>
> What would people recommend to do in such a case?
> Would it be better for Relion to gain correct the single frames first and
> then start MotionCor2 inside Relion?
>
> Thanks in advance,
> Thomas
>
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