Hi,
In RELION's implementation, each frame is aligned against sum
of all other frames and the shifts are normalised such that
the first frame always has zero shifts.
Then all frames are shifted accordingly, to make a reference
for the next iteration.
Thus, the first frame never moves.
When RELION calls UCSF MotionCor2, it adds "-FmRef 0" to override
its default behavior and make it the same as RELION's convention.
(Otherwise, Bayesian Polishing might behave badly when shifts are
very large)
Best regards,
Takanori Nakane
On 2019/10/22 22:30, Alpay Burak Seven wrote:
> Dear developers and users of Motion Correction algorithm from UCSF
> MotionCor2 and the relion implementation of it.
>
> What is the reference frame for the final averaged micrograph?
> According to the manual of MotionCor2 (corresponding entry attached
> below), i think the reference frame is the central frame. However, I
> could not find any information on Relion implementation of the
> MotionCor2 except the below line in the motioncorr_runner code
> // Always take the first frame to be aligned as the origin of the motion
> command += " -FmRef 0";
>
>
> This information kind of conflicts with the MotionCor2 Manual.
>
> Can anyone clarify which version uses which frame as a reference for
> averaging the frames and how to control exactly which frame we would
> like to use?
>
> Thank you. Best regards
> Alpay
>
> MotionCor2 Manual
> "The output and log files list the shifts relative to the first frame.
> However the
> correction is relative to the central frame by default. “-FmRef” is a
> switch that allows
> to choose the reference either the central frame by giving it a non-zero
> value or the
> first frame by setting it zero."
>
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