Motion corr preaverage frames

Dear all,
is there a way to prealign a certain amount of frames beforehand? I might have saved too many fractions for motion corr to work properly (too less dose in each fraction).

Are you referring to an EER dataset and the EER Number of Fractions parameter of an Import Movies job?

IME it works even with very low dose (e.g. 0.15 e-/A2/fm for 20 frames, 3e- total, it’s fine).

If it’s really not working you can try reducing the number of patches/knots for Patch Motion, or instead use MotionCor3 and use -Group to group frames before alignment.

I do not have EER data.
My micrographs are 1.1A/px, 47e/A2 total dose, saved in 40 frames.
Apparently there was another issue why motion corr didnt work when I posted the thread. It seems to work now.
This is one of the outputs:


OK, looks good! Those parameters are not low dose or finely fractionated IMO, in particular > 1e-/Å2/fm is actually a high per-frame dose.

Shawn (MotionCor2+ author) recommends throwing the first frame if the per-frame dose is > 1 e-/Å2, and grouping 2 frames if it is ~0.3 e-/Å2 or less. BTW 0.3e-/Å2/fm or less is required in order to get Thon rings from water. In SPA I usually shoot for ~80-100 frames ~0.3-0.6 e-/Å2/fm. For ET it’s more like 0.15e-/Å2/fm for 20 frames, because CTF estimation can be difficult at higher tilts.

With respect to dose rate for the K3 it should be ~15 e-/px/s for non-CDS and ~7e-/px/s for CDS. On FalconX it should be substantially lower, on DE Apollo it could be ~30 eps. (Based on published data, I have not used them).


Falcon 4i is good to about 12 e-/pix/s, vanilla 4 is OK up to about 10 e-/pix/s. I usually aim for 6-8 depending on mag and other conditions.

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It’s a falcon 3.
Do you also drop the first frame like Daniel suggested?

Not initially. If it jumps excessively, then I will.

@Dario the numbers I gave are just rules of thumb Shawn determined by testing various parameters with small ~100 image apoF datasets. @rbs_sci is right, in general you should see how your own data behaves.

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