please give me an advice what limit to set for the “Full-frame motion distance” in the job “Curate exposures”. Does it depend on particle size and other factors?
At what extent may it affect the final map quality (resolution and b-factor; overall resolution is ~3.4 A) if to increase the upper limit from 20px to 80px (particle size is 150px)?
Is the next statement correct – “If CTF fit <5 A, no need to limit the full frame motion distance”?
Does this parameter become more critical when the molecule has flexible domains?
Thank you!
Full frame motion is a metric for how much drift there is in the micrograph. CryoSPARC’s Patch Motion Correction is generally pretty good at correcting even extreme drift (much better than MotionCor2 or RELIONCor in my experience) so I generally check the extreme micrographs to see whether they’re usable or not, but I equally don’t apply and hard-and-fast cutoff, it just depends on the data. If a micrograph is really that bad, particles won’t get picked or will get removed during 2D classification and heterogeneous refinement anyway…
Dear rbs_sci,
thank you for advice!
By the way, shall we limit the local particle motion like below?
And if yes, what is a optimal value?
What do you think about exclusion of the first frame during Patch Motion Correction because it has the biggest motion and maybe the least predictable ?
Thanks!
A motion plot like that I would take as an indication that the ice vapourised during image acquisition, or had some other pathology which meant it was unfavourable for use.
Agree with @rbs_sci, if you run RBMC you will see there is some high resolution information in the first frame (frame = 0) and many are hopeful the first frame will be useful for zero dose extrapolation. Also if you have .eer movies you can also re-process with different number of frame so e-/frame changes. Dose weighting should take care of the rest.
@andro for you initial question about patch motion correction, in some cases the inputting the hyper parameter from RBMC as “Dose Weights” to another Patch Motion job can give slight improvements.
