Hi,
> "too few valid local trajectories to fit local motion model"
> Does it indicate the bad movie quality? Or is it caused by wrong
settings?
This means that many patches were rejected because trajectories
did not converge. So only the global trajectory was applied.
You might be able to fix this by reducing the number of patches,
grouping frames and/or increasing the B factor. That being said,
I would not worry about this. I do not spend time optimising
parameters for initial motion correction. As long as you run Bayesian
Polishing afterwards, initial trajectories are not very important (see
our preprint).
Best regards,
Takanori Nakane
On 2018/10/06 0:33, Chen Sun wrote:
> Dear Relion users and developers,
>
>
>
> I have two questions regarding motion correction with relion/3.0-beta-sm52.
>
>
>
> 1. I have been running motion correction with relion's own implementation but it skipped some of the movies and reported the following error message:
>
>
> "too few valid local trajectories to fit local motion model"
>
>
>
> Does it indicate the bad movie quality? Or is it caused by wrong settings?
>
>
> Here is the printed command:
>
>
> `which relion_run_motioncorr` --i Import/job001/movies.star --o MotionCorr/job018/ --first_frame_sum 1 --last_frame_sum 0 --use_own --j 1 --bin_factor 1 --bfactor 150 --angpix 0.9 --voltage 300 --dose_per_frame 1.2 --preexposure 0 --patch_x 5 --patch_y 5 --gainref micrographs/Movies/Gain.mrc --gain_rot 0 --gain_flip 0 --dose_weighting
>
>
>
>
> 2. When I run motioncor2 with relion's GUI, some of the movies were summed and corrected into totally black images. The other movies are fine.
>
>
> Here are my settings for motioncor2:
>
>
> `which relion_run_motioncorr` --i Import/job001/movies.star --o MotionCorr/job018/ --first_frame_sum 1 --last_frame_sum 0 --use_motioncor2 --motioncor2_exe /apps/motioncor2/1.1.0/motioncor2 --gpu "2" --bin_factor 1 --bfactor 150 --angpix 0.9 --voltage 300 --dose_per_frame 1.2 --preexposure 0 --patch_x 5 --patch_y 5 --gainref micrographs/Movies/Gain.mrc --gain_rot 0 --gain_flip 0 --dose_weighting
>
>
> Has anyone also faced these problems before? And how did you work around them? Any help would be appreciated.
>
>
> Best,
> Chen
>
>
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