preprocess_segment_averages.csh

[zehrea]

Hello,

I am using the original mirp for relion 3.0. One of the steps that uses "preprocess_segment_averages.csh" to generate segment averages for classification of the protofilament number often gives corrupted stacks (not all but still many). I then, to get around this error, need to manually modify particles-scaled-helical-track-length-SAs.star to get rid of images that exceed stack size. Why are some stacks corrupted and how one can modify your preprocess_segment_averages.csh to mitigate this issue?
I know there is mirpv2, but we have not manage to install it yet.

ERROR:
readMRC: Image number 83 exceeds stack size 81 of image 000083@Extract/job024/Micrographs/0735_SAs_norm.mrcs

When I use preprocess_segment_averages.csh in the later step "REFINED SEGMENT AVERAGES" I do not get corrupted stack error

Thanks,
Elena