Hi,
> Thanks a lot Takanori for your help! Unfortunately the artifacts are within the mask and like you said I do have a very tight box. I understand you cannot do "--pad 1.5" in the current GUI. But can you do this using command line? I just submitted a job using command line with --pad 1.5 and it seems running normally at least for now.
I checked the code and realized that "--pad" indeed accepts
non-integers. This has not been tested as much as pad 1 or 2,
so you should be careful.
I don't recommend such a tight box; recall signal delocalization
due to CTF.
> Another unrelated question is about the Polishing jobs in Relion3. So in Relion2 Polishing jobs generate a reconstruction that be directed used in PostProcessing while in Relion3 it doesn't generate this anymore. Is there any way in Relion3 to turn on this in Polishing jobs? I understand it is recommended to re-run a Refine3D job after Polishing to potentially further improve the map, but in this dataset I found the improvement is minimum but took 13 days to re-run a Refine3D job due to the large box size..
You can run 'relion_reconstruct' using previous orientations.
Best regards,
Takanori Nakane
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