I have been running several Apo tests on a new system. When slicing through homogeneous refinement masks I see what appears to be streaks or missing planes (1st image). Manually generated masks also show the same behavior, even more clear at the minimum threshold. Any suggestions on what might be causing these?
Many thanks!
Are you sure this isn’t just an artefact of visualization in Chimera? Do you see the same artefacts using other visualization approaches, for example EMAN or relion_display?
Thank you for the suggestion, Oliver. It is entirely possible it is a Chimera artifact, as I do not see the streaks in EMAN/Relion and they are much reduced in ChimeraX. I didn’t recall seeing this artifact with my previous data and it got me worried. But the streaks also show up in masks from a few test EMDB structures as well.
Thanks again!