Also, while you're in the code, the Shake code needs to be aware of the minimalist preset that has the "Show bondable atoms" view setting turned off. It only shows like this when executing a shake from a recipe (might also be from manual shake, haven't tried it.)

hi @NinjaGreg can you send some log files fom situations where you're noticing these visualization bugs? also please let me know what OS and version of the client you're using. thanks!
also @NinjaGreg just in case the log file doesn't catch the reason for the bug, please let me know some steps i can take to try to recreate it from my system.
Hi, sorry to be so slow, got busy irl. I run MacOS, M1 chip, client version build id V24-20230404-1e75494fe4-macos_x64. I was running a recipe AFK3 on a puzzle, with view set to minimalist. I think any recipe that does a shake in the middle would exhibit this behavior. Not clear how useful the logs would be since I am usually running three parallel clients, but it should be easy to recreate. Let me know if not and I'll close all but one client, clear the logs and run it.
Note: while this isn't really an important bug, it's just odd.