Maybe requested before, maybe a bit of a long shot…
I think it could be super useful to have a little GUI/interactive job that makes the input job’s Viewing Direction Distribution interactive. You could draw a little polygon on it, then it would output particles from within that polygon (and I guess an excluded category too).
I think this could be helpful in a few ways. You could confirm which views populate which “hot-spots” for over representation in your plots, thus assisting in attempts to re-balance. As well, you could look specifically at less well represented regions, do downstream 2Ds, pipe this into Topaz and try and boost these views, etc.
Regardless, thanks devs for the great software.
Cheers,
NAC
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You can also use star2bild.py to make Relion-style distribution plots for ChimeraX and then simply look at what views/parts of the structure are sticking in 3D.
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+1 to this - it seems like rebalancing views based on 3d classification of particles would be much more efficient than using 2D views, especially when trying to find rare 2D views
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Looks like Sami Chaaban made this for STAR files. Would still love to see this sort of thing incorporated into CryoSPARC.
https://twitter.com/sami_chaaban/status/1695508724637405354?s=20
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I came across this post when looking to see if anyone had made this exact feature. I couldn’t find what I wanted either so I ended up making it myself. It’s a simple tool to select particles from the viewing direction distribution plots and you can try it out here github.com/robertstass/ViewSelect
Let me know what you think!
Rob
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Hey @robertstass – thanks for sharing, this looks like a great tool!
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No problem! I hope that by sharing this I might be able to find some example projects where this script really makes a difference. In my case, in the example below, selecting the small group of particles in the blue and orange circles revealed some 2D classes I hadn’t seen before.
Unfortunately I have struggled to pick many more of these views but maybe I haven’t found the right settings for Topaz. I think it is still helpful just to be able to troubleshoot issues like this. Hopefully some other people might be more lucky! Let me know if you are.
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Really excited to try this on one of my projects when I get the chance. As you said, it is super informative, even if piping into topaz to pump those rare views doesn’t work out in every instance.
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