Is it possible to re-center 2D particles after 2D classification?
I’m working with a protein complex that contains a large domain and a small satellite domain.
In the 2D-class averages the large domain sits neatly in the centre, while the small domain is always pushed to the corner of the box, rendering it perpetually blurry.
I would like to shift the particles so that the small domain is centred before the next round of 2D classification, hoping to improve its visibility and alignment.
Any suggestions are welcome!
If you can make a mask around that area then you can use the Volume Alignment Tools job to center on that mask and apply that operation to an attached particle stack as well.
You can try changing the “Re-center mask threshold” setting and also try “Re-center mask binary”. Some combination of those settings has helped me in the past for a very similar issue.
and then run 2D with “recentering” off, if the goal is to get 2D classification of the area. Can also reextract with this recentering applied in a much smaller box size, appropriate for the area of interest not the whole particle
Hi seandworkman, thanks for the suggestion, it worked perfectly! I can now see previously hidden regions; they’re still blurry, but at last they’re visible.
