Oli Clarke
@olibclarke.bsky.social
CryoEM, membrane proteins and whatnot
Tried this starting directly from blob-picked particles - no 2D classification. Still works.
The SGD meanders around for 5000 iterations going nowhere, and then suddenly starts to converge at iteration 5400 (this animation ends at iter 5900):
The SGD meanders around for 5000 iterations going nowhere, and then suddenly starts to converge at iteration 5400 (this animation ends at iter 5900):
October 2, 2025 at 6:47 PM
Tried this starting directly from blob-picked particles - no 2D classification. Still works.
The SGD meanders around for 5000 iterations going nowhere, and then suddenly starts to converge at iteration 5400 (this animation ends at iter 5900):
The SGD meanders around for 5000 iterations going nowhere, and then suddenly starts to converge at iteration 5400 (this animation ends at iter 5900):
Initial attempt at replicating in relion (parameters in next post). This is for Aca2-RNA, using a 100k subset of the 2D-classified particles (no prior 3D cleanup).
A 1-class ab initio in relion, then local refinement in relion (1.8deg searches+blush) gives a nominally 3.3Å map; 3.5 Å w/out blush.
A 1-class ab initio in relion, then local refinement in relion (1.8deg searches+blush) gives a nominally 3.3Å map; 3.5 Å w/out blush.
September 26, 2025 at 2:28 AM
Initial attempt at replicating in relion (parameters in next post). This is for Aca2-RNA, using a 100k subset of the 2D-classified particles (no prior 3D cleanup).
A 1-class ab initio in relion, then local refinement in relion (1.8deg searches+blush) gives a nominally 3.3Å map; 3.5 Å w/out blush.
A 1-class ab initio in relion, then local refinement in relion (1.8deg searches+blush) gives a nominally 3.3Å map; 3.5 Å w/out blush.