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--- eman2:e2tomo_atpsyn [2026/06/04 20:46] – muyuanchen
+++ eman2:e2tomo_atpsyn [2026/06/04 20:47] (current) – muyuanchen
@@ Line 202: / Line 202: @@
 This should improve the structure features at the F1 head domain, but the FSC resolution does not necessarily improve here. Because the even/odd half set only are only aligned to the "neutral" struture of their half-set and never see each other, there is a possiblity that they converge to slightly different states, and the FSC resolution decrease even though the feature in each half-set improves. This is less of a problem in datasets with more particles since the "neutral" state would be better defined, but here there are some uncertainties with only 5 tomograms...
+{{http://blake.bcm.edu/dl/EMAN2/atpsyn_cmp_focus_refine.png| Focus refinement comparison | width="600"}}
 To visualize the dynamics, run the following.
@@ Line 212: / Line 214: @@
 {{http://blake.bcm.edu/dl/EMAN2/atpsyn_f1_motion.gif | F1 head motion | width="600"}}
-Finally, we can refine the local motion of the F1 domain a bit more, without the neural network part. Depending on the particle count and the type of motion, this sometimes improve the resolution of the target domain.
-<code>
-e2gmm_spt_refine_iter.py gmm_01/threed_03.hdf --initpts spt_02/threed_07_seg.pdb --startres 10 --maskpp mask_01.hdf --mask mask_f1.hdf
-</code>
-{{http://blake.bcm.edu/dl/EMAN2/atpsyn_cmp_focus_refine.png| Focus refinement comparison | width="600"}}