alignments3D
key.Ab-initio reconstruction
;Homogeneous refinement
to find improved alignments for a final set of particles;Homogeneous refinement
;3D Classification (BETA)
with particles from step 2 or 3 and a mask from step 4;Number of classes
Target resolution
Initialization mode
Batch size per class
Auto-tune initial class similarity
& Target class ESS fraction
Auto-tune initial class similarity
is set to True, the job will automatically tune the class similarity score so that initially, the average particle has a significant likelihood of belonging to multiple classes (characterized by the Effective Sample Size, or ESS, of the probability distribution over classes). The Target class ESS fraction
parameter defines the target ESS as a fraction of the total number of classes. This fraction can typically be set between 0.1 and 0.9.alignments3D
alignments3D
key set (e.g., from an ab-initio job, from homogeneous refinement, from an imported EMPIAR particle dataset, etc.), however the quality of the alignments may affect the resulting classes.PCA/simple: particles per reconstruction
).PCA: number of reconstructions
;PCA: number of components
;vseries play
command) are shown below:alignments3D
from the Homogeneous refinement
job)Number of classes
: 100Target resolution
: 6Ã…Initialization mode
: PCAalignments3D
);Homogeneous Reconstruction Only
to obtain a consensus reconstruction;Homogeneous Reconstruction Only
job, we obtain the following 3D map:particles.star
in EMPIAR-10256
Number of classes
: 24Target resolution
: 6Ã…Initialization mode
: PCA