Table 1. Intensity thresholds for pre-processing Challenge cryo-EM density maps.

For each cryo-EM map, the suggested contour level for visualization is given (column 2), as well as our computed threshold for small voxels (column 4). The percent of voxels larger than each threshold is provided (column 3: suggested contour level, column 5: computed threshold), as well as the absolute difference between these two thresholds (column 6). The percent of voxels larger than the threshold is equivalent to the percent of voxels from the cryo-EM map that are used in constructing the affinity matrix, A.

map	EMDB contour	% voxels > τ	computed τ	% voxels > τ	difference in %
AQPO	NA	NA	2.49	5	NA
Epsilon-15 7.3 Å	1.6	6	1.32	9	3
GroEL 4 Å	0.60	11	0.77	7	4
GroEL+GroES 7.7Å	0.61	37	0.75	27	9
GroEL+GroES 23.5Å	.029	5	.087	3	2
Mm-cpn 4.3 Å	0.38	2	0.45	1	1
Mm-cpn 8.0 Å	0.78	7	0.95	11	4
Ribosome 6.4 Å	3.5	2	5.5	1	1
Ribosome 7.4 Å	0.17	13	0.49	5	8
Ribosome 8.9 Å	70.4	5	88.5	4	1
Rotavirus 3.8 Å	1.04	4	0.98	5	1