3D Class Indexes) parameter. In this case, the probability for each particle will be summed between the selected classes, and then compared to the threshold. So if a particle gets 0.33 in class 0 (good), 0.33 in class 1 (good) and 0.33 in class 2 (bad), and the threshold is 0.6, this particle will have 0.33+0.33 = 0.66 score and therefore be retained.
3D Class Indexes: (Optional) Comma-separated list of class indexes. Specify this when using the
particles_all_classesoutput from Ab-initio reconstruction. A particle is selected if the sum of the posterior probabilities is greater than the given
3D Class Threshold. For example, to sum all classes from a 3 class ab-initio reconstruction, enter
3D Class Threshold: (Optional) A number between 0 and 1. If specified, excludes particles with smaller total 3D ab-initio class posterior probabilities. Typical values range from 0.5 to 0.9. If the
3D Class Indexesparameter is specified, this value is compared to the sum of probabilities from inputs slots
particles.alignments_class_1, etc.; otherwise compared with
2D Class Threshold: (Optional) A number between 0 and 1. If specified, excludes particles with smaller 2D class posterior probabilities. Compared with probabilities from the
particlesoutput from a previous 2D Classification or Ab-Initio Reconstruction job into the
particlesinput slot and expand it to see which input are still required based on the specified parameters.
particles_all_classesoutput from an Ab-initio reconstruction job with at least 3 classes.