Particle Box Size and Speed
Various algorithms in EMAN2 will depend non-linearly on the box size of the particle. Sometimes (such as the case with FFTs), this behavior will appear bizzare. For example refinements with a box size of 45 pixels will run roughly twice as fast as those with a box size of 47, and 44 is about 20% faster than 45.
The following plot shows how long it takes to compute one similarity matrix element for a noisy particle aligned to a noise-free reference with the rotate-translate-flip aligner, refine alignment enabled with the dot comparator, and a phase residual for a similarity metric. ie - typical options for a real refinement:
