Q: What does the "shrink=n" do in Refine commmand? It doesn't look like changing the size of subfiles like proc2d shrink=n does?
A: (DavidWoolford) - I had a look at the source code and it looks like refine uses the shrink parameter to run classesbymra - there it is used to mean shrink the particle images prior to classification. Hence it speeds things up by disregarding high frequency information. However, when the classes are finally generated the original images are used, and this involves involves an iterative alignment, so in a sense the high frequency information can still be resolved. So conceptually this flag speeds things up at at no penalty.
A: (Steve Ludtke) - Yes, shrink= in refine will cause the classification process to occur on shrunken images and projections, increasing the speed of classification considerably. In some cases it may even improve classification accuracy, however, it likely isn't a good idea to use it during the final rounds of a high resolution refinement. The 'no penalty' is only true if you believe the high resolution information is completely negligible when aligning or classifying particles.