I am new to cisTEM and have got confused about the differences between auto refine and manual refine. Does auto refinement always start from a global search followed by local refinement for the N best matching projections for each cycle? And the percentage of particles used for each cycle and the total number of cycles are automatically determined by the program? I have seen manual refinement allows me to choose local search and no. of cycles to run, but what's the percentage of particles should I use? If I put 100%, will 100% of the particles be used for each refinement cycle? In the documentation it says "A refinement should always be finished with a few cycles using 100% of the data", so if I use less than 100%, should I run a few more cycles using 100%?
Also I have seen from previous post that for 3D classification, it's better to run a global refinement with a single class, followed by ~50 rounds of local refinement for desired number of classes simply because it is much faster. But in my practice I didn't really see it's faster... Is that because I used 100% of the particles for local refinement?