Q: The class-averages produced by startnrclasses don't seem to show the number of particles in each class when displayed in the matrix view. How can we fix this ?
A: Hi. Two points here. First, you should really consider using refine2d.py rather than startnrclasses. startnrclasses is really only suitable for bootstrapping the refine2d.py process, or getting a very rough view of characteristic views of your particles.
With respect to the actual question, you are right, this certainly should not happen. Please try installing a current snapshot version of EMAN (rather than 1.8) and see if that clears up the problem. If not please email details of the system and installation to sludtke@bcm.edu, and we'll try to help you debug the problem.