Question:
We have a bit of a problem with our refinement 
Some of the classsums look a bit off centered and it gets worse as I do more rounds of refinement. Our structure looks more funny as I refine further. We wonder if it's worth removing the bad classsums in the initial rounds of refinements to get the rough shape of the molecule (if yes, how?).
I started with a Gaussian sphere as initial model and used these commands:
refine 2 mask=25 pad=128 hard=25 ang=10 classkeep=1 classiter=8 median phasecls refine 10 mask=25 pad=128 hard=25 ang=10 classkeep=1 classiter=5 median phasecls refine 14 mask=25 pad=128 hard=25 ang=10 classkeep=1 classiter=3 median phasecls refine 16 mask=25 pad=128 hard=25 ang=8 classkeep=1 classiter=8 median phasecls refine 24 mask=25 pad=128 hard=25 ang=8 classkeep=1 classiter=5 median phasecls refine 32 mask=25 pad=128 hard=25 ang=8 classkeep=1 classiter=3 shrink=8 median phasecls refine 42 mask=25 pad=128 hard=25 ang=8 classkeep=1 classiter=3 shrink=8 median phasecls refine 44 mask=25 pad=128 hard=25 ang=6 classkeep=1 classiter=8 shrink=8 median phasecls
Answer: (dwoolford, Nov 20th 2007) - This has happened to me before - try generating a better starting model - use refine2d.py to generate some unbiased class sums, pick a bunch of good classes from the result, and then use startcsym (or is it startAny) to generate a starting model. You should be able to tell if you're getting the off-center problem very early in the refinement - i.e. just do several (or even 1) refinments, and check that the class sums look normal.
Answer: (dwoolford, Nov 20th 2007) - If you want to remove bad class sums from the classes.?.img, you can do it in v2 - just remove the class sum and it's associated projection using the delete option, then save (to a different filename) - then call make3d with the pruned image - all that make3d requires is the Euler angles, which are stored in the .hed file.