Q: Does e2make3d.py work on tomographic stacks?
A: Yes, but the stacks must already have been aligned and have their Euler angles stored in the image headers. If you haven't done this you can use IMOD to perform alignment and then convert the output into a format suitable for eman2 using e2ali2img.py. Then you can reconstruct the data using the zsample parameter in the fourier reconstructor. There will be more information available on this aspect of eman2 as the source code matures.