Q: Does e2make3d.py work on tomographic stacks?
A: Yes, it is now possible to directly reconstruct aligned stacks (.ali) files from imod using the corresponding .tlt file. In fact, the Fourier reconstruction algorithm used in EMAN2 has produced substantially better results than either back-projection or SIRT in a number of cases.
Run e2make3d.py --help for more options. Pay particular attention to the various parameters impacting reconstruction size, because the default would be to make a cube using the maximum dimension. ie - if you reconstructed a 2k x 2k stack using default options, it would try to do a 2k x 2k x 2k volume !!! (a very bad thing).
You may also want to consider using a mode other than the default 2-pixel interpolation in the Fourier reconstruction. For sparsely sampled tomography data, using a larger interpolation kernel can produce structures which are better localized on the Z axis. However, this will also cause some radial intensity dampening in the final reconstruction (which can be corrected).