Can we use reconstruct3d to reconstruct cisTEM par files? I've tried using the imported stack and an output .par, or exporting to Frealign, but I just get a NaN volume. I've also tried normalizing particles or not, inverting contrast or not, etc., and the output indicates normal termination. From reading the code so far I haven't figured this out.
I mainly want to reconstruct maps using your reconstruct3d, but not normalizing so I have the direct particle intensity scale.