This is reporting the same problem discussed in the post entitled “The ab initio reconstructions generated wrong initial models” (The ab initio reconstructions generated wrong initial models)
I didn’t get any response to my recent question in this thread so I wondered if it was still “live” - hence the new post. Anyway, I have datasets from two different icosahedral viruses that both generate nice 2D classes but give a squashed ab initio model. I have tried all the tricks discussed in the above post i.e. using an increased resolution range e.g. 15 to 8 Ang and setting initial and final minibatch sizes to 1000. I even resorted to setting the symmetry to I1 (which I know is not recommended), which unsurprisingly gave a more virus-shaped volume, but it looked highly dubious!
Here are some 2D classes from ~2.5k particles:
and here is the output from an ab initio reconstruction run with default parameters:
Any advice much appreciated.