Squashed ab initio model for icosahedral virus



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.



Hi @lawsond,

This type of failure mode is (as you’ve seen) unfortunately common for the ab-initio reconstruction algorithm. The algorithm finds that the “squashed” model is locally optimal and explains images better than any other nearby model, and therefore does not explore far enough to find the correct symmetric model.
Generally, tweaking the parameters that you already mentioned (initial/final resolution, minibatch size, etc) can help the algorithm explore farther before locking in to an incorrect solution. However, this is also not guaranteed to work for highly symmetric particles, since the problem really is just non-convex and has many local optima.

What makes you feel that the result with symmetry directly enforced was dubious? In our hands, we have generally got good results with symmetry enforced for virus particles, and octahedral symmetry, but not for high-degree C or D symmetry.


Hi Ali,

Thanks for your comments. As it happens, yesterday I had a tip from another cryoSPARC user who had experience with icosahedral virus processing. He had seen the same thing with generating the ab initio model in C1, but then found that refinement in I1 was able to sort it out (i.e. “re-inflate” the volume). So, I tried the same thing and actually ended up with something sensible. The structure is already known and docks nicely into the map.

Regarding the “dubious” ab initio models produced by enforcing I1, they looked too featureless with no hint of the prominent projections on the 5-fold axes that were clearly visible in the 2D classes (in fact there were holes on the 5-folds!). For a fair comparison I also did a refinement job with this ab initio model, but it didn’t recover the projections.

Thanks again