Octahedral symmetry with apoferritin


we are testing our new K3 installation. Collected apoferritin. Processing in C1 yielded a 3A map that looks reasonable. However when I impose octahedral sym (“O”) it produces a terrible reconstruction. Am I missing something? thanks!!!

Hi @orangeboomerang, this can sometimes happen if the “symmetry alignment” that happens at the start of the refinement with “O” symmetry fails to correctly align the starting structure.

If you have any other apoF structure that is already symmetry aligned, you can try using that as an initial model. Or, you can download the C1 map and in Chimera, rotate and re-output it to be aligned to the symmetry axes, then use that as the initial model.

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hi, thanks @apunjani

I had guessed that might be the issue and I ended up re-aligning the axes as you had suggested. Was planning on reporting back when the job finished. So far it’s better: currently at 3.9A on iteration 5, and can see clear secondary structure in the downloaded map. Thanks.

Great! Thanks for letting us know.