Align 3D maps - exhaustive search?

Utilities
1

Hi,

Align 3D maps is very useful, when it finds the correct alignment, but it often fails in cases of pseudosymmetry, even when the correct solution is clearly identifiable visually.

Without knowing the algorithm I am not sure why this is, but I am guessing it is optimized for speed, perhaps searching with limited angular increments.

Is there (or could there be) a way to force it do do an exhaustive search within the specified bounds, accepting that it will take longer to do so?

One option would also to be add a minimum bound for the search angle, as well as a maximum - that would allow constraining something which is approximately a C2 rotation to 160-200 degrees, for example.

Cheers
Oli

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2

Hi @olibclarke,

Do you only Align3D failing in this manner when pseudo-symmetry is present?

Thanks,
Kye

3

That’s certainly where I have noticed it most - not sure if i have a non-pseudosymm example, but if you want examples where Align3D fails and something like Chimera fitmap #1 #0 search 100 radius 5 succeeds, I am happy to send them through as I come across them!

Cheers
Oli

EDIT:

Can confirm - we also see failures (or at least suboptimal solutions) with non-pseudosymmetric complexes, where fitmap in Chimera does a lot better. This can be important when one wants to use the updated particle alignments for local refinement.

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4

Hi @olibclarke,

Thanks for providing your example. We have noted this failure mode.

Best,
Kye

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