Symmetry equivalent positions in 3DVA


I have a particle with D3 symmetry which has a small protein bound to it somewhat randomly and sparsely. I refine in D3, expand the D3 sym, then run 3DVA. The results I get are basically just morphing between the bound protein stuck to symmetry equivalent parts of my D3 protein. It’s bound in the exact same way, just on the other side of my D3 protein. I am interpreting this as having no motion/flexing because it is just morphing between two different symmetry equivalent positions. Is that fair?

Also, the sparsely bound protein looks roughly D3 symmetrized in these output maps, despite having done sym expansion prior to 3DVA. I’m guessing this is due to D3 symmetrization of noise during the initial refinement?


I think you need the mask to focus a single asymmetric unit and binding interface, otherwise all the duplicate expanded AUs with their binding/unbinding mode will need to be represented by a large number of different 3DVA components that add/subtract the binding partner at the different sites.

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