3dflex custom meshes

The 3dflex paper and documentation only say that the domain boundaries in a custom 3dflex mesh provide additional “inductive bias.”

Can you provide additional information on how the custom mesh is used? There is a restraint that flow on the mesh elements is similar within each domain?

Hi @DanielAsarnow!

In essence, yes, you’re right — similar meshes will flow in similar ways. Custom meshes are most useful when two domains are expected to either move away from or slide past each other.

For example, if we consider this dataset (EMPIAR 10261) in which we have two Fabs bound to the channel ECD:

it would be reasonable to expect that those Fabs independently flex forward/backward/left/right. However, the default mesh puts them both in the same grid of tetrahedral cells

Because we model flexible movement by deforming these cells, moving the Fabs away from each other would require expanding the central plane of tetras to a degree which, in other regions, would represent non-physical deformation of protein density and is thus not allowed.

Defining a custom mesh allows for each Fab to be placed in its own mesh:

which in turn allows the deformation model to capture the bending and flexing of the Fabs, since there is no set of tetra cells joining the two:

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