Ability to override the number of asymmetric units to search during helical refinement

[msleutel]

We’ve found that for cases with an extremely small rise (e.g. smaller than 0.5Å) that convergence to find the global minimum of the error landscape can be challenging. For these cases, there can be degeneracy in the rise. I’m pasting the error landscape result from a symmetry search job below where the function is searching over 32 asymmetric units (rises).

Changing the rise search range to 200 rises ‘sharpens‘ the error plot:

It would be interesting to see if this would also translate into improved helical refinement results when one would be able to tweak this parameter during Helix Refine.

[egelman]

It appears that in Helix Refine the number of subunits used for the symmetry search is not properly determined and is not an adjustable parameter. Here is our own example where there is a very small helical rise:

If the search was done over many more subunits, then one would see a clear minimum in this plot, rather than all values of the rise (from 0.62 to 0.76 Å) giving the same mean squared error.