Implement solvation model from

[geoffwoollard]

This model is a fixed PS envelope, with this functional form and constant values.

The phases are sampled uniformly.

The constants were fit to agree with explicit water from MD simulations. These could be free parameters that the user can input, with defaults from Parkhurst et al.

The authors incorporate this in multislice, and dynamically mask in real space for each slice.

I think a simple/fast implementation where the water is just added onto the protein density is desirable.

References

• Parkhurst, J. M., Cavalleri, A., Dumoux, M., Basham, M., Clare, D., Siebert, C. A., … Essex, J. W. (2024). Computational models of amorphous ice for accurate simulation of cryo-EM images of biological samples. Ultramicroscopy, 256(October 2023), 113882. http://doi.org/10.1016/j.ultramic.2023.113882

[mjo22]

This is a repeat of #236, could you pick one of these issues to keep open?