Daniel R. Roe

Currently goes by lipid chain only.

If mask1 is residues 1 to 10 and mask2 is residues 11 to 15, want a 10x5 matrix, not 15x15 (lots of wasted space).

Something like: ``` rotate usedata Rmatrix aroundz ``` for only rotations around Z.

Currently during `diagmatrix` eigenvalues calculated from a mass-weighted covariance matrix are always converted to frequencies. There should be an option not to do this, and if it happens things like...

If time is present in trajectory files, use it when setting up data sets.

Give the user an indication that something is still happening.

1. By residue functionality. 2. Only specify part that needs to be remapped.

- Enable 3d dataset OP scalar. - Identify voxels that correspond to ligand (with/without Gaussian, similar to volumetric mapping) for certain calculations. - Scripts from T. Balius, S. Ramsey &...

For atom types not currently handled by `surf`.

Otherwise in parallel each thread writes to the same file.