NGL cell visualization
NGL constructs the unit cell by using 6 floating point numbers: a, b, c, alpha, beta and gamma. Most of the structure file types supported by NGL (pdb, gro, etc.) also contain only these 6 numbers, some formats don't support storing the cell information at all. With 6 numbers one can reconstruct the cell shape, but not the orientation. To know the orientation we need the complete lattice vectors which is a 3x3 matrix.
This is becoming an issue for entries where the cell orientation does not match the typical direction, but is e.g. pointing in a completely random direction: lattice_vectors = [[-1, 1, 1], [1, -1, 1], [1, 1, -1]].
@jrudz: Is there any structure file format that supports storing the full 3x3 lattice vectors? The file format should also be supported by NGL. I tried something with the .gro format, but I could not get e.g. MDAnalysis to write the full 9 components, maybe there is a way. It somehow seems odd that the structure files don't store the lattice orientation: maybe I'm missing something obvious...?
If there is no such format, we need to get the lattice vectors from the archive, which complicates things somewhat, but is not impossible. Another solution might be to use some other generic comment/remark field of e.g. the PDB format to store this information.