Now 6 atoms are being created at X, -X, Y, -Y, Z, and -Z, 100 Angstrom from the origin. This is
required so that the CoM is at the origin, to allow the CoM-pivot vector to be unchanged at
[1, 0, 0] so that the axis alpha angle of pi/2 creates an axis parallel to Z. The origin to atom
distance check has also been loosened due to the PDB truncation artifact.
