This script will draw a CGO cylinder representing a rotation axis for a given transformation.
The idea is to align two molecules/domains/chains/selections (using cmd.super) and extract the trasformation (TTT) matrix (T). The direction of the rotation axis, and a point are obtained from T and are used to create a cgo object representing the axis. The script generates two measures: one in the graphical screen (the rotation axis value, and the norm of the translation vector along the rotation axis) and some basic information in the command-line (the transformation matrix, the rotation angle, distance between centroids, and some pml lines that you can use to reproduce the axis...)
As always with these type of things, you have to use it at your own risk. I did not try all possible combinations, but if you find a bug, do not hesitate to contact me (firstname.lastname@example.org) or try to modify the code ..→