I would like to surface colour a filament within an EM map using cylindrical geometry (scolor geometry cylindrical). 

However, the electron density of the filament does not lie perfectly on the x, y or z axis. Is there a way of using two marker points placed at each end (on the longitudinal axis) of the filament to define the orientation of the cylindrical geometry and scolor the filament accordingly?

My attempts to do this whilst executing the following command didn’t seem to work:

scolor #0 geometry cylindrical axis sel cmap 5,gold:10,red:15,blue

Many thanks for any suggestions/help,

R.