Hi Luca, "Define Axes" or command "define axis" gives a cylinder along the major inertia axis. To have all three (major, intermediate, minor) reported in the Reply Log, instead use the command "measure inertia." That command always does atom mass-weighting, and by default shows an ellipsoid. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/define.html#axis> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#inertia> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 23, 2012, at 7:51 AM, Luca Pellegrini wrote:

Hello, Can you please explain how the inertia axis is calculated in:

Tools -> Structural analysis -> Structure Measurements -> Define Axes

when one uses the 'Selected atoms' and 'Mass weighting' option? Formally one can define three principal axes of inertia for an object, but only one axis seems to be calculated. Thanks, Luca