[Chimera-users] Time evolution of the crossing angle between helices during MD trajectories

[George Tzotzos]

In Chimera’s Structure Measurement tool, for a given protein, clicking on the Define axes gives the Cartesian coordinates of the centre of each helix as well as its direction. Selecting two helices (say helix 5 and 6) gives the angle and distance between these helices. I take it that the distance is defined as that between the centroids of the centre of mass of the two helices.

The question is whether it is possible to work out the time evolution of the crossing angle between to helices during an MD trajectory. 

MD Movie/Analysis/Plots/Angles plots the angle between three atoms rather than the crossing angle of the chosen helices. Am I right? Missing something?

Thanks in advance for your help

George