I am trying to calculate distances in a unique structure in which alpha-helices stack into sheets, as in beta-sheets. I wish to calculate the distance between two facing sheets and between helices along each sheet. The structure theoretically contains tens of thousands of helices in each sheet (the content of the asymmetric unit is only one helix and the rest are a result of symmetry operations). 

I tried creating planes, one for each sheet, and calculate their distances, but I get zero since the planes are not exactly parallel. 

I also tried calculating centroid to centroid distance (I used 4 helices for each sheet), but there is an angle between the centroids and therefore I get a longer value then expected. Same when calculating axis to axis distance. 

Is there a good way to calculate such things with chimera? and if so, I would appreciate an explanation for an "alpha-helical sheet" containing structure, as well as for facing beta-sheets containing structure (in case there is a difference in the explanation).

Thank you in advance,

Einav