I would like to calculate the relative rotation of one helix relative to another in a dimer to see how the contact surface between the two changes,if at all. I am unsure how to set this up.

COOR HELIX with a double atom selection will do that (corman.doc)

In principle obtaining two HELIX time series (correl.doc) and then computing the helical axes dot product should also work, but I had some trouble with the HELIX time series recently. Instead, I computed the dot product of vectors from CA of residue i to CA of residue i+14 (where i may be different for each helix).

wouldnt that calculate the angle between helix axes? I am interested in the rotation of one helix on its axis relative to the surface of the other helix- like if two rolling pins on top of one another roll on eachother and the contact surface changes

The proper way to do this is to first discuss with your supervisor to find out what would be a reasonable physical quantity (equation!) to use for this purpose, then come back and ask how this can be implemented in CHARMM.

Lennart Nilsson Karolinska Institutet Stockholm, Sweden

I was thinking more of the helix crossing angle when I first read the question. I've used the CA-CB bond vector of selected side chains as a measure of rotation around the helical axis.