Hi Bobby, The "measure rotation #0 #1" command determines the axis of rotation as a vector and then reports the angle of rotation in a right-hand sense around that vector that carries #0 into #1. You are right it there could be an ambiguity. The sign of the axis vector can be flipped. Then the rotation angle reported would be (360 - angle). Notice the possibilities are (angle) and (360-angle). It always reports the one that has the angle <= 180 degrees. So "measure rotation" always gives a consistent result -- the angle <= 180 degrees. This doesn't solve your problem. If you compare the rotation of models B and C to A you may have B rotated by 10 degrees and C rotated by 15 degrees. But it would be nice to know if those rotations are in opposite directions about the same axis (25 degrees apart), or in the same directions (5 degrees apart), or if they are around different rotation axes. In general B and C will be rotated into A about axes that are not parallel. If the two rotation axes point more or less in the same direction then it still might make sense to say that the rotations are approximately in opposite or approximately in the same direction. In order to assess this you should look at the coordinates of the rotation axis vector that are reported by the "measure rotation" command in the Reply Log. From this you can observe if the axis vectors are roughly opposite one another. To quantify this further you may want to consider the angle between the rotation vectors. Tom

I am using the measure rotation command in chimera to calculate the degree of rotation between two dimers, which make up a tetramer. I am using the following commands to accomplish this:

mmaker #1:.A,.B #0:.A,.B pair ss write relative #0 #1 /tmp/ab-aligned.pdb close #1 open #1 /tmp/ab-aligned.pdb mmaker #1:.C,.D #0:.C,.D pair ss measure rotation #0 #1

I have noticed that when I use the "measure rotation" command that can get two different answers. I realize that the two answers are the result of an arbitrary decision made by the measure tool that result in a +/- of the same angle (i.e. 6 versus 174 degrees). Since I am looking at more several crystal structures, is there a way to force "measure rotation" to always make the same decision so that I know what relative direction the rotations are in to each other?

Thanks _______________________________ Bobby W. Laird