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