[Chimera-users] question about "measure rotation"

Bobby Laird bobbylaird at tamu.edu
Wed May 25 14:09:40 PDT 2011

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?

Bobby W.  Laird

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