[Chimera-users] question about "measure rotation"
Tom Goddard
goddard at sonic.net
Wed May 25 15:27:12 PDT 2011
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
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