From: Josh Vermaas (
Date: Fri Jun 27 2014 - 10:15:58 CDT

Hi Bo,

I believe its the center of geometry by default (which would minimize
the RMSD after the center of geometry translation is applied). The way I
like to think about it is that there is a translation that aligns the
center of geometry, then a rotation that minimizes the RMSD, all tucked
away in a 4x4 transformation matrix.
-Josh Vermaas

On 6/26/14, 5:27 PM, James Chen wrote:
> Hi,
> I wonder what is the center of rotation for the transformation matrix
> which I obtained by applying
> %measure fit $atomselect1 $atomselect2
> Thanks!
> Bo