Hi Katryna, I think what you want is available, but only via keyboard shortcuts. You have to first enable shortcuts as described here: <http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/accelerator...

The you can use the "comparing domain orientation" shortcuts "ab" and "ai" described briefly here: <http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/accelerator...

and in a more detailed example here: <http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/accelerator...

A limitation is that the residue numbers and chain IDs need to be the same between the different orientations being compared. The output is two rectangular slabs and in the Reply Log, RMSD, number of atom pairs, and angle of rotation. I don't see anything about translation, however. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Sep 11, 2008, at 9:39 AM, KATRYNA CISEK wrote:

Dear Chimera developer, I would like to analyze a set of dimer structures based on a reference dimer structure. Unfortunately a simple RMSD calculation does not capture the translational/rotational shift that occurs. Is it possible to extract a plane of rotation and degree of rotation between two structures in chimera? Thanks, Katryna