On Jul 24, 2009, at 7:20 AM, Stefano Ciurli wrote:
Hello Elaine, I am writing to ask you the following: I need to define the relative orientation of two domains of a protein, and I am not sure about how to do it. I was thinking of approximating the domains as ellipsoids and then calculate the angles between the axes of the ellipsoids. I wonder if you have a better way to define the orientation, or if Chimera can do things like calculate ellipsoids axes and their orientation. Regards Stefano
Hi Stefano, There is an Axes tool (under Tools... Structure Analysis). It does not give ellipsoids, just the long axis, shown as a cylinder. You can define axes for helices or for any set of atoms (e.g. a domain), and then choose any two axes for an angle calculation. For details, see <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ structuremeas/structuremeas.html#axes> or just click the Help button on the dialog to see your local copy of this information. Eventually we want to also allow defining centroids and planes, but only the axes measurements are available currently. Please send chimera questions to chimera-users@cgl.ucsf.edu rather than to me personally, unless private data are included. This allows others to benefit, or to answer the question if I am unavailable. 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