Hi Andy, It just occurred to me that the "align" command changed recently. The link in my previous message goes to the man page for the latest and greatest, which allows you to specify two sets of atoms. The centroids of the sets are aligned. The older version of "align" (such as in the most recent production release, 1.2422) only allows two atoms rather than two sets of atoms to be used: http://www.cgl.ucsf.edu/chimera/1.2422/docs/UsersGuide/midas/align.html Currently the newer version of "align" is available in the August Linux snapshots http://www.cgl.ucsf.edu/chimera/download.html#snapshots and *untested* builds for other platforms http://www.cgl.ucsf.edu/chimera/alpha-downloads.html Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Sep 7, 2007, at 10:49 AM, Elaine Meng wrote:
You might be able to do what you want even without a visual representation of the axes, using the "align" command and then rotating 90 degrees around various axes with "turn" http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/align.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html