Hi Andy, You can measure atom-atom distances, or you can measure the distance between the helix axes. There are several ways to measure atom-atom distances, including Ctrl- click to select the first atom, Shift-Ctrl-click to select the second atom, and then clicking "Create" in the "Distances" tool (under Tools... Structure Analysis): http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/struc... You would have to display the atoms to pick them from the screen, but you could undisplay them after that. Or instead of picking from the screen, you could name them in a distance command, for example: distance :10.a@ca :10.b@ca In that case the atoms never need to be displayed; to see the distance you would need to look at the "Distances" tool. If instead you want to use the helix axes for the measurements, use the "Axes" tool (under Tools... Structure Analysis): http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/struc... Using that tool, define the helix axes, and then in the resulting list choose the two of interest with the mouse. That will show the axis- axis distance and crossing angle on the dialog and in the Reply Log. I hope this helps, 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 Jul 28, 2008, at 10:35 AM, Thomas Goddard wrote:
HI Tom How do I compute and show the distance between 2 regions (2 alpha helixes) of 2 crystal structures (docked in the density maps), similar portions of each is already highlighted/selected to show the DNA binding region (without showing the atoms).
THanks Andy
Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908