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

Hi Wally, You can use the setattr command, for example: setattr m stickScale 1.5 setattr m ballScale 0.5 http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#attrnam... Or, if you'd rather do something interactive/graphical: (a) select all molecule models (or at least one atom or bond from each) (b) open Selection Inspector by clicking button near lower right corner of the Chimera window or by choosing Actions... Inspect from the menu (c) Inspect "Molecule model" and change the ball scale and/or stick scale as desired These parameters are also in the individual molecule model attributes panels that can be opened from Model Panel, but it is too tedious to set the values individually for multiple models. Another possibility is to change the "New Molecules" Preferences to set those values as desired for subsequently opened molecule models (Favorites... Preferences, change to New Molecules category). 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 Jul 28, 2008, at 12:05 PM, Walter Novak wrote:

Hi All, This is probably a simple question, but the answer is eluding me. Say I have 20 models open. How can I globally change the stick scale and ball scale for all models. Thanks, Wally