Hi Chuck, I'm not sure if this is exactly what you mean, but the new command (in daily builds only, not version 1.3) "measure rotation" reports the transformation of one model relative to another and can create a rod that shows the axis of rotation. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html> Alternatively, you can create arbitrary shapes with specified coordinates (including rods, arrows, etc.) in the BILD format and then read in that BILD file. That requires already knowing what coordinates you want the shape(s) to have. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html> And a final alternative, if you just want lines or sticks that connect existing atoms, you can create them as "pseudobonds" using a simple input format read in by the PseudoBond Reader tool. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader.h...

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. 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 Jul 7, 2009, at 9:04 AM, Charles Letner, Ph.D. wrote:

Hello, Is there a way to display a vector between two sets of coordinates in Chimera? If the approach is to write a python, any chance I could get a nudge in the right direction on chimera commands to work with? I've written a minimal amount of python code but not related to Chimera. Cheers, Chuck