Hi James, It is a shortcoming of raytracing from Chimera that the global (Side View) clipping is not included, as listed in the Limitations here: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/raytracing.html However, you may be able to get what you want by using Per-Model Clipping (under Tools... Depiction): http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/per-model/ per-model.html You would have to turn this on for each model individually that you want to clip, and it takes a little practice moving the plane around with the mouse. It is especially useful when you want to clip one model but not another, but if you do want to clip them all with the same plane, there is an option to "align plane" of one model with that for another. Experiment a little and you will see what I mean... If you are clipping surfaces, you may also want to use Surface Capping (if you aren't already). Finally, if you are using the production release from November, you might also want to try a newer build. After the November release, we changed the default lighting in Chimera to give a brighter appearance in raytraced images. 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 Feb 18, 2008, at 9:28 AM, James Fethiere wrote:

Hi, I'm trying to save an image of an EM map with atomic models fitting in and can't get pov-ray to write-out the displayed image. Using the side view panel, I cut out part of the surface and models to get the view I want. When I save the image without pov-ray, I get what is displayed but when I try using the pov-ray option, I get the full map and models without the clipping I imposed using the side view mode. What would be the right procedure? Thanks James