Hi Monica, Sorry, it is a current limitation of raytracing from Chimera, as noted in the documentation: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/raytracing.html> "parts of objects cut away with the global clipping planes in Chimera will still be shown in the raytraced image" However, you may be able to get what you want using Per-Model Clipping (under Tools... Depiction), as that type of clipping is translated into the information sent to POV-Ray. Here are more details on using that tool: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/per-model/ per-model.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu 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 Aug 31, 2008, at 10:14 AM, Monica Tello wrote:

I am having trouble saving my images when they have a surface clipped to show the inside. If I have a surface around my ligand and is partially clipped, at the time of saving the image: - If I save it without using POV-ray, it saves the exact same view as on the screen, with the surface clipped. - If I use POV-ray, it saves it with the full surface around the ligand, ignoring the clipping I had done. I have tried modifying several POV-ray settings but nothing has worked! Have you got any suggestions?

Thanks!

Monica