Hi Fabian, Both the atom spheres (CPK representation) and molecular surface are triangulations rather than the exact smooth surfaces, and when both are shown, parts of the spheres poke through above the surface. The ideal surfaces would overlap exactly, at least in the convex areas, so even then you might expect some show-through, although it wouldn't look so bumpy. The simplest way to avoid it is to use a different atom representation. However, you must be doing this for some reason, so here is my best idea: You could "fake" the CPK representation by using ball-and-stick instead, but with increased ball scale factor (ballScale=0.25 by default, whereas 1 would give the VDW radius and be the same as the CPK representation). The ball scale factor can be changed in the Selection Inspector ("molecule model" section), or in the molecule model attributes panel, or with a command something like: setattr m ballScale 0.85 <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.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 21, 2008, at 11:22 AM, Fabian Glaser wrote:
Thanks for your answer. But even if teh surface is 0% transparent I see the CPK balls "sticking out", and they don't look nice. Maybe there is a way of slightly enlarging the surface?
THanks a lot for your kind help,
Fabian