Hi Liz, The default transparency is "single-layer," which is nicer for de-emphasizing transparent parts relative to nontransparent ones. However, you can instead show all layers, for example with the command: ~set single This is also a checkbox setting in the Effects tool. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/set.html#singlelayer> However, sometimes in Chimera multiple transparent layers don't end up looking as nice as you would hope. There may be weird artifacts, essentially errors, in rendering multiple layers of transparency from more than one model or both ribbons and surfaces. If it looks good, then great; if not, you could try showing one of the isosurfaces as (nontransparent) mesh and seeing if that shows what you want to show. More about the problem with multiple transparent models: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2008-February/002335.html> 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 On Aug 17, 2013, at 11:20 AM, Elizabeth Montabana wrote:

Hi All I have a difference map that I'd like to have set to 50% transparent overlaid with the original data map set to 70% transparent. If I do this, I cease to see any off the difference map. Is there anyway to accomplish this in Chimera? thanks Liz Montabana Graduate Student Agard Lab, UCSF