Hi Ashley, I assume you are using the Animation tool. In my tests, it worked to gradually fade in from 70% to 0% transparent, but not in the opposite direction, to fade out. In general when something doesn’t work we recommend using Chimera menu: Help… Report a Bug and including a description (and possibly attaching a file) as needed to reproduce that problem, as well as including your email address for feedback such as notification of a fix. However, I’ll do that for you since I already generated a test session. The workaround is to instead make a Chimera command file for your movie content. I understand, however, that this could be much more work depending on how complicated your movie is. For a relatively simple movie with things like spinning around, zooming, and changing colors and transparency, it would be a pretty short script. For example, Chimera commands to open 1gcn, show surface, gradually go from 0% to 70% transparent surface and roll around Y axis: open 1gcn surface transparency 70,s frames 120; wait 120 turn y 2 180 See info on creating movie content: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html#content> I hope this helps. Sorry for the inconvenience, 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 Nov 2, 2015, at 10:17 AM, Ashley Acevedo <acevedo.ashley@gmail.com> wrote:

Hi,

I'm trying to animate a change in surface transparency. I have made a scene with my molecule at 0% transparency and a second scene with the same molecule at 70% transparency. The problem that I'm having is that when I set the transparency in one scene that transparency setting is carried over to my other scene, so I end up not being able to animate changes in transparency. Is there a solution to this problem?

I'm using Chimera version 1.10.2 on a mac.

Thanks, Ashley