Hi Scott, This looks to me like a graphics driver bug, and you should use the Chimera Report a Bug dialog if you wish to discuss it further with us. Probably updating your graphics driver is the only hope of fixing it. If you have another computer you can try it on, you can see if it depends on the computer which would support the theory that it is the system graphics driver at fault. Tom On Oct 23, 2013, at 11:03 AM, Elaine Meng wrote:

Hi Scott, Short answer is I have no idea what could be happening. I tried to reproduce the problem, but in my case making the surface transparent didn't make any part of it disappear. I tried to use a similar situation (partial surface, gradient background, etc.) It may be something specific to your computer or the structure, which we would need to be able to reproduce to solve.

You could save session with the surface at zero transparency, then use Help... Report a Bug, including your email address and a short description of the problem and how to reveal it starting from that session (e.g. command: transparency 1,s), and of course attaching the session file. Thanks 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 Oct 23, 2013, at 9:43 AM, Scott Classen wrote:

...

Hello, I'm trying to fade a surface to 100 transparent with the following command

transparency 100,s #2 frames 30; wait 30

and when the surface goes from 0% transparent to 1% transparent I see the following clipping at the top of the surface:

<zero.png> <one.png>

What is causing this and how can I eliminate it?

Thanks, Scott

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