[Chimera-users] Changes in transparency during animation

Elaine Meng meng at cgl.ucsf.edu
Mon Nov 2 12:32:09 PST 2015

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
transparency 70,s frames 120; wait 120
turn y 2 180

See info on creating movie content:

I hope this helps.  Sorry for the inconvenience,
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 at 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

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