[Chimera-users] Multiple transparent objects

Daniel Asarnow dasarnow at gmail.com
Mon Dec 12 12:02:11 PST 2016

I'm having some trouble with a movie of a morph between structures of the
same protein bound to two different ligands. The basic idea is a closeup of
the binding pocket, and as the morph progresses the initial ligand becomes
transparent while the second one becomes opaque. The result is a similar
effect to crossfade, only the morph animation is playing simultaneously.

I've tried both the screen capture and ray tracing methods, with the
following results:

Screen capture

   - When a ligand is almost entirely transparent, a white silhouette is
   shown at the highest z-order, blocking what's behind.
   - There is a "pop up" effect when the ligands suddenly switch z-order at
   the beginning and end of my animation.
   - Single-layer and flat transparency options don't help.

Ray tracing

   - Multiple transparency is fine.
   - Reflections and shadows are not made transparent.
      - E.g. when one ligand is 100% transparent, the reflections and
      shadows are still visible as white lines and dark spots.

Maybe someone here has some insights on my transparency problems?

A way to use crossfade instead would be even better.

I can record movies with the two ligands separately and then crossfade them
manually with ffmpeg. However, it would be nice to have this working
entirely in chimera, especially for some more complicated animations I have
in the works.

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