Hi,

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.

Best,

-da