[Chimera-users] Multiple transparent objects

Tom Goddard goddard at sonic.net
Mon Dec 12 14:14:51 PST 2016

Hi Daniel,

  Chimera does not correctly display two transparent models — one will appear on top of the other one.  The simplest and most practical solution is to fade out one ligand by making it transparent, and immediately after fade in the other ligand, instead of having both ligands intermingled as one fades out and one fades in.  If you don’t like that you can try putting both ligands in a single model.  Still won’t look great with the one transparent layer setting because you won’t be able to see through one ligand to the other, and if you turn off one transparent layer, then multiple layers don’t even look right within a single molecule model.  The way to get exactly what you want is as you suggest, record two times, each with only one ligand and blend the result with ffmpeg.  Multiple transparent layers is difficult to do right.


> On Dec 12, 2016, at 12:02 PM, Daniel Asarnow wrote:
> 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
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