Hi Yao,

  Yes ChimeraX is not showing silhouette edges on molecules behind transparent surfaces. This is because ChimeraX silhouette edges are drawn where the depth of the scene makes a jump.  The depth at a pixel is the depth of the front-most object, so the transparent surface causes ChimeraX not to see the depth of the molecule, hence no silhouette edge on the molecule.

  I just added some code that separately draws the silhouette edges for opaque models and transparent models, so in tonight’s ChimeraX daily build it will draw silhouettes on molecules under transparent surfaces.

Tom

Here’s a picture Elaine Meng made illustrating the problem you described, showing Chimera on left and ChimeraX on right.

On Aug 30, 2019, at 12:21 AM, YAO HE <yaohe@ucla.edu> wrote:

Hi,

I am using ChimeraX now to show the overlay between atomic model and transparent EM densities. However, when I enable the silhouette feature, only the transparent EM densities are affected. I am wondering if it is possible to also silhouette the atomic model inside. Just like "setattr M silhouette true #3" in Chimera.

Best,

Yao

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