[chimerax-users] silhouette of transparent density

[Alexis Rohou]

Hi Tom,

This is great! I'd often wished I could get silhouettes of opaque models
behind transparent surfaces.

However, there are also circumstances where the effect of having
silhouettes only around the outermost (front-most, I guess) surface is
very nice. A number of figures of membrane proteins were published
recently like that - the micelle is shown as a low-resolution
very-transparent blob with silhouette, and the volume surface of the TM
domain is shown inside it without silhouette. Makes for a nice visual
effect.

My question: could we perhaps have this new feature switchable via the
set command?

Cheers,
Alexis

On 8/30/19 11:08 AM, Tom Goddard wrote:
> 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 at ucla.edu
>> <mailto:yaohe at 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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>
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