[chimerax-users] silhouette of transparent density

[Alexis Rohou]

Hi Tom,

No - I'm not sure! I'm working on a couple myself at the moment, so I'll
try with the new version :)

Either way, I understand your point - I was only asking in case it was only
a small delta of effort on top of the work you'd just completed. I'm happy
with and grateful for whatever features you & the team can deliver.

Cheers,
Alexis

On Fri, Aug 30, 2019 at 2:47 PM Tom Goddard <goddard at sonic.net> wrote:

> Hi Alexis,
>
>   I’d prefer not to add super obscure options like turning off silhouette
> edges behind transparent surfaces.  I think almost no one will use it and
> we have hundreds of other feature requests that I think would get use if we
> had time to implement them.  Are you sure the figures you describe would
> not actually look better if both the outer transparent surface and inner
> opaque transmembrane surface were both silhouetted?
>
> Tom
>
>
> On Aug 30, 2019, at 12:05 PM, Alexis Rohou <a.rohou at gmail.com> wrote:
>
> 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.
>
> <Screen Shot 2019-08-30 at 9.33.44 AM.png>
>
> On Aug 30, 2019, at 12:21 AM, YAO HE <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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