[chimerax-users] silhouette of transparent density

[Tom Goddard]

Hi Tristan,

  It would be nice to not have silhouette edges on meshes.  The algorithm relies on the depth of the entire scene, it is computed after the whole scene is rendered (or now after opaque and transparent models are rendered) and cannot exclude any models since the same code that computes depth is also drawing the colors.  It would take new code that rerenders everything in order to be able to exclude specific models from the silhouette depth calculation.  So it is unlikely we can do this — it is too complex.  So if meshes are shown I recommend not using silhouettes.

	Rom

> On Aug 30, 2019, at 1:45 PM, Tristan Croll <tic20 at cam.ac.uk> wrote:
> 
> Along the same lines, it might be nice to have the option to turn silhouettes off for wireframe surfaces. Those have a tendency to become very “heavy” looking with silhouettes, particularly when zoomed out - they can end up obscuring everything behind them. 
>  
> 
> On 30 Aug 2019, at 20:05, Alexis Rohou <a.rohou at gmail.com <mailto: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 <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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