[chimerax-users] silhouette of transparent density

[Tom Goddard]

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 <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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