[chimerax-users] silhouette of transparent density

[Yazan Abbas]

Hi Alexis,

Have you tried achieving the desired effect by outputting multiple images from chimeraX, then using layers and transparency in illustrator (or equivalent program)? I’ve been using that trick to show a silhouetted atomic model in semi-transparent density: top layer contains all the elements including the opaque density, bottom layer includes all the elements minus the surface I want to make transparent, then I adjust top layer transparency. Now that chimeraX is implementing that feature, I don't need to do that but perhaps you can do something similar to selectively silhouette an object or map.

Best,

Yazan
On Aug 30, 2019, 6:12 PM -0400, Tom Goddard <goddard at sonic.net>, wrote:
> Hi Alexis,
>
>   To add the option requires that it be added to a command to set it, also it would need to be saved in sessions, and it would need to be documented in the manual — it would be about twice the work that was needed to make silhouettes show under transparent surfaces (which involved no user interface, session or documentation changes).  It would be a small effort, maybe 4 hours work, but we have years of unimplemented feature requests, so it needs to be well justified.
>
>   Let me know what you find as you make some new figures.
>
> 	Tom
>
> > On Aug 30, 2019, at 3:04 PM, Alexis Rohou <a.rohou at gmail.com> wrote:
> >
> > 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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