silhouette of transparent density
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
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@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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@ucla.edu <mailto:yaohe@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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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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@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@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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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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@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@gmail.com <mailto:a.rohou@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@ucla.edu <mailto:yaohe@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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
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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@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@ucla.edu <mailto:yaohe@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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
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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@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@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@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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing listChimeraX-users@cgl.ucsf.edu Manage subscription:http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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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@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@sonic.net <mailto:goddard@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@gmail.com <mailto:a.rohou@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@ucla.edu <mailto:yaohe@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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
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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@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@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@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@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@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 > _______________________________________________ > ChimeraX-users mailing list > ChimeraX-users@cgl.ucsf.edu > Manage subscription: > http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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I have not, but thanks for the suggestion! Cheers, Alexis On Aug 30, 2019, 3:30 PM -0700, Yazan Abbas <yazan.abbas@gmail.com>, wrote:
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@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@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@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@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@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 > > _______________________________________________ > > ChimeraX-users mailing list > > ChimeraX-users@cgl.ucsf.edu > > Manage subscription: > > http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users > > > _______________________________________________ > ChimeraX-users mailing list > ChimeraX-users@cgl.ucsf.edu > Manage subscription: > http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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Hi Tom, Thank you for the help. Best, Yao On Fri, Aug 30, 2019 at 11:08 AM Tom Goddard <goddard@sonic.net> 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@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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (5)
-
Alexis Rohou -
Tom Goddard -
Tristan Croll -
YAO HE -
Yazan Abbas