Appearance of thick edges
Hi all, While playing around with lighting settings, thick black lines appear on the edges of my model (picture attached) that do not go away when I reset lighting conditions. Is it a "feature" or a bug? I tried playing around with all or most of the lighting options to find one that would get rid of them, but that didn't work. Thanks, Yazan
Hi Yazan, Those are “silhouettes” and you can toggle them on and off with the icon that looks like a seahorse outline in the Graphics tab of the Toolbar, or with the “set” command. <http://rbvi.ucsf.edu/chimerax/docs/user/tools/graphics.html> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/set.html#silhouettes> The thickness and color of the lines are also adjustable with the “set” command. See also “making images” list of image-related commands: <http://rbvi.ucsf.edu/chimerax/docs/user/images.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 10, 2019, at 9:07 AM, Yazan Abbas <yazan.abbas@gmail.com> wrote:
Hi all, While playing around with lighting settings, thick black lines appear on the edges of my model (picture attached) that do not go away when I reset lighting conditions. Is it a "feature" or a bug?
I tried playing around with all or most of the lighting options to find one that would get rid of them, but that didn't work. Thanks, Yazan
Hi Elaine, The thin silhouettes at the edges in my image are intentional, it is the thicker silhouettes where the model curves that are bothering me. They seem to intensify as the clipping changes, or when I rotate the model. In other figures I am preparing, the silhouettes are even more intense especially in cartoon helix tube mode and around the the curved parts of the tube (see image attached). They just appeared at one point in my session and I can't make them go away. They were definitely not there before even when silhouettes were turned on. Yazan On Wed, Jul 10, 2019 at 8:30 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Yazan, Those are “silhouettes” and you can toggle them on and off with the icon that looks like a seahorse outline in the Graphics tab of the Toolbar, or with the “set” command.
<http://rbvi.ucsf.edu/chimerax/docs/user/tools/graphics.html> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/set.html#silhouettes>
The thickness and color of the lines are also adjustable with the “set” command.
See also “making images” list of image-related commands: <http://rbvi.ucsf.edu/chimerax/docs/user/images.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 10, 2019, at 9:07 AM, Yazan Abbas <yazan.abbas@gmail.com> wrote:
Hi all, While playing around with lighting settings, thick black lines appear on the edges of my model (picture attached) that do not go away when I reset lighting conditions. Is it a "feature" or a bug?
I tried playing around with all or most of the lighting options to find one that would get rid of them, but that didn't work. Thanks, Yazan
Hi Yazan, Try increasing silhouetteDepthJump: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/set.html#silhouetteDepthJum...> Probably you tried the flat lighting preset which made it smaller than the initial default. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 11, 2019, at 1:51 PM, Yazan Abbas <yazan.abbas@gmail.com> wrote:
Hi Elaine,
The thin silhouettes at the edges in my image are intentional, it is the thicker silhouettes where the model curves that are bothering me. They seem to intensify as the clipping changes, or when I rotate the model. In other figures I am preparing, the silhouettes are even more intense especially in cartoon helix tube mode and around the the curved parts of the tube (see image attached). They just appeared at one point in my session and I can't make them go away. They were definitely not there before even when silhouettes were turned on.
Yazan
Hi Elaine, Thank you very much for your help, that setting did it. I didn't realise the parameters changes and wouldn't have known to look for it. Best, Yazan On Thu, Jul 11, 2019 at 5:06 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Yazan, Try increasing silhouetteDepthJump:
< http://rbvi.ucsf.edu/chimerax/docs/user/commands/set.html#silhouetteDepthJum...
Probably you tried the flat lighting preset which made it smaller than the initial default. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 11, 2019, at 1:51 PM, Yazan Abbas <yazan.abbas@gmail.com> wrote:
Hi Elaine,
The thin silhouettes at the edges in my image are intentional, it is the thicker silhouettes where the model curves that are bothering me. They seem to intensify as the clipping changes, or when I rotate the model. In other figures I am preparing, the silhouettes are even more intense especially in cartoon helix tube mode and around the the curved parts of the tube (see image attached). They just appeared at one point in my session and I can't make them go away. They were definitely not there before even when silhouettes were turned on.
Yazan
As the ChimeraX documentation explains, the silhouette edge calculation does depend on the depth jump between neighboring pixels as a fraction of the clip plane separation. https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/set.html#silhouetteDep... <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/set.html#silhouetteDep...> Please check the documentation before asking questions. You ask a lot of questions that are already answered in the documentation. Tom
On Jul 11, 2019, at 1:51 PM, Yazan Abbas <yazan.abbas@gmail.com> wrote:
Hi Elaine,
The thin silhouettes at the edges in my image are intentional, it is the thicker silhouettes where the model curves that are bothering me. They seem to intensify as the clipping changes, or when I rotate the model. In other figures I am preparing, the silhouettes are even more intense especially in cartoon helix tube mode and around the the curved parts of the tube (see image attached). They just appeared at one point in my session and I can't make them go away. They were definitely not there before even when silhouettes were turned on.
Yazan
On Wed, Jul 10, 2019 at 8:30 PM Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: Hi Yazan, Those are “silhouettes” and you can toggle them on and off with the icon that looks like a seahorse outline in the Graphics tab of the Toolbar, or with the “set” command.
<http://rbvi.ucsf.edu/chimerax/docs/user/tools/graphics.html <http://rbvi.ucsf.edu/chimerax/docs/user/tools/graphics.html>> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/set.html#silhouettes <http://rbvi.ucsf.edu/chimerax/docs/user/commands/set.html#silhouettes>>
The thickness and color of the lines are also adjustable with the “set” command.
See also “making images” list of image-related commands: <http://rbvi.ucsf.edu/chimerax/docs/user/images.html <http://rbvi.ucsf.edu/chimerax/docs/user/images.html>>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 10, 2019, at 9:07 AM, Yazan Abbas <yazan.abbas@gmail.com <mailto:yazan.abbas@gmail.com>> wrote:
Hi all, While playing around with lighting settings, thick black lines appear on the edges of my model (picture attached) that do not go away when I reset lighting conditions. Is it a "feature" or a bug?
I tried playing around with all or most of the lighting options to find one that would get rid of them, but that didn't work. Thanks, Yazan
<Screenshot from 2019-07-11 16-47-21.png>_______________________________________________ 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>
participants (3)
-
Elaine Meng -
Tom Goddard -
Yazan Abbas