Hi, Is there any way to avoid this effect where silhouettes lead to an apparent flood fill? The helix in the upper left of this clip shows what I mean: [image: image.png]
I was able to work around it a bit by making the silhouettes thinner than I'd like, and aggressively supersampling. It seems severe with any silhouette width greater than 1.
Thanks and best, -da
Hi Daniel, Another parameter to play with is the graphics silhouettes "depthJump" value. In this case you could try increasing it. I've had similar problems, and at least part of the time, could solve them by fiddling with this value.
http://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#silhouettes
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 3, 2020, at 7:38 PM, Daniel Asarnow asarnow@msg.ucsf.edu wrote:
Hi, Is there any way to avoid this effect where silhouettes lead to an apparent flood fill? The helix in the upper left of this clip shows what I mean: <image.png>
I was able to work around it a bit by making the silhouettes thinner than I'd like, and aggressively supersampling. It seems severe with any silhouette width greater than 1.
Thanks and best, -da
Hi Daniel,
It is the silhouette depth jump parameter that is causing this. The default values is 0.03 and if you increase it
graphics silhouette depthJump 0.1
that might solve your issue. Let me explain what this parameter means. A black silhouette edge is drawn at a pixel if a neighbor pixel differs in depth by 0.03 times the full depth of the scene (between near and far clip planes). It is surprising to me that your helix has neighboring 2d pixels that differ in depth by more than 3% of the scene depth. But the helix axis is almost aligned with the view direction so two adjacent pixels on the helix can be at quite different depths. But also the full depth of your scene must be quite small, only a few times deeper than the length of the entire helix I guess. Maybe there is a bug here.
Tom
On May 4, 2020, at 10:20 AM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Daniel, Another parameter to play with is the graphics silhouettes "depthJump" value. In this case you could try increasing it. I've had similar problems, and at least part of the time, could solve them by fiddling with this value.
http://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#silhouettes
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 3, 2020, at 7:38 PM, Daniel Asarnow asarnow@msg.ucsf.edu wrote:
Hi, Is there any way to avoid this effect where silhouettes lead to an apparent flood fill? The helix in the upper left of this clip shows what I mean: <image.png>
I was able to work around it a bit by making the silhouettes thinner than I'd like, and aggressively supersampling. It seems severe with any silhouette width greater than 1.
Thanks and best, -da
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Tom and Elaine,
Thanks for the answer. I had found a workaround on this issue and hope you can help me understand this -- if I clip the plane using the buttons (Clip/Clip rotate) available in "Right Mouse" panel and I don't see this thick black edge anymore. Is it because the Clipping mode designated for the buttons is for front and back clipping?
Obviously, the depthJump 0.1 solves the problem (thanks for the tip)!
Thanks! Ray
On Mon, May 4, 2020 at 11:50 AM Tom Goddard goddard@sonic.net wrote:
Hi Daniel,
It is the silhouette depth jump parameter that is causing this. The default values is 0.03 and if you increase it
graphics silhouette depthJump 0.1that might solve your issue. Let me explain what this parameter means. A black silhouette edge is drawn at a pixel if a neighbor pixel differs in depth by 0.03 times the full depth of the scene (between near and far clip planes). It is surprising to me that your helix has neighboring 2d pixels that differ in depth by more than 3% of the scene depth. But the helix axis is almost aligned with the view direction so two adjacent pixels on the helix can be at quite different depths. But also the full depth of your scene must be quite small, only a few times deeper than the length of the entire helix I guess. Maybe there is a bug here.
TomOn May 4, 2020, at 10:20 AM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Daniel, Another parameter to play with is the graphics silhouettes "depthJump"
value. In this case you could try increasing it. I've had similar problems, and at least part of the time, could solve them by fiddling with this value.
<
http://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#silhouettes
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 3, 2020, at 7:38 PM, Daniel Asarnow asarnow@msg.ucsf.edu
wrote:
Hi, Is there any way to avoid this effect where silhouettes lead to an
apparent flood fill? The helix in the upper left of this clip shows what I mean:
<image.png>
I was able to work around it a bit by making the silhouettes thinner
than I'd like, and aggressively supersampling. It seems severe with any silhouette width greater than 1.
Thanks and best, -da
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 Ray,
It does not make sense to me that clip planes would help the silhouette edge problem. To understand this you could send me an example session using ChimeraX menu Help / Report a Bug.... Even with small protein fragments I don't observe this silhouette problem.
Tom
On May 4, 2020, at 4:38 PM, Ray Y.-R. Wang wangyr@msg.ucsf.edu wrote:
Hi Tom and Elaine,
Thanks for the answer. I had found a workaround on this issue and hope you can help me understand this -- if I clip the plane using the buttons (Clip/Clip rotate) available in "Right Mouse" panel and I don't see this thick black edge anymore. Is it because the Clipping mode designated for the buttons is for front and back clipping?
Obviously, the depthJump 0.1 solves the problem (thanks for the tip)!
Thanks! Ray
On Mon, May 4, 2020 at 11:50 AM Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote: Hi Daniel,
It is the silhouette depth jump parameter that is causing this. The default values is 0.03 and if you increase it
graphics silhouette depthJump 0.1that might solve your issue. Let me explain what this parameter means. A black silhouette edge is drawn at a pixel if a neighbor pixel differs in depth by 0.03 times the full depth of the scene (between near and far clip planes). It is surprising to me that your helix has neighboring 2d pixels that differ in depth by more than 3% of the scene depth. But the helix axis is almost aligned with the view direction so two adjacent pixels on the helix can be at quite different depths. But also the full depth of your scene must be quite small, only a few times deeper than the length of the entire helix I guess. Maybe there is a bug here.
TomOn May 4, 2020, at 10:20 AM, Elaine Meng <meng@cgl.ucsf.edu mailto:meng@cgl.ucsf.edu> wrote:
Hi Daniel, Another parameter to play with is the graphics silhouettes "depthJump" value. In this case you could try increasing it. I've had similar problems, and at least part of the time, could solve them by fiddling with this value.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#silhouettes http://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#silhouettes>
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 3, 2020, at 7:38 PM, Daniel Asarnow <asarnow@msg.ucsf.edu mailto:asarnow@msg.ucsf.edu> wrote:
Hi, Is there any way to avoid this effect where silhouettes lead to an apparent flood fill? The helix in the upper left of this clip shows what I mean: <image.png>
I was able to work around it a bit by making the silhouettes thinner than I'd like, and aggressively supersampling. It seems severe with any silhouette width greater than 1.
Thanks and best, -da
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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Since (as Tom said) the silhouette depthjump is defined as a fraction of the distance between near and far clip planes, if you make that near-far distance larger, it makes the depthjump effectively larger as well. Also if you'd used the flat lighting, depthjump is changed from 0.03 to 0.01.
http://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#silhouettes
Whether the mouse clipping mode affects the near-far (nonrotatable) or back-front (rotatable) clip planes depends on the situation... I guess in your case it was affecting near-far clipping.
http://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode http://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#clipping
Elaine
On May 4, 2020, at 5:23 PM, Tom Goddard goddard@sonic.net wrote:
Hi Ray,
It does not make sense to me that clip planes would help the silhouette edge problem. To understand this you could send me an example session using ChimeraX menu Help / Report a Bug.... Even with small protein fragments I don't observe this silhouette problem.
Tom
On May 4, 2020, at 4:38 PM, Ray Y.-R. Wang wangyr@msg.ucsf.edu wrote:
Hi Tom and Elaine,
Thanks for the answer. I had found a workaround on this issue and hope you can help me understand this -- if I clip the plane using the buttons (Clip/Clip rotate) available in "Right Mouse" panel and I don't see this thick black edge anymore. Is it because the Clipping mode designated for the buttons is for front and back clipping?
Obviously, the depthJump 0.1 solves the problem (thanks for the tip)!
Thanks! Ray
On Mon, May 4, 2020 at 11:50 AM Tom Goddard goddard@sonic.net wrote: Hi Daniel,
It is the silhouette depth jump parameter that is causing this. The default values is 0.03 and if you increase it
graphics silhouette depthJump 0.1that might solve your issue. Let me explain what this parameter means. A black silhouette edge is drawn at a pixel if a neighbor pixel differs in depth by 0.03 times the full depth of the scene (between near and far clip planes). It is surprising to me that your helix has neighboring 2d pixels that differ in depth by more than 3% of the scene depth. But the helix axis is almost aligned with the view direction so two adjacent pixels on the helix can be at quite different depths. But also the full depth of your scene must be quite small, only a few times deeper than the length of the entire helix I guess. Maybe there is a bug here.
TomOn May 4, 2020, at 10:20 AM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Daniel, Another parameter to play with is the graphics silhouettes "depthJump" value. In this case you could try increasing it. I've had similar problems, and at least part of the time, could solve them by fiddling with this value.
http://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#silhouettes
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 3, 2020, at 7:38 PM, Daniel Asarnow asarnow@msg.ucsf.edu wrote:
Hi, Is there any way to avoid this effect where silhouettes lead to an apparent flood fill? The helix in the upper left of this clip shows what I mean: <image.png>
I was able to work around it a bit by making the silhouettes thinner than I'd like, and aggressively supersampling. It seems severe with any silhouette width greater than 1.
Thanks and best, -da
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 and Elaine,
Thanks for trying to explain this to me. @Tom, I will send a session to you through the HELP channel soon.
Cheers, Ray
On Mon, May 4, 2020 at 5:44 PM Elaine Meng meng@cgl.ucsf.edu wrote:
Since (as Tom said) the silhouette depthjump is defined as a fraction of the distance between near and far clip planes, if you make that near-far distance larger, it makes the depthjump effectively larger as well. Also if you'd used the flat lighting, depthjump is changed from 0.03 to 0.01.
< http://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#silhouettes
Whether the mouse clipping mode affects the near-far (nonrotatable) or back-front (rotatable) clip planes depends on the situation... I guess in your case it was affecting near-far clipping.
http://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode http://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#clipping
Elaine
On May 4, 2020, at 5:23 PM, Tom Goddard goddard@sonic.net wrote:
Hi Ray,
It does not make sense to me that clip planes would help the
silhouette edge problem. To understand this you could send me an example session using ChimeraX menu Help / Report a Bug.... Even with small protein fragments I don't observe this silhouette problem.
TomOn May 4, 2020, at 4:38 PM, Ray Y.-R. Wang wangyr@msg.ucsf.edu wrote:
Hi Tom and Elaine,
Thanks for the answer. I had found a workaround on this issue and hope
you can help me understand this -- if I clip the plane using the buttons (Clip/Clip rotate) available in "Right Mouse" panel and I don't see this thick black edge anymore. Is it because the Clipping mode designated for the buttons is for front and back clipping?
Obviously, the depthJump 0.1 solves the problem (thanks for the tip)!
Thanks! Ray
On Mon, May 4, 2020 at 11:50 AM Tom Goddard goddard@sonic.net wrote: Hi Daniel,
It is the silhouette depth jump parameter that is causing this. The
default values is 0.03 and if you increase it
graphics silhouette depthJump 0.1that might solve your issue. Let me explain what this parameter
means. A black silhouette edge is drawn at a pixel if a neighbor pixel differs in depth by 0.03 times the full depth of the scene (between near and far clip planes). It is surprising to me that your helix has neighboring 2d pixels that differ in depth by more than 3% of the scene depth. But the helix axis is almost aligned with the view direction so two adjacent pixels on the helix can be at quite different depths. But also the full depth of your scene must be quite small, only a few times deeper than the length of the entire helix I guess. Maybe there is a bug here.
TomOn May 4, 2020, at 10:20 AM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Daniel, Another parameter to play with is the graphics silhouettes
"depthJump" value. In this case you could try increasing it. I've had similar problems, and at least part of the time, could solve them by fiddling with this value.
<
http://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#silhouettes
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 3, 2020, at 7:38 PM, Daniel Asarnow asarnow@msg.ucsf.edu
wrote:
Hi, Is there any way to avoid this effect where silhouettes lead to an
apparent flood fill? The helix in the upper left of this clip shows what I mean:
<image.png>
I was able to work around it a bit by making the silhouettes thinner
than I'd like, and aggressively supersampling. It seems severe with any silhouette width greater than 1.
Thanks and best, -da
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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Thanks, Tom - depthJump fixes the problem completely!
Are there other thresholds to trigger silhouette drawing? I'm thinking of instances like the shifted helices in the lower right here, where there's no silhouette between the khaki and salmon models. BTW the upper left helix shows how well depthJump 0.1 works here.
[image: image.png]
Best, -da
On Mon, May 4, 2020 at 11:48 AM Tom Goddard goddard@sonic.net wrote:
Hi Daniel,
It is the silhouette depth jump parameter that is causing this. The default values is 0.03 and if you increase it
graphics silhouette depthJump 0.1that might solve your issue. Let me explain what this parameter means. A black silhouette edge is drawn at a pixel if a neighbor pixel differs in depth by 0.03 times the full depth of the scene (between near and far clip planes). It is surprising to me that your helix has neighboring 2d pixels that differ in depth by more than 3% of the scene depth. But the helix axis is almost aligned with the view direction so two adjacent pixels on the helix can be at quite different depths. But also the full depth of your scene must be quite small, only a few times deeper than the length of the entire helix I guess. Maybe there is a bug here.
TomOn May 4, 2020, at 10:20 AM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Daniel, Another parameter to play with is the graphics silhouettes "depthJump"
value. In this case you could try increasing it. I've had similar problems, and at least part of the time, could solve them by fiddling with this value.
<
http://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#silhouettes
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 3, 2020, at 7:38 PM, Daniel Asarnow asarnow@msg.ucsf.edu
wrote:
Hi, Is there any way to avoid this effect where silhouettes lead to an
apparent flood fill? The helix in the upper left of this clip shows what I mean:
<image.png>
I was able to work around it a bit by making the silhouettes thinner
than I'd like, and aggressively supersampling. It seems severe with any silhouette width greater than 1.
Thanks and best, -da
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Daniel, As far as I know it's a fiddle, trying to find the happy medium value of "depthJump" by trial and error. There may not be a perfect separation between the edges you want and those you don't. Best, Elaine
On May 6, 2020, at 3:54 PM, Daniel Asarnow asarnow@msg.ucsf.edu wrote:
Thanks, Tom - depthJump fixes the problem completely!
Are there other thresholds to trigger silhouette drawing? I'm thinking of instances like the shifted helices in the lower right here, where there's no silhouette between the khaki and salmon models. BTW the upper left helix shows how well depthJump 0.1 works here.
<image.png>
Best, -da
On Mon, May 4, 2020 at 11:48 AM Tom Goddard goddard@sonic.net wrote: Hi Daniel,
It is the silhouette depth jump parameter that is causing this. The default values is 0.03 and if you increase it
graphics silhouette depthJump 0.1that might solve your issue. Let me explain what this parameter means. A black silhouette edge is drawn at a pixel if a neighbor pixel differs in depth by 0.03 times the full depth of the scene (between near and far clip planes). It is surprising to me that your helix has neighboring 2d pixels that differ in depth by more than 3% of the scene depth. But the helix axis is almost aligned with the view direction so two adjacent pixels on the helix can be at quite different depths. But also the full depth of your scene must be quite small, only a few times deeper than the length of the entire helix I guess. Maybe there is a bug here.
TomOn May 4, 2020, at 10:20 AM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Daniel, Another parameter to play with is the graphics silhouettes "depthJump" value. In this case you could try increasing it. I've had similar problems, and at least part of the time, could solve them by fiddling with this value.
http://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#silhouettes
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 3, 2020, at 7:38 PM, Daniel Asarnow asarnow@msg.ucsf.edu wrote:
Hi, Is there any way to avoid this effect where silhouettes lead to an apparent flood fill? The helix in the upper left of this clip shows what I mean: <image.png>
I was able to work around it a bit by making the silhouettes thinner than I'd like, and aggressively supersampling. It seems severe with any silhouette width greater than 1.
Thanks and best, -da
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 Daniel,
The silhouettes outline edges where the depth changes. With your two overlapping helix cylinders there is no depth change at the boundary between the two helices, so no silhouette edge. Silhouettes are not designed to draw boundaries between different models, only to highlight the 3d appearance by clarifying where a jump in depth occurs because a foreground object is far in front of a background object which may have the same color making the difference in depth not obvious.
If one model is selected and the other is not that can show a boundary line between two models. The color of the selection outline can also be changed from its normal green to say black. I don't expect this to work well, but you could try.
Tom
On May 6, 2020, at 3:59 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Daniel, As far as I know it's a fiddle, trying to find the happy medium value of "depthJump" by trial and error. There may not be a perfect separation between the edges you want and those you don't. Best, Elaine
On May 6, 2020, at 3:54 PM, Daniel Asarnow asarnow@msg.ucsf.edu wrote:
Thanks, Tom - depthJump fixes the problem completely!
Are there other thresholds to trigger silhouette drawing? I'm thinking of instances like the shifted helices in the lower right here, where there's no silhouette between the khaki and salmon models. BTW the upper left helix shows how well depthJump 0.1 works here.
<image.png>
Best, -da
On Mon, May 4, 2020 at 11:48 AM Tom Goddard goddard@sonic.net wrote: Hi Daniel,
It is the silhouette depth jump parameter that is causing this. The default values is 0.03 and if you increase it
graphics silhouette depthJump 0.1that might solve your issue. Let me explain what this parameter means. A black silhouette edge is drawn at a pixel if a neighbor pixel differs in depth by 0.03 times the full depth of the scene (between near and far clip planes). It is surprising to me that your helix has neighboring 2d pixels that differ in depth by more than 3% of the scene depth. But the helix axis is almost aligned with the view direction so two adjacent pixels on the helix can be at quite different depths. But also the full depth of your scene must be quite small, only a few times deeper than the length of the entire helix I guess. Maybe there is a bug here.
TomOn May 4, 2020, at 10:20 AM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Daniel, Another parameter to play with is the graphics silhouettes "depthJump" value. In this case you could try increasing it. I've had similar problems, and at least part of the time, could solve them by fiddling with this value.
http://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#silhouettes
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 3, 2020, at 7:38 PM, Daniel Asarnow asarnow@msg.ucsf.edu wrote:
Hi, Is there any way to avoid this effect where silhouettes lead to an apparent flood fill? The helix in the upper left of this clip shows what I mean: <image.png>
I was able to work around it a bit by making the silhouettes thinner than I'd like, and aggressively supersampling. It seems severe with any silhouette width greater than 1.
Thanks and best, -da
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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participants (4)
-
Daniel Asarnow -
Elaine Meng -
Ray Y.-R. Wang -
Tom Goddard