[chimerax-users] Silhouettes cause fill

[Ray Y.-R. Wang]

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 at 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 at 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 at 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 at 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 0.1
> >>
> >> 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 at 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 at 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
> >> >
> >> >
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> >>
> >>
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