[chimerax-users] Silhouettes cause fill

[Tom Goddard]

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 at 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 at 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 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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