<div dir="ltr">Hi Tom and Elaine, <div><br></div><div>Thanks for trying to explain this to me. @Tom, I will send a session to you through the HELP channel soon.</div><div><br></div><div>Cheers,</div><div>Ray </div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, May 4, 2020 at 5:44 PM Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">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.<br>
<br>
<<a href="http://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#silhouettes" rel="noreferrer" target="_blank">http://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#silhouettes</a>><br>
<br>
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.<br>
<br>
<<a href="http://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode" rel="noreferrer" target="_blank">http://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode</a>><br>
<<a href="http://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#clipping" rel="noreferrer" target="_blank">http://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#clipping</a>><br>
<br>
Elaine<br>
<br>
<br>
> On May 4, 2020, at 5:23 PM, Tom Goddard <<a href="mailto:goddard@sonic.net" target="_blank">goddard@sonic.net</a>> wrote:<br>
> <br>
> Hi Ray,<br>
> <br>
> 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.<br>
> <br>
> Tom<br>
> <br>
> <br>
>> On May 4, 2020, at 4:38 PM, Ray Y.-R. Wang <<a href="mailto:wangyr@msg.ucsf.edu" target="_blank">wangyr@msg.ucsf.edu</a>> wrote:<br>
>> <br>
>> Hi Tom and Elaine, <br>
>> <br>
>> 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? <br>
>> <br>
>> Obviously, the depthJump 0.1 solves the problem (thanks for the tip)!<br>
>> <br>
>> Thanks!<br>
>> Ray<br>
>> <br>
>> On Mon, May 4, 2020 at 11:50 AM Tom Goddard <<a href="mailto:goddard@sonic.net" target="_blank">goddard@sonic.net</a>> wrote:<br>
>> Hi Daniel,<br>
>> <br>
>> It is the silhouette depth jump parameter that is causing this. The default values is 0.03 and if you increase it<br>
>> <br>
>> graphics silhouette depthJump 0.1<br>
>> <br>
>> 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.<br>
>> <br>
>> Tom<br>
>> <br>
>> > On May 4, 2020, at 10:20 AM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" target="_blank">meng@cgl.ucsf.edu</a>> wrote:<br>
>> > <br>
>> > Hi Daniel,<br>
>> > 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.<br>
>> > <br>
>> > <<a href="http://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#silhouettes" rel="noreferrer" target="_blank">http://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#silhouettes</a>><br>
>> > <br>
>> > I hope this helps,<br>
>> > Elaine<br>
>> > -----<br>
>> > Elaine C. Meng, Ph.D. <br>
>> > UCSF Chimera(X) team<br>
>> > Department of Pharmaceutical Chemistry<br>
>> > University of California, San Francisco<br>
>> > <br>
>> > <br>
>> >> On May 3, 2020, at 7:38 PM, Daniel Asarnow <<a href="mailto:asarnow@msg.ucsf.edu" target="_blank">asarnow@msg.ucsf.edu</a>> wrote:<br>
>> >> <br>
>> >> Hi,<br>
>> >> 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:<br>
>> >> <image.png><br>
>> >> <br>
>> >> 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.<br>
>> >> <br>
>> >> Thanks and best,<br>
>> >> -da<br>
>> > <br>
>> > <br>
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</blockquote></div>