Don't want silhouettes on volume meshes

[glander@…]

The following bug report has been submitted:
Platform:        Darwin-19.2.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-12-18)
Description
Silhouettes should not be drawn on volume meshes by default, as the mesh looks very dark.

Log:
UCSF ChimeraX version: 0.91 (2019-12-18)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 9333 fromDatabase emdb

Opened emd_9333.map, grid size 320,320,320, pixel 1.06, shown at level 0.321,
step 2, values float32  

> volume #1 style mesh

> set bgColor white

> graphics silhouettes true

> save /Users/goddard/Desktop/image1.png supersample 3




OpenGL version: 4.1 ATI-3.4.19
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
File attachment: image1.png

image1.png​

[goddard@…]

Added by email2trac

[Tom Goddard]

Here is Gabe's report of this problem.

Begin forwarded message:

From: Gabriel Lander
Subject: silhouettes on mesh in ChimeraX
Date: January 18, 2020 at 4:01:35 PM PST
To: Tom Goddard

Hi Tom,
One of the "go-to" representations to demonstrate the quality of a modeled PDB in an EM density is sticks shown in a volume mesh. In Chimera when you turn on silhouettes they would only show around the atoms, but not the mesh. This is not the case in ChimeraX, and renderings with silhouettes and meshes look really messy. Is there a way to specifically turn off silhouettes on meshes but not atoms?
Thanks,
-gabe

[Tom Goddard]

I agree the silhouette edges look bad on meshes. ChimeraX cannot turn off silhouette edges on just meshes. It uses the scene depth at each pixel to compute the edges and the mesh contributes to the scene depth. This is a different method than Chimera used. It has the advantage that it renders basically as fast as without silhouettes where Chimera renders about 2x slower with silhouettes. The Chimera method won't work in ChimeraX because ChimeraX uses modern OpenGL (core profile) which no longer supports drawing linewidth greater than 1. The Chimera algorithm worked by drawing the edges of every triangle in the scene with linewidth 2 and slightly behind the triangle. This linewidth 1 only limitation of modern OpenGL also is a problem with meshes on retina displays where the lines are too thin and hard to see.

At any rate, there are ways to provide silhouette edges only on some models but not meshes. But they are hard to implement.

So the best advice I have is show the atomic model and mesh without silhouettes or use Chimera.