id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
2127	Silhouettes on transparent drawings	tic20@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        Linux-3.10.0-957.12.2.el7.x86_64-x86_64-with-centos-7.6.1810-Core
ChimeraX Version: 0.91 (2019-06-25)
Description
Cartoon tethers (and I suppose other drawings?) with opacity set to zero still get outlined when silhouettes is true.

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.91 (2019-06-25)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6o6c

6o6c title:  
RNA polymerase II elongation complex arrested at a CPD lesion [more info...]  
  
Chain information for 6o6c #1  
---  
Chain | Description  
A | DNA-directed RNA polymerase II subunit RPB1  
B | DNA-directed RNA polymerase II subunit RPB2  
C | DNA-directed RNA polymerase II subunit RPB3  
D | DNA-directed RNA polymerases I, II, and III subunit RPABC1  
E | DNA-directed RNA polymerases I, II, and III subunit RPABC2  
F | DNA-directed RNA polymerases I, II, and III subunit RPABC3  
G | DNA-directed RNA polymerase II subunit RPB9  
H | DNA-directed RNA polymerases I, II, and III subunit RPABC5  
I | DNA-directed RNA polymerase II subunit RPB11  
J | DNA-directed RNA polymerases I, II, and III subunit RPABC4  
K | RNA (5'-R(P*ap*up*CP*GP*ap*GP*ap*GP*G)-3')  
L | DNA (5'-D(P*GP*GP*ap*GP*ap*ap*GP*GP*ap*GP*CP*ap*GP*ap*GP*C)-3')  
M | DNA (27-mer)  
  
Non-standard residues in 6o6c #1  
---  
MG — magnesium ion  
ZN — zinc ion  
  
  

> show selAtoms ribbons

> style selAtoms stick

Changed 30166 atom styles  

> set bgColor white

> set silhouettes true

> cofr centerOfView

> cofr centerOfView showPivot true

> usage cartoon style

cartoon style [atoms] [width a number] [thickness a number] [arrows true or
false] [arrowsHelix true or false] [arrowScale arrowScale] [xsection xsection]
[sides sides] [divisions divisions] [barScale a number] [barSides barSides]
[modeHelix modeHelix] [radius radius]  
— set cartoon style for secondary structures in specified models  
arrowScale: a number ≥ 1.0 and ≤ 5.0  
xsection: one of barbell, oval, piping, rectangle, round, or square  
sides: an even integer ≥ 3 and ≤ 24  
divisions: an integer ≥ 2 and ≤ 40  
barSides: an even integer ≥ 3 and ≤ 24  
modeHelix: one of default, tube, or wrap  
radius: a number or auto  

> usage cartoon tether

cartoon tether [structures] [scale scale] [shape shape] [sides sides] [opacity
opacity]  
— set cartoon tether options for specified structures  
scale: a number ≥ 0.0 and ≤ 1.0  
shape: one of cone, cylinder, or steeple  
sides: an integer ≥ 3 and ≤ 24  
opacity: a number ≥ 0.0 and ≤ 1.0  

> cartoon tether opacity 0




OpenGL version: 3.3.0 NVIDIA 415.27
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

}}}
"	enhancement	closed	normal		Graphics		duplicate		Elaine Meng				all	ChimeraX