Opened 4 years ago

Last modified 4 years ago

#4628 assigned defect

Boxy silhouettes in saved images

Reported by: c.waudby@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Graphics Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.2.2 (2021-05-08 05:48:20 UTC)
Description
I get weird black boxes around background-exposed edges when saving figures with silhouettes. Sometimes this also appears in the main view, but turning silhouettes off and on again usually resets this - but they always appear in saved files. Happened in v1.1.1 and updated to v.1.2.2 and same problem occurs.

Log:
UCSF ChimeraX version: 1.2.2 (2021-05-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/chris/Library/Containers/com.apple.mail/Data/Library/Mail
> Downloads/A657E53C-D5B5-47FE-9768-1A5B36DCA455/ribosome_31_cor_new_large.pdb"
> format pdb

Chain information for ribosome_31_cor_new_large.pdb #1  
---  
Chain | Description  
0 | No description available  
1 | No description available  
3 | No description available  
6 7 8 9 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
s | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> color /1 gray(90%)

> color /3 gray(90%)

> color /A gray(50%)

> color /B gray(50%)

> color /C gray(70%)

> color /D gray(70%)

> color /E gray(70%)

> color /F gray(50%)

> color /G gray(70%)

> color /I gray(70%)

> color /J gray(70%)

> color /K gray(70%)

> color /L gray(50%)

> color /M gray(70%)

> color /N gray(70%)

> color /0 gray(50%)

> color /O gray(50%)

> color /P gray(50%)

> color /Q gray(50%)

> color /R gray(70%)

> color /S gray(70%)

> color /T gray(50%)

> color /U gray(50%)

> color /V gray(50%)

> color /W gray(70%)

> color /X gray(50%)

> color /x gray(70%)

> color /Y gray(70%)

> color /Z gray(50%)

> color /w gray(50%)

> color /y gray(50%)

> color /z gray(50%)

> surface /0 resolution 8

1 Gaussian surfaces, threshold level 0.076  

> surface /1 resolution 8

1 Gaussian surfaces, threshold level 0.104  

> surface /3 resolution 8

1 Gaussian surfaces, threshold level 0.111  

> surface /6 resolution 8

1 Gaussian surfaces, threshold level 0.075  

> surface /7 resolution 8

1 Gaussian surfaces, threshold level 0.074  

> surface /8 resolution 8

1 Gaussian surfaces, threshold level 0.074  

> surface /9 resolution 8

1 Gaussian surfaces, threshold level 0.075  

> surface /Z resolution 8

1 Gaussian surfaces, threshold level 0.080  

> surface /Y resolution 8

1 Gaussian surfaces, threshold level 0.076  

> surface /A resolution 8

1 Gaussian surfaces, threshold level 0.074  

> surface /B resolution 8

1 Gaussian surfaces, threshold level 0.074  

> surface /C resolution 8

1 Gaussian surfaces, threshold level 0.076  

> surface /D resolution 8

1 Gaussian surfaces, threshold level 0.077  

> surface /E resolution 8

1 Gaussian surfaces, threshold level 0.076  

> surface /F resolution 8

1 Gaussian surfaces, threshold level 0.076  

> surface /G resolution 8

1 Gaussian surfaces, threshold level 0.075  

> surface /H resolution 8

1 Gaussian surfaces, threshold level 0.075  

> surface /I resolution 8

1 Gaussian surfaces, threshold level 0.075  

> surface /J resolution 8

1 Gaussian surfaces, threshold level 0.076  

> surface /K resolution 8

1 Gaussian surfaces, threshold level 0.076  

> surface /L resolution 8

1 Gaussian surfaces, threshold level 0.075  

> surface /M resolution 8

1 Gaussian surfaces, threshold level 0.078  

> surface /N resolution 8

1 Gaussian surfaces, threshold level 0.077  

> surface /O resolution 8

1 Gaussian surfaces, threshold level 0.074  

> surface /P resolution 8

1 Gaussian surfaces, threshold level 0.079  

> surface /Q resolution 8

1 Gaussian surfaces, threshold level 0.076  

> surface /R resolution 8

1 Gaussian surfaces, threshold level 0.077  

> surface /S resolution 8

1 Gaussian surfaces, threshold level 0.075  

> surface /T resolution 8

1 Gaussian surfaces, threshold level 0.075  

> surface /U resolution 8

1 Gaussian surfaces, threshold level 0.075  

> surface /V resolution 8

1 Gaussian surfaces, threshold level 0.074  

> surface /W resolution 8

1 Gaussian surfaces, threshold level 0.076  

> surface /X resolution 8

1 Gaussian surfaces, threshold level 0.076  

> surface /s resolution 8

1 Gaussian surfaces, threshold level 0.075  

> surface /w resolution 8

1 Gaussian surfaces, threshold level 0.078  

> surface /x resolution 8

1 Gaussian surfaces, threshold level 0.075  

> surface /y resolution 8

1 Gaussian surfaces, threshold level 0.075  

> surface /z resolution 8

1 Gaussian surfaces, threshold level 0.075  

> hide /6 surfaces

> hide /7 surfaces

> hide /8 surfaces

> hide /9 surfaces

> hide /H surfaces

> color /1 gray(90%)

> color /3 gray(90%)

> color /A gray(50%)

> color /B gray(50%)

> color /C gray(70%)

> color /D gray(70%)

> color /E gray(70%)

> color /F gray(50%)

> color /G gray(70%)

> color /I gray(70%)

> color /J gray(70%)

> color /K gray(70%)

> color /L gray(50%)

> color /M gray(70%)

> color /N gray(70%)

> color /0 gray(50%)

> color /O gray(50%)

> color /P gray(50%)

> color /Q gray(50%)

> color /R gray(70%)

> color /S gray(70%)

> color /T gray(50%)

> color /U gray(50%)

> color /V gray(50%)

> color /W gray(70%)

> color /X gray(50%)

> color /x gray(70%)

> color /Y gray(70%)

> color /Z gray(50%)

> color /w gray(50%)

> color /y gray(50%)

> color /z gray(50%)

> set bgColor white

> hide atoms

> lighting soft

> graphics silhouettes

Current silhouette settings:  
enabled: False  
width: 2  
color: 0,0,0  
depth jump: 0.03  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/1040-bb.pdb

Chain information for 1040-bb.pdb #2  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/1062-bb.pdb

Chain information for 1062-bb.pdb #3  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/1325-bb.pdb

Chain information for 1325-bb.pdb #4  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/10089-bb.pdb

Chain information for 10089-bb.pdb #5  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/10126-bb.pdb

Chain information for 10126-bb.pdb #6  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/10566-bb.pdb

Chain information for 10566-bb.pdb #7  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/10670-bb.pdb

Chain information for 10670-bb.pdb #8  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/10829-bb.pdb

Chain information for 10829-bb.pdb #9  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/11058-bb.pdb

Chain information for 11058-bb.pdb #10  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/11324-bb.pdb

Chain information for 11324-bb.pdb #11  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/12437-bb.pdb

Chain information for 12437-bb.pdb #12  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/12490-bb.pdb

Chain information for 12490-bb.pdb #13  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/13748-bb.pdb

Chain information for 13748-bb.pdb #14  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/13814-bb.pdb

Chain information for 13814-bb.pdb #15  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/13913-bb.pdb

Chain information for 13913-bb.pdb #16  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/14332-bb.pdb

Chain information for 14332-bb.pdb #17  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/14794-bb.pdb

Chain information for 14794-bb.pdb #18  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/14839-bb.pdb

Chain information for 14839-bb.pdb #19  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/14984-bb.pdb

Chain information for 14984-bb.pdb #20  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/15300-bb.pdb

Chain information for 15300-bb.pdb #21  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/15381-bb.pdb

Chain information for 15381-bb.pdb #22  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/15501-bb.pdb

Chain information for 15501-bb.pdb #23  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/15547-bb.pdb

Chain information for 15547-bb.pdb #24  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/15628-bb.pdb

Chain information for 15628-bb.pdb #25  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/15712-bb.pdb

Chain information for 15712-bb.pdb #26  
---  
Chain | Description  
$ | No description available  
  

> color ~#1 & :1-8 gray(80%)

> color ~#1 & :9-114 gray(20%)

> color ~#1 & :90-110 red

> color ~#1 & :115-163 gray(70%)

> color ~#1 & :164-180 magenta

> cartoon style thickness 0.6

> view matrix camera
> -0.8215,0.27347,0.50035,427.78,-0.51228,0.031354,-0.85823,-306.19,-0.25039,-0.96137,0.11434,283.22

> hide /6 surfaces

> hide /7 surfaces

> hide /8 surfaces

> hide /9 surfaces

> hide /H surfaces

> hide /7

> clip near 20

> clip near -5

> clip near -5

> clip near 3

> clip near 1

> clip near 1

> clip near 1

> clip near -.5

> graphics silhouettes true

> save /Users/chris/Desktop/test7.png supersample 3 transparentBackground true
> pixelSize 0.2

> graphics silhouettes false

> save /Users/chris/Desktop/test7.png supersample 3 transparentBackground true
> pixelSize 0.2

> save /Users/chris/Desktop/test7.png supersample 3 transparentBackground true
> pixelSize 0.1

> save /Users/chris/Desktop/test7.png supersample 3 pixelSize 0.1

> save /Users/chris/Desktop/test7.png supersample 2 pixelSize 0.1

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> save /Users/chris/Desktop/test7.png supersample 2 pixelSize 0.1

> save /Users/chris/Desktop/test7.png supersample 4 pixelSize 0.1

> save /Users/chris/Desktop/test7.png supersample 1 pixelSize 0.1

> save /Users/chris/Desktop/test7.png pixelSize 0.1

> graphics quality 2

> save /Users/chris/Desktop/test7.png pixelSize 0.1

> ui tool show "Side View"

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> close #3

> close #1

> close

> open "/Users/chris/Library/Containers/com.apple.mail/Data/Library/Mail
> Downloads/A657E53C-D5B5-47FE-9768-1A5B36DCA455/ribosome_31_cor_new_large.pdb"
> format pdb

Chain information for ribosome_31_cor_new_large.pdb #1  
---  
Chain | Description  
0 | No description available  
1 | No description available  
3 | No description available  
6 7 8 9 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
s | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> hide atoms

> show surfaces

> lighting soft

> set bgColor white

> graphics silhouettes

Current silhouette settings:  
enabled: True  
width: 2  
color: 0,0,0  
depth jump: 0.03  

> color /1 gray(90%)

> color /3 gray(90%)

> color /A gray(50%)

> color /B gray(50%)

> color /C gray(70%)

> color /D gray(70%)

> color /E gray(70%)

> color /F gray(50%)

> color /G gray(70%)

> color /I gray(70%)

> color /J gray(70%)

> color /K gray(70%)

> color /L gray(50%)

> color /M gray(70%)

> color /N gray(70%)

> color /0 gray(50%)

> color /O gray(50%)

> color /P gray(50%)

> color /Q gray(50%)

> color /R gray(70%)

> color /S gray(70%)

> color /T gray(50%)

> color /U gray(50%)

> color /V gray(50%)

> color /W gray(70%)

> color /X gray(50%)

> color /x gray(70%)

> color /Y gray(70%)

> color /Z gray(50%)

> color /w gray(50%)

> color /y gray(50%)

> color /z gray(50%)

> surface /0 resolution 8

1 Gaussian surfaces, threshold level 0.076  

> surface /1 resolution 8

1 Gaussian surfaces, threshold level 0.104  

> surface /3 resolution 8

1 Gaussian surfaces, threshold level 0.111  

> surface /6 resolution 8

1 Gaussian surfaces, threshold level 0.075  

> surface /7 resolution 8

1 Gaussian surfaces, threshold level 0.074  

> surface /8 resolution 8

1 Gaussian surfaces, threshold level 0.074  

> surface /9 resolution 8

1 Gaussian surfaces, threshold level 0.075  

> surface /Z resolution 8

1 Gaussian surfaces, threshold level 0.080  

> surface /Y resolution 8

1 Gaussian surfaces, threshold level 0.076  

> surface /A resolution 8

1 Gaussian surfaces, threshold level 0.074  

> surface /B resolution 8

1 Gaussian surfaces, threshold level 0.074  

> surface /C resolution 8

1 Gaussian surfaces, threshold level 0.076  

> surface /D resolution 8

1 Gaussian surfaces, threshold level 0.077  

> surface /E resolution 8

1 Gaussian surfaces, threshold level 0.076  

> surface /F resolution 8

1 Gaussian surfaces, threshold level 0.076  

> surface /G resolution 8

1 Gaussian surfaces, threshold level 0.075  

> surface /H resolution 8

1 Gaussian surfaces, threshold level 0.075  

> surface /I resolution 8

1 Gaussian surfaces, threshold level 0.075  

> surface /J resolution 8

1 Gaussian surfaces, threshold level 0.076  

> surface /K resolution 8

1 Gaussian surfaces, threshold level 0.076  

> surface /L resolution 8

1 Gaussian surfaces, threshold level 0.075  

> surface /M resolution 8

1 Gaussian surfaces, threshold level 0.078  

> surface /N resolution 8

1 Gaussian surfaces, threshold level 0.077  

> surface /O resolution 8

1 Gaussian surfaces, threshold level 0.074  

> surface /P resolution 8

1 Gaussian surfaces, threshold level 0.079  

> surface /Q resolution 8

1 Gaussian surfaces, threshold level 0.076  

> surface /R resolution 8

1 Gaussian surfaces, threshold level 0.077  

> surface /S resolution 8

1 Gaussian surfaces, threshold level 0.075  

> surface /T resolution 8

1 Gaussian surfaces, threshold level 0.075  

> surface /U resolution 8

1 Gaussian surfaces, threshold level 0.075  

> surface /V resolution 8

1 Gaussian surfaces, threshold level 0.074  

> surface /W resolution 8

1 Gaussian surfaces, threshold level 0.076  

> surface /X resolution 8

1 Gaussian surfaces, threshold level 0.076  

> surface /s resolution 8

1 Gaussian surfaces, threshold level 0.075  

> surface /w resolution 8

1 Gaussian surfaces, threshold level 0.078  

> surface /x resolution 8

1 Gaussian surfaces, threshold level 0.075  

> surface /y resolution 8

1 Gaussian surfaces, threshold level 0.075  

> surface /z resolution 8

1 Gaussian surfaces, threshold level 0.075  

> hide /6 surfaces

> hide /7 surfaces

> hide /8 surfaces

> hide /9 surfaces

> hide /H surfaces

> color /1 gray(90%)

> color /3 gray(90%)

> color /A gray(50%)

> color /B gray(50%)

> color /C gray(70%)

> color /D gray(70%)

> color /E gray(70%)

> color /F gray(50%)

> color /G gray(70%)

> color /I gray(70%)

> color /J gray(70%)

> color /K gray(70%)

> color /L gray(50%)

> color /M gray(70%)

> color /N gray(70%)

> color /0 gray(50%)

> color /O gray(50%)

> color /P gray(50%)

> color /Q gray(50%)

> color /R gray(70%)

> color /S gray(70%)

> color /T gray(50%)

> color /U gray(50%)

> color /V gray(50%)

> color /W gray(70%)

> color /X gray(50%)

> color /x gray(70%)

> color /Y gray(70%)

> color /Z gray(50%)

> color /w gray(50%)

> color /y gray(50%)

> color /z gray(50%)

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/1040-bb.pdb

Chain information for 1040-bb.pdb #2  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/1062-bb.pdb

Chain information for 1062-bb.pdb #3  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/1325-bb.pdb

Chain information for 1325-bb.pdb #4  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/10089-bb.pdb

Chain information for 10089-bb.pdb #5  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/10126-bb.pdb

Chain information for 10126-bb.pdb #6  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/10566-bb.pdb

Chain information for 10566-bb.pdb #7  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/10670-bb.pdb

Chain information for 10670-bb.pdb #8  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/10829-bb.pdb

Chain information for 10829-bb.pdb #9  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/11058-bb.pdb

Chain information for 11058-bb.pdb #10  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/11324-bb.pdb

Chain information for 11324-bb.pdb #11  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/12437-bb.pdb

Chain information for 12437-bb.pdb #12  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/12490-bb.pdb

Chain information for 12490-bb.pdb #13  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/13748-bb.pdb

Chain information for 13748-bb.pdb #14  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/13814-bb.pdb

Chain information for 13814-bb.pdb #15  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/13913-bb.pdb

Chain information for 13913-bb.pdb #16  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/14332-bb.pdb

Chain information for 14332-bb.pdb #17  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/14794-bb.pdb

Chain information for 14794-bb.pdb #18  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/14839-bb.pdb

Chain information for 14839-bb.pdb #19  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/14984-bb.pdb

Chain information for 14984-bb.pdb #20  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/15300-bb.pdb

Chain information for 15300-bb.pdb #21  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/15381-bb.pdb

Chain information for 15381-bb.pdb #22  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/15501-bb.pdb

Chain information for 15501-bb.pdb #23  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/15547-bb.pdb

Chain information for 15547-bb.pdb #24  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/15628-bb.pdb

Chain information for 15628-bb.pdb #25  
---  
Chain | Description  
$ | No description available  
  

> open /Users/chris/Documents/Work/rnc-relaxation/tomek-
> binding/structures-67/selected/15712-bb.pdb

Chain information for 15712-bb.pdb #26  
---  
Chain | Description  
$ | No description available  
  

> color ~#1 & :1-8 gray(80%)

> color ~#1 & :9-114 gray(20%)

> color ~#1 & :90-110 red

> color ~#1 & :115-163 gray(70%)

> color ~#1 & :164-180 magenta

> cartoon style thickness 0.6

> view matrix camera
> -0.8215,0.27347,0.50035,427.78,-0.51228,0.031354,-0.85823,-306.19,-0.25039,-0.96137,0.11434,283.22

> clip near 20

> clip near 10

> clip near -20

> clip near -5

> clip near -5

> clip near .2

> clip near -.4

> clip near -.2

> clip near -.1

> clip near +.1

> clip near -.1

> clip near +.1

> clip near +.1

> save /Users/chris/Desktop/test7.png pixelSize 0.1

> set bgColor white

> set bgColor gray

> set bgColor gray

> set bgColor gray

> set bgColor white

> set bgColor white

> set bgColor black

> set bgColor white

> set bgColor white

> set bgColor gray

> set bgColor white

> save /Users/chris/Desktop/test7.png pixelSize 0.1

> ui tool show "Side View"

> help help:user/preferences.html#clipping

> ui tool show "Side View"

> hide atoms

> save /Users/chris/Desktop/test7.png

> save /Users/chris/Desktop/test7.tif

> help help:contact.html

Populating font family aliases took 930 ms. Replace uses of missing font
family "-apple-system" with one that exists to avoid this cost.  




OpenGL version: 4.1 INTEL-16.2.16
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,2
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 512 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 1554.100.64.0.0 (iBridge: 18.16.14556.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 11.3.1 (20E241)
      Kernel Version: Darwin 20.4.0
      Time since boot: 1 day 13:35

Graphics/Displays:

    Intel Iris Plus Graphics:

      Chipset Model: Intel Iris Plus Graphics
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x8a53
      Revision ID: 0x0007
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        HP 24fw:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 75.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 3CM0240P3C   
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Adapter Type: DVI or HDMI
          Automatically Adjust Brightness: Yes
          Adapter Firmware Version: ff.c1

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.4.1
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.3
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.2
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.2
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.4
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.7
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 1.1.1
    matplotlib: 3.3.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0

Change History (4)

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Boxy silhouettes in saved images

Reported by Chris Waudby

comment:2 by Tom Goddard, 4 years ago

The silhouette noise has been reported twice before #4541 (​https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/4541) and #4273. All reports have been on the exact same model MacBookPro16,2 using macOS Big Sur and the problem does not occur on other Mac computers I tested on. It appears to be a graphics driver bug only seen on this exact model of Mac laptop. In the previous report the user did extensive testing for me but I could not figure out any way to work around the graphics driver bug. Probably if I had this exact model of Mac laptop I could figure out how to work around the driver bug -- but without directly testing on such a machine I have no way to debug it.

Sorry I have no solution. Apple has no interest in improving the cross-platform OpenGL graphics driver since they use their own proprietary Metal graphics library. The even deprecated OpenGL a few years ago. So I would not expect Apple to ever fix this in a macOS update.

My only recommendation if you need silhouettes in images is to save a ChimeraX session on the Mac, then copy it to a different machine (Mac, Windows, or Linux) and make the images on the machine with working graphics.

in reply to:  3 ; comment:3 by c.waudby@…, 4 years ago 

Hi Tom,

Thanks for the quick response. That’s pretty extraordinary, but I’ll give that a go tomorrow and hopefully a colleague will be able to help me out! It’s doubly frustrating as I just need to re-create a figure I made on my old laptop in response to some reviewer comments :)

Best,

Chris

in reply to:  4 ; comment:4 by goddard@…, 4 years ago 

Just tested on another Mac for silhouette noise on a new Mac Mini (model Macmini9,1) with Apple M1 processor.  Silhouettes are correct including when image saved.  Not surprising.
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