silhouettes → tiny boxes

[xin_gu@…]

The following bug report has been submitted:
Platform:        macOS-14.2.1-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Hi! Thank you so much for your help in advance. I have been having this issue with my chimeraX displaying my cryoEM data. It's strange that whenever I open a density map, if I opaque it, there are a many broken little pieces (look like display artefects) on the map. Also with models, when I export, sometimes I will also see weird looking shapes near the edge of models. Are there ways to solve this? I tried to delete and then reinstall newer version of ChimeraX, it didn't help... Thank you!

Log:
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/xingu/Dropbox (HMS)/Midnolin proteasome structural
> paper/ChimeraX/Sessions/CryoEM/AAA_Density_PSMD14_Distances.cxs" format
> session

Opened j1332_highRes_resampled.mrc as #5, grid size 440,440,440, pixel 0.825,
shown at level 0.14, step 2, values float32  
Opened J268_highres_resampled.mrc as #6, grid size 440,440,440, pixel 0.825,
shown at level 0.14, step 2, values float32  
Opened J1144_deephighRes.mrc as #7, grid size 440,440,440, pixel 0.825, shown
at level 0.14, step 2, values float32  
Opened J1146_deephighRes.mrc as #8, grid size 440,440,440, pixel 0.825, shown
at level 0.14, step 2, values float32  
Log from Thu Jan 11 22:17:31 2024UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open "/Users/Chris/Desktop/Most Recent Models from Susan 010324/All Models
> Colored.cxs"

Opened j1332_highRes_resampled.mrc as #5, grid size 440,440,440, pixel 0.825,
shown at level 0.14, step 2, values float32  
Opened J268_highres_resampled.mrc as #6, grid size 440,440,440, pixel 0.825,
shown at level 0.14, step 2, values float32  
Opened J1144_deephighRes.mrc as #7, grid size 440,440,440, pixel 0.825, shown
at level 0.14, step 2, values float32  
Opened J1146_deephighRes.mrc as #8, grid size 440,440,440, pixel 0.825, shown
at level 0.14, step 2, values float32  
Log from Mon Jan 8 16:16:33 2024UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open "/Users/Chris/Desktop/Most Recent Models from Susan 010324/All Models
> Colored.cxs"

Opened j1332_highRes_resampled.mrc as #5, grid size 440,440,440, pixel 0.825,
shown at level 0.14, step 2, values float32  
Opened J268_highres_resampled.mrc as #6, grid size 440,440,440, pixel 0.825,
shown at level 0.14, step 2, values float32  
Opened J1144_deephighRes.mrc as #7, grid size 440,440,440, pixel 0.825, shown
at level 0.14, step 2, values float32  
Log from Sat Jan 6 18:38:43 2024UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open "/Users/Chris/Desktop/Most Recent Models from Susan 010324/All Atomic
> Models Colored.cxs"

Log from Sat Jan 6 18:11:44 2024UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/Chris/Desktop/Most Recent Models from Susan
> 010324/MINDUbl_j1332_231230.pdb"

Chain information for MINDUbl_j1332_231230.pdb #1  
---  
Chain | Description  
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  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | 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  
y | No description available  
z | No description available  
  

> open "/Users/Chris/Desktop/Most Recent Models from Susan
> 010324/conf2_j268_noZFAND4_240103.pdb"

Chain information for conf2_j268_noZFAND4_240103.pdb #2  
---  
Chain | Description  
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  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | 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  
y | No description available  
  

> open "/Users/Chris/Desktop/Most Recent Models from Susan
> 010324/conf1B_j1146_231114.pdb"

Chain information for conf1B_j1146_231114.pdb #3  
---  
Chain | Description  
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  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | 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  
y | No description available  
  

> open "/Users/Chris/Desktop/Most Recent Models from Susan
> 010324/conf1A_j1144_231114.pdb"

Chain information for conf1A_j1144_231114.pdb #4  
---  
Chain | Description  
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  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | 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  
y | No description available  
  

> hide #!1 models

> hide #!3 models

> hide #!4 models

> hide #!2 models

> show #!2 models

> show #!1 models

> hide #!2 models

> show #!3 models

> show #!4 models

> show #!2 models

> show cartoons

> hide atoms

> set bgColor white

> graphics silhouettes true

> lighting soft

[Repeated 1 time(s)]

> select A

Expected an objects specifier or a keyword  

> select #4/y:380-410

273 atoms, 272 bonds, 31 residues, 1 model selected  

> select #4/y:380-410

273 atoms, 272 bonds, 31 residues, 1 model selected  

> select clear

> select /y

1698 atoms, 1702 bonds, 1 pseudobond, 204 residues, 5 models selected  

> ui tool show "Color Actions"

> color sel light coral

> select /A

12413 atoms, 12613 bonds, 3 pseudobonds, 1571 residues, 6 models selected  

> select /n

5368 atoms, 5433 bonds, 11 pseudobonds, 720 residues, 8 models selected  

> delete atoms (#!1-4 & sel)

> delete bonds (#!1-4 & sel)

> select /o

5260 atoms, 5324 bonds, 16 pseudobonds, 704 residues, 8 models selected  

> delete atoms (#!1-4 & sel)

> delete bonds (#!1-4 & sel)

> select /p

5063 atoms, 5135 bonds, 20 pseudobonds, 657 residues, 8 models selected  

> delete atoms (#!1-4 & sel)

> delete bonds (#!1-4 & sel)

> select /q

5520 atoms, 5620 bonds, 16 pseudobonds, 692 residues, 8 models selected  

> delete atoms (#!1-4 & sel)

> delete bonds (#!1-4 & sel)

> select /r

5728 atoms, 5840 bonds, 8 pseudobonds, 748 residues, 8 models selected  

> delete atoms (#!1-4 & sel)

> delete bonds (#!1-4 & sel)

> select /s

6388 atoms, 6500 bonds, 4 pseudobonds, 824 residues, 8 models selected  

> delete atoms (#!1-4 & sel)

> delete bonds (#!1-4 & sel)

> select /t

6436 atoms, 6556 bonds, 4 pseudobonds, 824 residues, 8 models selected  

> delete atoms (#!1-4 & sel)

> delete bonds (#!1-4 & sel)

> select /A

12413 atoms, 12613 bonds, 3 pseudobonds, 1571 residues, 6 models selected  

> color sel light sky blue

> select /B

12092 atoms, 12266 bonds, 4 pseudobonds, 1528 residues, 6 models selected  

> color sel light sky blue

> select /C

11796 atoms, 11953 bonds, 3 pseudobonds, 1490 residues, 6 models selected  

> color sel light sky blue

> select /D

12140 atoms, 12341 bonds, 3 pseudobonds, 1509 residues, 7 models selected  

> color sel light sky blue

> select /E

10566 atoms, 10710 bonds, 15 pseudobonds, 1325 residues, 7 models selected  

> color sel light sky blue

> select /F

11233 atoms, 11387 bonds, 7 pseudobonds, 1429 residues, 8 models selected  

> color sel light sky blue

> select /G

7471 atoms, 7607 bonds, 954 residues, 4 models selected  

> color sel white smoke

> select /H

7185 atoms, 7339 bonds, 921 residues, 4 models selected  

> color sel white smoke

> select /I

8085 atoms, 8205 bonds, 1022 residues, 4 models selected  

> color sel white smoke

> select /J

7548 atoms, 7652 bonds, 956 residues, 4 models selected  

> color sel white smoke

> select /K

7059 atoms, 7161 bonds, 4 pseudobonds, 921 residues, 8 models selected  

> color sel white smoke

> select /L

7472 atoms, 7608 bonds, 948 residues, 4 models selected  

> color sel white smoke

> select /M

7654 atoms, 7794 bonds, 975 residues, 4 models selected  

> color sel white smoke

> select /N

5948 atoms, 6052 bonds, 792 residues, 4 models selected  

> color sel silver

> select /n

Nothing selected  

> select /N

5948 atoms, 6052 bonds, 792 residues, 4 models selected  

> color sel silver

> select /O

6668 atoms, 6776 bonds, 884 residues, 4 models selected  

> color sel silver

> select /P

6364 atoms, 6480 bonds, 816 residues, 4 models selected  

> color sel silver

> select /Q

6312 atoms, 6444 bonds, 788 residues, 4 models selected  

> color sel silver

> select /R

6196 atoms, 6320 bonds, 796 residues, 4 models selected  

> color sel silver

> select /S

6572 atoms, 6692 bonds, 848 residues, 4 models selected  

> color sel silver

> select /T

6660 atoms, 6792 bonds, 852 residues, 4 models selected  

> color sel silver

> select /U

26004 atoms, 26457 bonds, 12 pseudobonds, 3334 residues, 8 models selected  

> color sel lavender

> select /V

14097 atoms, 14367 bonds, 2 pseudobonds, 1731 residues, 6 models selected  

> color sel lemon chiffon

> select /W

14198 atoms, 14385 bonds, 2 pseudobonds, 1742 residues, 6 models selected  

> color sel lemon chiffon

> select /X

13172 atoms, 13354 bonds, 2 pseudobonds, 1668 residues, 6 models selected  

> color sel lemon chiffon

> select /Y

12504 atoms, 12736 bonds, 1518 residues, 4 models selected  

> color sel lemon chiffon

> select /Z

9160 atoms, 9332 bonds, 1148 residues, 4 models selected  

> color sel lemon chiffon

> select /a

12048 atoms, 12280 bonds, 1500 residues, 4 models selected  

> color sel lemon chiffon

> select /b

5836 atoms, 5916 bonds, 764 residues, 4 models selected  

> color sel thistle

> select /c

8890 atoms, 9054 bonds, 6 pseudobonds, 1130 residues, 8 models selected  

> color sel dark sea green

> select /d

8453 atoms, 8625 bonds, 6 pseudobonds, 1039 residues, 8 models selected  

> color sel lemon chiffon

> select /e

1287 atoms, 1321 bonds, 4 pseudobonds, 147 residues, 8 models selected  

> color sel lemon chiffon

> select /f

24186 atoms, 24598 bonds, 8 pseudobonds, 3132 residues, 8 models selected  

> color sel light cyan

> select /g

Nothing selected  

> select /y

1698 atoms, 1702 bonds, 1 pseudobond, 204 residues, 5 models selected  

> color sel light coral

> select /z

471 atoms, 481 bonds, 59 residues, 1 model selected  

> color sel tan

> select clear

> save "/Users/Chris/Desktop/Most Recent Models from Susan 010324/All Atomic
> Models Colored.cxs"

——— End of log from Sat Jan 6 18:11:44 2024 ———

opened ChimeraX session  

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!1 models

> show #!4 models

> show #!1 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> hide #!1 models

> open "/Users/Chris/Desktop/Most Recent Models from Susan
> 010324/UblC_j1332/j1332_highRes_resampled.mrc"

Opened j1332_highRes_resampled.mrc as #5, grid size 440,440,440, pixel 0.825,
shown at level 0.13, step 2, values float32  

> open "/Users/Chris/Desktop/Most Recent Models from Susan
> 010324/Conf2_j268/J268_highres_resampled.mrc"

Opened J268_highres_resampled.mrc as #6, grid size 440,440,440, pixel 0.825,
shown at level 0.127, step 2, values float32  

> open "/Users/Chris/Desktop/Most Recent Models from Susan
> 010324/Conf1A_j1144/J1144_deephighRes.mrc"

Opened J1144_deephighRes.mrc as #7, grid size 440,440,440, pixel 0.825, shown
at level 0.115, step 2, values float32  

> hide #!6 models

> hide #!7 models

> show #!1 models

> volume #7 level 0.14

> volume #6 level 0.14

> volume #5 level 0.14

> color zone #5 near #1 distance 4.95

> surface dust #5 size 8.25

> volume zone #5 nearAtoms #1 range 4.95

> hide #!5 models

> hide #!1 models

> show #!6 models

> show #!2 models

> color zone #6 near #2 distance 4.95

> surface dust #6 size 8.25

> volume zone #6 nearAtoms #2 range 4.95

> hide #!2 models

> hide #!6 models

> show #!7 models

> show #!4 models

> color zone #7 near #4 distance 4.95

> surface dust #7 size 8.25

> volume zone #7 nearAtoms #4 range 4.95

> hide #!4 models

> show #!5 models

> hide #!7 models

> hide #!5 models

> show #!5 models

> show #!7 models

> hide #!5 models

> select clear

> show #!5 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!5 models

> show #!5 models

> hide #!7 models

> show #!7 models

> hide #!5 models

> show #!5 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!7 models

> show #!7 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> hide #!7 models

> show #!7 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!7 models

> hide #!5 models

> show #!7 models

> hide #!7 models

> show #!5 models

> hide #!5 models

> show #!7 models

> show #!5 models

> hide #!7 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> show #!7 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> hide #!5 models

> show #!4 models

> show #!1 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> save "/Users/Chris/Desktop/Most Recent Models from Susan 010324/All Models
> Colored.cxs"

——— End of log from Sat Jan 6 18:38:43 2024 ———

opened ChimeraX session  

> open "/Users/Chris/Desktop/Most Recent Models from Susan
> 010324/Conf1B_j1146/J1146_deephighRes.mrc"

Opened J1146_deephighRes.mrc as #8, grid size 440,440,440, pixel 0.825, shown
at level 0.117, step 2, values float32  

> hide #!1 models

> show #!4 models

> show #!3 models

> hide #!4 models

> surface dust #8 size 8.25

> color zone #8 near #3 distance 4.95

> volume zone #8 nearAtoms #3 range 4.95

> hide #!3 models

> show #!7 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!7 models

> volume #8 level 0.14

> volume #8 level 0.08

> volume #8 level 0.4

> volume #8 level 0.08

> volume #8 level 0.04

> volume #8 level 0.3

> volume #8 level 0.2

> volume #8 level 0.14

> show #!7 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!7 models

> show #!7 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!7 models

> show #!7 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!7 models

> save "/Users/Chris/Desktop/Most Recent Models from Susan 010324/All Models
> Colored.cxs"

——— End of log from Mon Jan 8 16:16:33 2024 ———

opened ChimeraX session  

> hide #!8 models

> show #!1 models

> show #!2 models

> show #!3 models

> show #!4 models

> select A/

Expected an objects specifier or a keyword  

> select A /

Expected an objects specifier or a keyword  

> select / A

12413 atoms, 12613 bonds, 3 pseudobonds, 1571 residues, 6 models selected  

> select / H

7185 atoms, 7339 bonds, 921 residues, 4 models selected  

> delete atoms sel

> delete bonds sel

> select / I

8085 atoms, 8205 bonds, 1022 residues, 4 models selected  

> delete atoms sel

> delete bonds sel

> select / J

7548 atoms, 7652 bonds, 956 residues, 4 models selected  

> delete atoms sel

> delete bonds sel

> select / K

7059 atoms, 7161 bonds, 4 pseudobonds, 921 residues, 8 models selected  

> delete atoms (#!1-4 & sel)

> delete bonds (#!1-4 & sel)

> select / L

7472 atoms, 7608 bonds, 948 residues, 4 models selected  

> delete atoms sel

> delete bonds sel

> select / M

7654 atoms, 7794 bonds, 975 residues, 4 models selected  

> delete atoms sel

> delete bonds sel

> select / N

5948 atoms, 6052 bonds, 792 residues, 4 models selected  

> delete atoms sel

> delete bonds sel

> select / O

6668 atoms, 6776 bonds, 884 residues, 4 models selected  

> delete atoms sel

> delete bonds sel

> select / P

6364 atoms, 6480 bonds, 816 residues, 4 models selected  

> delete atoms sel

> delete bonds sel

> select / Q

6312 atoms, 6444 bonds, 788 residues, 4 models selected  

> delete atoms sel

> delete bonds sel

> select / R

6196 atoms, 6320 bonds, 796 residues, 4 models selected  

> delete atoms sel

> delete bonds sel

> select / S

6572 atoms, 6692 bonds, 848 residues, 4 models selected  

> delete atoms sel

> delete bonds sel

> select / T

6660 atoms, 6792 bonds, 852 residues, 4 models selected  

> delete atoms sel

> delete bonds sel

> select / U

26004 atoms, 26457 bonds, 12 pseudobonds, 3334 residues, 8 models selected  

> delete atoms (#!1-4 & sel)

> delete bonds (#!1-4 & sel)

> select / V

14097 atoms, 14367 bonds, 2 pseudobonds, 1731 residues, 6 models selected  

> delete atoms (#!1-4 & sel)

> delete bonds (#!1-4 & sel)

> select / W

14198 atoms, 14385 bonds, 2 pseudobonds, 1742 residues, 6 models selected  

> delete atoms (#!1-4 & sel)

> delete bonds (#!1-4 & sel)

> select / X

13172 atoms, 13354 bonds, 2 pseudobonds, 1668 residues, 6 models selected  

> delete atoms (#!1-4 & sel)

> delete bonds (#!1-4 & sel)

> select / Y

12504 atoms, 12736 bonds, 1518 residues, 4 models selected  

> delete atoms sel

> delete bonds sel

> select / Z

9160 atoms, 9332 bonds, 1148 residues, 4 models selected  

> delete atoms sel

> delete bonds sel

> select / a

12048 atoms, 12280 bonds, 1500 residues, 4 models selected  

> delete atoms sel

> delete bonds sel

> select / b

5836 atoms, 5916 bonds, 764 residues, 4 models selected  

> delete atoms sel

> delete bonds sel

> select / d

8453 atoms, 8625 bonds, 6 pseudobonds, 1039 residues, 8 models selected  

> delete atoms (#!1-4 & sel)

> delete bonds (#!1-4 & sel)

> select / e

1287 atoms, 1321 bonds, 4 pseudobonds, 147 residues, 8 models selected  

> delete atoms (#!1-4 & sel)

> delete bonds (#!1-4 & sel)

> select / f

24186 atoms, 24598 bonds, 8 pseudobonds, 3132 residues, 8 models selected  

> delete atoms (#!1-4 & sel)

> delete bonds (#!1-4 & sel)

> select / g

Nothing selected  

> select / G

7471 atoms, 7607 bonds, 954 residues, 4 models selected  

> delete atoms sel

> delete bonds sel

> select / z

471 atoms, 481 bonds, 59 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select / y

1698 atoms, 1702 bonds, 1 pseudobond, 204 residues, 5 models selected  

> delete atoms (#!1-4 & sel)

> delete bonds (#!1-4 & sel)

> hide #!3 models

> hide #!2 models

> select clear

> save "/Users/Chris/Desktop/Most Recent Models from Susan
> 010324/AAA_Density_PSMD14_Distances.cxs"

——— End of log from Thu Jan 11 22:17:31 2024 ———

opened ChimeraX session  

> hide #!1 models

> show #!8 models

> volume #8 color #b2b2b26d




OpenGL version: 4.1 INTEL-22.1.29
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
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: 2020.61.1.0.0 (iBridge: 21.16.2057.0.0,0)
      OS Loader Version: 580~1053

Software:

    System Software Overview:

      System Version: macOS 14.2.1 (23C71)
      Kernel Version: Darwin 23.2.0
      Time since boot: 37 days, 23 hours, 39 minutes

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 Support: Metal 3
      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


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9
File attachment: Screenshot 2024-02-22 at 1.58.06 PM.png

Screenshot 2024-02-22 at 1.58.06 PM.png​

[xin_gu@…]

Added by email2trac

[pett]

Hi Xin,

Thanks for reporting this problem. It is a known problem with the graphics of that particular Mac model. The only "solutions" are to not use silhouettes or use another Mac. Sorry!

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

info from previous tickets:

The incorrect silhouette edge display in ChimeraX is caused by defective Apple Intel graphics driver in your specific laptop model MacBookPro16,2. It has been reported many times. Only Apple could fix that. They won't fix it because they've replaced Intel graphics with their Apple Silicon chips. Sorry I have no solution, other than use a different computer, or just don't use silhouette edges.

Here are details from the previous report ticket #5129:

Several people have reported this bug, tickets #4768, #4628, #4541, #4273. All reports are on the exact same MacBookPro16,2 model with Intel graphics. It appears to be a bug in the Mac OpenGL graphics driver that effects only this one model of Mac. Unfortunately Apple has no interest in improving their graphics drivers for the community standard OpenGL library, they deprecated OpenGL a few years ago when Mac switched to their proprietary Metal graphics. Only Apple can fix this. In working many hours with previous reporters we did not find any way to work around the graphics driver bug. Sorry to say but the only solution to get functioning ChimeraX graphics is to use a different computer. Another option is to use our older Chimera program which uses a much older generation OpenGL and does not seem to have this problem.

I believe this problem was only observed in past reports when silhouette edges were being used. If that is the case for you the best solution is to not use silhouettes.