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#7905 closed defect (limitation)
Bus Error computing surface of 2cse biological assembly
| Reported by: | Eric Pettersen | Owned by: | Tom Goddard |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Surface | Version: | |
| Keywords: | Cc: | kristen.browne@…, michal.stolarczyk@…, phil.cruz@… | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-12.3.1-arm64-arm-64bit
ChimeraX Version: 1.6.dev202210202104 (2022-10-20 21:04:43 UTC)
Description
Last time you used ChimeraX it crashed.
"time surface #1 enclose #1" on biological assembly of 2cse
Fatal Python error: Bus error
Current thread 0x000000010416c580 (most recent call first):
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/surface/gridsurf.py", line 86 in ses_surface_geometry
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/molsurf.py", line 235 in calculate_surface_geometry
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/surface/surfacecmds.py", line 195 in _calculate_surface
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/threadq.py", line 47 in
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/threadq.py", line 47 in apply_to_list
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/surface/surfacecmds.py", line 162 in surface
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 38 in run
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/std_commands/time.py", line 19 in time
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 319 in execute
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 284 in event_loop
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 888 in init
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1039 in
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
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===== Log before crash start =====
UCSF ChimeraX version: 1.6.dev202210202104 (2022-10-20)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/pett/Downloads/2cse-assembly1.cif format mmcif
2cse-assembly1.cif title:
Features of Reovirus Outer-Capsid Protein mu1 Revealed by Electron and Image
Reconstruction of the virion at 7.0-A Resolution [more info...]
Chain information for 2cse-assembly1.cif #1
---
Chain | Description
1 1-10 1-11 1-12 1-13 1-14 1-15 1-16 1-17 1-18 1-19 1-2 1-20 1-21 1-22 1-23
1-24 1-25 1-26 1-27 1-28 1-29 1-3 1-30 1-31 1-32 1-33 1-34 1-35 1-36 1-37 1-38
1-39 1-4 1-40 1-41 1-42 1-43 1-44 1-45 1-46 1-47 1-48 1-49 1-5 1-50 1-51 1-52
1-53 1-54 1-55 1-56 1-57 1-58 1-59 1-6 1-60 1-7 1-8 1-9 | Minor core protein
lambda 3
A A-10 A-11 A-12 A-13 A-14 A-15 A-16 A-17 A-18 A-19 A-2 A-20 A-21 A-22 A-23
A-24 A-25 A-26 A-27 A-28 A-29 A-3 A-30 A-31 A-32 A-33 A-34 A-35 A-36 A-37 A-38
A-39 A-4 A-40 A-41 A-42 A-43 A-44 A-45 A-46 A-47 A-48 A-49 A-5 A-50 A-51 A-52
A-53 A-54 A-55 A-56 A-57 A-58 A-59 A-6 A-60 A-7 A-8 A-9 B B-10 B-11 B-12 B-13
B-14 B-15 B-16 B-17 B-18 B-19 B-2 B-20 B-21 B-22 B-23 B-24 B-25 B-26 B-27 B-28
B-29 B-3 B-30 B-31 B-32 B-33 B-34 B-35 B-36 B-37 B-38 B-39 B-4 B-40 B-41 B-42
B-43 B-44 B-45 B-46 B-47 B-48 B-49 B-5 B-50 B-51 B-52 B-53 B-54 B-55 B-56 B-57
B-58 B-59 B-6 B-60 B-7 B-8 B-9 C C-10 C-11 C-12 C-13 C-14 C-15 C-16 C-17 C-18
C-19 C-2 C-20 C-21 C-22 C-23 C-24 C-25 C-26 C-27 C-28 C-29 C-3 C-30 C-31 C-32
C-33 C-34 C-35 C-36 C-37 C-38 C-39 C-4 C-40 C-41 C-42 C-43 C-44 C-45 C-46 C-47
C-48 C-49 C-5 C-50 C-51 C-52 C-53 C-54 C-55 C-56 C-57 C-58 C-59 C-6 C-60 C-7
C-8 C-9 J J-10 J-11 J-12 J-13 J-14 J-15 J-16 J-17 J-18 J-19 J-2 J-20 J-21 J-22
J-23 J-24 J-25 J-26 J-27 J-28 J-29 J-3 J-30 J-31 J-32 J-33 J-34 J-35 J-36 J-37
J-38 J-39 J-4 J-40 J-41 J-42 J-43 J-44 J-45 J-46 J-47 J-48 J-49 J-5 J-50 J-51
J-52 J-53 J-54 J-55 J-56 J-57 J-58 J-59 J-6 J-60 J-7 J-8 J-9 K K-10 K-11 K-12
K-13 K-14 K-15 K-16 K-17 K-18 K-19 K-2 K-20 K-21 K-22 K-23 K-24 K-25 K-26 K-27
K-28 K-29 K-3 K-30 K-31 K-32 K-33 K-34 K-35 K-36 K-37 K-38 K-39 K-4 K-40 K-41
K-42 K-43 K-44 K-45 K-46 K-47 K-48 K-49 K-5 K-50 K-51 K-52 K-53 K-54 K-55 K-56
K-57 K-58 K-59 K-6 K-60 K-7 K-8 K-9 L L-10 L-11 L-12 L-13 L-14 L-15 L-16 L-17
L-18 L-19 L-2 L-20 L-21 L-22 L-23 L-24 L-25 L-26 L-27 L-28 L-29 L-3 L-30 L-31
L-32 L-33 L-34 L-35 L-36 L-37 L-38 L-39 L-4 L-40 L-41 L-42 L-43 L-44 L-45 L-46
L-47 L-48 L-49 L-5 L-50 L-51 L-52 L-53 L-54 L-55 L-56 L-57 L-58 L-59 L-6 L-60
L-7 L-8 L-9 P P-10 P-11 P-12 P-13 P-14 P-15 P-16 P-17 P-18 P-19 P-2 P-20 P-21
P-22 P-23 P-24 P-25 P-26 P-27 P-28 P-29 P-3 P-30 P-31 P-32 P-33 P-34 P-35 P-36
P-37 P-38 P-39 P-4 P-40 P-41 P-42 P-43 P-44 P-45 P-46 P-47 P-48 P-49 P-5 P-50
P-51 P-52 P-53 P-54 P-55 P-56 P-57 P-58 P-59 P-6 P-60 P-7 P-8 P-9 Q Q-10 Q-11
Q-12 Q-13 Q-14 Q-15 Q-16 Q-17 Q-18 Q-19 Q-2 Q-20 Q-21 Q-22 Q-23 Q-24 Q-25 Q-26
Q-27 Q-28 Q-29 Q-3 Q-30 Q-31 Q-32 Q-33 Q-34 Q-35 Q-36 Q-37 Q-38 Q-39 Q-4 Q-40
Q-41 Q-42 Q-43 Q-44 Q-45 Q-46 Q-47 Q-48 Q-49 Q-5 Q-50 Q-51 Q-52 Q-53 Q-54 Q-55
Q-56 Q-57 Q-58 Q-59 Q-6 Q-60 Q-7 Q-8 Q-9 R R-10 R-11 R-12 R-13 R-14 R-15 R-16
R-17 R-18 R-19 R-2 R-20 R-21 R-22 R-23 R-24 R-25 R-26 R-27 R-28 R-29 R-3 R-30
R-31 R-32 R-33 R-34 R-35 R-36 R-37 R-38 R-39 R-4 R-40 R-41 R-42 R-43 R-44 R-45
R-46 R-47 R-48 R-49 R-5 R-50 R-51 R-52 R-53 R-54 R-55 R-56 R-57 R-58 R-59 R-6
R-60 R-7 R-8 R-9 T T-10 T-11 T-12 T-13 T-14 T-15 T-16 T-17 T-18 T-19 T-2 T-20
T-21 T-22 T-23 T-24 T-25 T-26 T-27 T-28 T-29 T-3 T-30 T-31 T-32 T-33 T-34 T-35
T-36 T-37 T-38 T-39 T-4 T-40 T-41 T-42 T-43 T-44 T-45 T-46 T-47 T-48 T-49 T-5
T-50 T-51 T-52 T-53 T-54 T-55 T-56 T-57 T-58 T-59 T-6 T-60 T-7 T-8 T-9 | major
outer-capsid protein mu1
D D-10 D-11 D-12 D-13 D-14 D-15 D-16 D-17 D-18 D-19 D-2 D-20 D-21 D-22 D-23
D-24 D-25 D-26 D-27 D-28 D-29 D-3 D-30 D-31 D-32 D-33 D-34 D-35 D-36 D-37 D-38
D-39 D-4 D-40 D-41 D-42 D-43 D-44 D-45 D-46 D-47 D-48 D-49 D-5 D-50 D-51 D-52
D-53 D-54 D-55 D-56 D-57 D-58 D-59 D-6 D-60 D-7 D-8 D-9 E E-10 E-11 E-12 E-13
E-14 E-15 E-16 E-17 E-18 E-19 E-2 E-20 E-21 E-22 E-23 E-24 E-25 E-26 E-27 E-28
E-29 E-3 E-30 E-31 E-32 E-33 E-34 E-35 E-36 E-37 E-38 E-39 E-4 E-40 E-41 E-42
E-43 E-44 E-45 E-46 E-47 E-48 E-49 E-5 E-50 E-51 E-52 E-53 E-54 E-55 E-56 E-57
E-58 E-59 E-6 E-60 E-7 E-8 E-9 F F-10 F-11 F-12 F-13 F-14 F-15 F-16 F-17 F-18
F-19 F-2 F-20 F-21 F-22 F-23 F-24 F-25 F-26 F-27 F-28 F-29 F-3 F-30 F-31 F-32
F-33 F-34 F-35 F-36 F-37 F-38 F-39 F-4 F-40 F-41 F-42 F-43 F-44 F-45 F-46 F-47
F-48 F-49 F-5 F-50 F-51 F-52 F-53 F-54 F-55 F-56 F-57 F-58 F-59 F-6 F-60 F-7
F-8 F-9 G G-10 G-11 G-12 G-13 G-14 G-15 G-16 G-17 G-18 G-19 G-2 G-20 G-21 G-22
G-23 G-24 G-25 G-26 G-27 G-28 G-29 G-3 G-30 G-31 G-32 G-33 G-34 G-35 G-36 G-37
G-38 G-39 G-4 G-40 G-41 G-42 G-43 G-44 G-45 G-46 G-47 G-48 G-49 G-5 G-50 G-51
G-52 G-53 G-54 G-55 G-56 G-57 G-58 G-59 G-6 G-60 G-7 G-8 G-9 H H-10 H-11 H-12
H-13 H-14 H-15 H-16 H-17 H-18 H-19 H-2 H-20 H-21 H-22 H-23 H-24 H-25 H-26 H-27
H-28 H-29 H-3 H-30 H-31 H-32 H-33 H-34 H-35 H-36 H-37 H-38 H-39 H-4 H-40 H-41
H-42 H-43 H-44 H-45 H-46 H-47 H-48 H-49 H-5 H-50 H-51 H-52 H-53 H-54 H-55 H-56
H-57 H-58 H-59 H-6 H-60 H-7 H-8 H-9 I I-10 I-11 I-12 I-13 I-14 I-15 I-16 I-17
I-18 I-19 I-2 I-20 I-21 I-22 I-23 I-24 I-25 I-26 I-27 I-28 I-29 I-3 I-30 I-31
I-32 I-33 I-34 I-35 I-36 I-37 I-38 I-39 I-4 I-40 I-41 I-42 I-43 I-44 I-45 I-46
I-47 I-48 I-49 I-5 I-50 I-51 I-52 I-53 I-54 I-55 I-56 I-57 I-58 I-59 I-6 I-60
I-7 I-8 I-9 M M-10 M-11 M-12 M-13 M-14 M-15 M-16 M-17 M-18 M-19 M-2 M-20 M-21
M-22 M-23 M-24 M-25 M-26 M-27 M-28 M-29 M-3 M-30 M-31 M-32 M-33 M-34 M-35 M-36
M-37 M-38 M-39 M-4 M-40 M-41 M-42 M-43 M-44 M-45 M-46 M-47 M-48 M-49 M-5 M-50
M-51 M-52 M-53 M-54 M-55 M-56 M-57 M-58 M-59 M-6 M-60 M-7 M-8 M-9 N N-10 N-11
N-12 N-13 N-14 N-15 N-16 N-17 N-18 N-19 N-2 N-20 N-21 N-22 N-23 N-24 N-25 N-26
N-27 N-28 N-29 N-3 N-30 N-31 N-32 N-33 N-34 N-35 N-36 N-37 N-38 N-39 N-4 N-40
N-41 N-42 N-43 N-44 N-45 N-46 N-47 N-48 N-49 N-5 N-50 N-51 N-52 N-53 N-54 N-55
N-56 N-57 N-58 N-59 N-6 N-60 N-7 N-8 N-9 O O-10 O-11 O-12 O-13 O-14 O-15 O-16
O-17 O-18 O-19 O-2 O-20 O-21 O-22 O-23 O-24 O-25 O-26 O-27 O-28 O-29 O-3 O-30
O-31 O-32 O-33 O-34 O-35 O-36 O-37 O-38 O-39 O-4 O-40 O-41 O-42 O-43 O-44 O-45
O-46 O-47 O-48 O-49 O-5 O-50 O-51 O-52 O-53 O-54 O-55 O-56 O-57 O-58 O-59 O-6
O-60 O-7 O-8 O-9 S S-10 S-11 S-12 S-13 S-14 S-15 S-16 S-17 S-18 S-19 S-2 S-20
S-21 S-22 S-23 S-24 S-25 S-26 S-27 S-28 S-29 S-3 S-30 S-31 S-32 S-33 S-34 S-35
S-36 S-37 S-38 S-39 S-4 S-40 S-41 S-42 S-43 S-44 S-45 S-46 S-47 S-48 S-49 S-5
S-50 S-51 S-52 S-53 S-54 S-55 S-56 S-57 S-58 S-59 S-6 S-60 S-7 S-8 S-9 | major
capsid surface protein sigma-3
U U-10 U-11 U-12 U-13 U-14 U-15 U-16 U-17 U-18 U-19 U-2 U-20 U-21 U-22 U-23
U-24 U-25 U-26 U-27 U-28 U-29 U-3 U-30 U-31 U-32 U-33 U-34 U-35 U-36 U-37 U-38
U-39 U-4 U-40 U-41 U-42 U-43 U-44 U-45 U-46 U-47 U-48 U-49 U-5 U-50 U-51 U-52
U-53 U-54 U-55 U-56 U-57 U-58 U-59 U-6 U-60 U-7 U-8 U-9 | guanylyltransferase
V V-10 V-11 V-12 V-13 V-14 V-15 V-16 V-17 V-18 V-19 V-2 V-20 V-21 V-22 V-23
V-24 V-25 V-26 V-27 V-28 V-29 V-3 V-30 V-31 V-32 V-33 V-34 V-35 V-36 V-37 V-38
V-39 V-4 V-40 V-41 V-42 V-43 V-44 V-45 V-46 V-47 V-48 V-49 V-5 V-50 V-51 V-52
V-53 V-54 V-55 V-56 V-57 V-58 V-59 V-6 V-60 V-7 V-8 V-9 W W-10 W-11 W-12 W-13
W-14 W-15 W-16 W-17 W-18 W-19 W-2 W-20 W-21 W-22 W-23 W-24 W-25 W-26 W-27 W-28
W-29 W-3 W-30 W-31 W-32 W-33 W-34 W-35 W-36 W-37 W-38 W-39 W-4 W-40 W-41 W-42
W-43 W-44 W-45 W-46 W-47 W-48 W-49 W-5 W-50 W-51 W-52 W-53 W-54 W-55 W-56 W-57
W-58 W-59 W-6 W-60 W-7 W-8 W-9 | major core protein lambda 1
X X-10 X-11 X-12 X-13 X-14 X-15 X-16 X-17 X-18 X-19 X-2 X-20 X-21 X-22 X-23
X-24 X-25 X-26 X-27 X-28 X-29 X-3 X-30 X-31 X-32 X-33 X-34 X-35 X-36 X-37 X-38
X-39 X-4 X-40 X-41 X-42 X-43 X-44 X-45 X-46 X-47 X-48 X-49 X-5 X-50 X-51 X-52
X-53 X-54 X-55 X-56 X-57 X-58 X-59 X-6 X-60 X-7 X-8 X-9 Y Y-10 Y-11 Y-12 Y-13
Y-14 Y-15 Y-16 Y-17 Y-18 Y-19 Y-2 Y-20 Y-21 Y-22 Y-23 Y-24 Y-25 Y-26 Y-27 Y-28
Y-29 Y-3 Y-30 Y-31 Y-32 Y-33 Y-34 Y-35 Y-36 Y-37 Y-38 Y-39 Y-4 Y-40 Y-41 Y-42
Y-43 Y-44 Y-45 Y-46 Y-47 Y-48 Y-49 Y-5 Y-50 Y-51 Y-52 Y-53 Y-54 Y-55 Y-56 Y-57
Y-58 Y-59 Y-6 Y-60 Y-7 Y-8 Y-9 Z Z-10 Z-11 Z-12 Z-13 Z-14 Z-15 Z-16 Z-17 Z-18
Z-19 Z-2 Z-20 Z-21 Z-22 Z-23 Z-24 Z-25 Z-26 Z-27 Z-28 Z-29 Z-3 Z-30 Z-31 Z-32
Z-33 Z-34 Z-35 Z-36 Z-37 Z-38 Z-39 Z-4 Z-40 Z-41 Z-42 Z-43 Z-44 Z-45 Z-46 Z-47
Z-48 Z-49 Z-5 Z-50 Z-51 Z-52 Z-53 Z-54 Z-55 Z-56 Z-57 Z-58 Z-59 Z-6 Z-60 Z-7
Z-8 Z-9 | Sigma 2 protein
> time surf #1 enclose #1
> surface #1 enclose #1
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.6.dev202210202104 (2022-10-20)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple
Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.1
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac Studio
Model Identifier: Mac13,1
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 32 GB
System Firmware Version: 7459.101.3
OS Loader Version: 7459.101.3
Software:
System Software Overview:
System Version: macOS 12.3.1 (21E258)
Kernel Version: Darwin 21.4.0
Time since boot: 14 days 7:42
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 24
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
PHL 279P1:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.0.7
Babel: 2.10.3
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.1
charset-normalizer: 2.1.0
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.43.2
ChimeraX-AtomicLibrary: 8.0.2
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.dev202210202104
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
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-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-NIHPresets: 1.1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PhenixUI: 1.0.5
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
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
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.25
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.2
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 0.9.1
filelock: 3.7.1
fonttools: 4.34.4
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.33
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 4.12.0
ipykernel: 6.15.1
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 4.11.1
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.3
msgpack: 1.0.4
nest-asyncio: 1.5.5
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.3
numpy: 1.23.1
openvr: 1.16.802
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.1
pkginfo: 1.8.3
prompt-toolkit: 3.0.30
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6: 6.3.1
PyQt6-Qt6: 6.3.1
PyQt6-sip: 13.4.0
PyQt6-WebEngine: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.1
python-dateutil: 2.8.2
pytz: 2022.1
pyzmq: 23.2.0
qtconsole: 5.3.1
QtPy: 2.2.0
RandomWords: 0.3.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 63.3.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.3.0
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
urllib3: 1.26.11
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.8.1
Attachments (1)
Change History (7)
comment:1 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Surface |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Bus Error computing surface of 2cse biological assembly |
comment:2 by , 3 years ago
| Resolution: | → limitation |
|---|---|
| Status: | assigned → closed |
I duplicated this crash and reported in #7906.
It is using 69 Gbytes when it crashed. This machine and the one I tested on have 32 Gbytes of memory. It is no suprise that it crashed. It ran out of memory.
Surfacing one asymmetric unit (16000 atoms) with one SES surface generates a 10 million triangle surface in 15 seconds. So 60 units for a full capsid might be about 600 million triangles. The memory use per triangle is about 24 bytes, so about 14 Gbytes. But the calculation method generates extra surface (the exterior from rolling a ball across the atoms) that is at least as big, possibly twice as big for this very airy all CA atom structure. And then there is the grid memory use. The capisd is about 1000 Angstroms diameter and the grid uses in the calculation has 0.5 A spacing so about a 2000 by 2000 by 2000 grid of floats, so 32 Gbytes. The memory use adds up to about the 70 Gbytes.
It's not too feasible to compute an SES surface of this size. Denser structures of a million atoms would probably work but the capsid is hollow making the diameter large, and it is all CA atoms so the triangles used by the surface is vastly higher than a dense structure, basically triangulating every atom.
If you tried to write out such a surface (on a machine that had more memory, probably 128 GB of physical memory would be fine, maybe even 64 GB), the file size would be at least 14 Gbytes, probably not reasonable for NIH 3D pipeline. So some filtering should be done to not compute SES surfaces on such large structures. Maybe a simple atom limit of 500,000 atoms. But for pathological structures where the atoms are not packed (like this all CA structure), may also need to reject those.
It should be fine to produce lower resolution surfaces of these large virus capsid structures.
follow-up: 3 comment:3 by , 3 years ago
Hi Tom and Eric,
I have a couple of questions and comments about this memory usage situation. I don’t know if Eric’s scripts do this, but for 3D Print Exchange I tried to address this issue by varying the Chimera grid size for surfaces using a logarithmic scale based on the number of atoms:
# Scaling for Surface Grid Size based on atom count before adding H
# Maximum grid size is 2.5, minimum grid size is 0.5.
numAtoms = sum([len(m.atoms) for m in openModels.list(modelTypes=[Molecule])])
#numAtoms = len(openModels.list(modelTypes=[Molecule])[0].atoms)
lognumAtoms = math.log10(numAtoms)
gridSize = lognumAtoms - 3.2
if gridSize > 2.0:
gridSize = 2.0
if gridSize < 0.3:
gridSize = 0.3
Is this being done? If it is, perhaps we could modify it to require less memory usage, and if not we should implement it.
I don’t know about the memory usage of Chimera vs. ChimeraX, but these models were created successfully on the somewhat limited nodes that were used by 3DPX. I’m not 100% sure but doubt if we had 64 GB machines.
Thanks,
Phil
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Thursday, October 27, 2022 at 9:32 PM
To:
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>, Browne, Kristen (NIH/NIAID) [C] <kristen.browne@nih.gov>, Stolarczyk, Michal (NIH/NIAID) [C] <michal.stolarczyk@nih.gov>, pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>, Cruz, Phil (NIH/NIAID) [C] <phil.cruz@nih.gov>
Subject: [EXTERNAL] Re: [ChimeraX] #7905: Bus Error computing surface of 2cse biological assembly (was: ChimeraX bug report submission)
#7905: Bus Error computing surface of 2cse biological assembly
-------------------------------+-------------------------
Reporter: pett | Owner: Tom Goddard
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Surface | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
-------------------------------+-------------------------
Changes (by pett):
* status: new => assigned
* cc: kristen.browne@…, michal.stolarczyk@…, phil.cruz@… (added)
* component: Unassigned => Surface
* project: => ChimeraX
* platform: => all
* owner: (none) => Tom Goddard
Comment:
This is on top of being very slow (crashed after about 9 minutes). The
biological assembly is 150MB, so instead of attaching it I put it in
plato:/wynton/group/ferrin/usr.local/projects/chimerax/nobackup/pett/2cse-
assembly1.cif
--
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comment:4 by , 3 years ago
Hi Phil,
The gridSize parameter in Chimera would only be for Gaussian surfaces made with molmap and there is also a resolution parameter. Chimera was not able to reliably compute large solvent excluded surfaces (SES) it often just crashes with more than 20000 atoms, so I guess 3DPX didn't even try that. But the ChimeraX NIH 3D script is attempting an SES surface. The ChimeraX SES algorithm is reliable, doesn't crash unless it runs out of memory. But the SES surface for this 1 million atom virus would make a 14 Gbyte file, and with 600 million triangles it would need a graphics card with at least 16 GB of memory (RTX 3090 has 24 GB) and would probably render at a few frames per second. So that is not useful. So for large atomic models only lower resolution surfaces should be made. ChimeraX can make the Gaussian surfaces. We need to determine the correct number of atoms cutoff, what the resolution should be and what the grid size should be. The default grid size is 1/10 the resolution when using the ChimeraX surface command and that is probably too fine. The ChimeraX molmap command also produces the gaussian surfaces and uses a grid size that is 1/3 the resolution.
For virus capsids probably a 15 Angstrom resolution with grid size 5 Angstroms is reasonable. Maybe use that for all structures over 300,000 atoms.
follow-up: 5 comment:5 by , 3 years ago
Hi Tom,
My recollection was that supplying the “grid” keyword along with a value to the surface command in Chimera caused it to use a “more robust” algorithm. The actual command used to create the surface in the 3DPX script is:
rc("surface #0 grid " + gridSizeStr + " warnLarge false")
Is using this keyword forcing it to use the Gaussian surfaces? The molmap command isn’t used at all in the script. Also, the “grid” keyword isn’t documented as part of the surface command for Chimera so I’m not sure what exactly it is doing.
ChimeraX documentation says the gridSpacing keyword is used by both types of surfaces. So is it, or can it, use variable grid spacing for SES surfaces for NIH 3D?
If we do fall back to Gaussian surfaces, your suggestion of what to do for structures over 300,000 atoms sounds good.
Phil
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Friday, October 28, 2022 at 2:23 PM
To:
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>, Browne, Kristen (NIH/NIAID) [C] <kristen.browne@nih.gov>, Stolarczyk, Michal (NIH/NIAID) [C] <michal.stolarczyk@nih.gov>, pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>, Cruz, Phil (NIH/NIAID) [C] <phil.cruz@nih.gov>
Subject: [EXTERNAL] Re: [ChimeraX] #7905: Bus Error computing surface of 2cse biological assembly
#7905: Bus Error computing surface of 2cse biological assembly
---------------------------------+-------------------------
Reporter: pett | Owner: Tom Goddard
Type: defect | Status: closed
Priority: normal | Milestone:
Component: Surface | Version:
Resolution: limitation | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
---------------------------------+-------------------------
Comment (by Tom Goddard):
Hi Phil,
The gridSize parameter in Chimera would only be for Gaussian surfaces made
with molmap and there is also a resolution parameter. Chimera was not
able to reliably compute large solvent excluded surfaces (SES) it often
just crashes with more than 20000 atoms, so I guess 3DPX didn't even try
that. But the ChimeraX NIH 3D script is attempting an SES surface. The
ChimeraX SES algorithm is reliable, doesn't crash unless it runs out of
memory. But the SES surface for this 1 million atom virus would make a 14
Gbyte file, and with 600 million triangles it would need a graphics card
with at least 16 GB of memory (RTX 3090 has 24 GB) and would probably
render at a few frames per second. So that is not useful. So for large
atomic models only lower resolution surfaces should be made. ChimeraX can
make the Gaussian surfaces. We need to determine the correct number of
atoms cutoff, what the resolution should be and what the grid size should
be. The default grid size is 1/10 the resolution when using the ChimeraX
surface command and that is probably too fine. The ChimeraX molmap
command also produces the gaussian surfaces and uses a grid size that is
1/3 the resolution.
For virus capsids probably a 15 Angstrom resolution with grid size 5
Angstroms is reasonable. Maybe use that for all structures over 300,000
atoms.
--
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comment:6 by , 3 years ago
Oh! We told you the secret "grid" option in Chimera. Yes that is using the same reliable SES calculation that is used in ChimeraX. Even though I wrote the code I can not predict what a grid size of 2 Angstroms will do. The default is 0.5 Angstroms, and such a large value as 2.0 when you are rolling a probe sphere of radius 1.4 Angstroms over the molecule may behave badly. I guess I wouldn't expect the code to fail, but the resulting surface may be very ugly. But I guess you chose the value after lots of testing so it can work. At any rate, I would still suggest skipping SES surfaces on large atomic models and use Gaussian surfaces at low resolution.
Eric said his NIH 3D script was using large grid values, like 2, probably copied from your code, and it still crashed or ran over an hour. I tried grid 2 on the 2cse capsid. Initial memory use is 4 GB which is much lower. It completed in 34 minutes, ChimeraX was using 8 Gbytes of memory, the surface has 73 million triangles, and a saved GLTF file had a size of 2.2 Gbytes. The surface is not too pretty and probably much more detail than desired for NIH 3D use cases. I'll attach an image.
Version 0, edited 3 years ago by (next)
by , 3 years ago
| Attachment: | 2cse_grid_2.png added |
|---|
2cse virus capsid surface, 73 million triangles, made with "surface enclose #2 grid 2".
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This is on top of being very slow (crashed after about 9 minutes). The biological assembly is 150MB, so instead of attaching it I put it in plato:/wynton/group/ferrin/usr.local/projects/chimerax/nobackup/pett/2cse-assembly1.cif