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Opened 3 years ago
Closed 3 years ago
#8652 closed defect (nonchimerax)
Crash in multishadow
| Reported by: | 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: Linux-5.19.0-35-generic-x86_64-with-glibc2.36
ChimeraX Version: 1.6.dev202302242240 (2023-02-24 22:40:11 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00007f350fc59b80 (most recent call first):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/OpenGL/GL/VERSION/GL_1_5.py", line 125 in glBufferSubData
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 1647 in set_multishadow_view
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/graphics/view.py", line 239 in _draw_scene
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/graphics/view.py", line 177 in draw
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 73 in draw_new_frame
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 139 in _redraw_timer_callback
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/ui/gui.py", line 284 in event_loop
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/runpy.py", line 87 in _run_code
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.6.dev202302242240 (2023-02-24)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 6nts
Summary of feedback from opening 6nts fetched from pdb
---
notes | Fetching compressed mmCIF 6nts from
http://files.rcsb.org/download/6nts.cif
Fetching CCD MLL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/MLL/MLL.cif
Fetching CCD L2J from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/J/L2J/L2J.cif
6nts title:
Protein Phosphatase 2A (Aalpha-B56alpha-Calpha) holoenzyme in complex with a
Small Molecule Activator of PP2A (SMAP) [more info...]
Chain information for 6nts #1
---
Chain | Description | UniProt
A | Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha
isoform | 2AAA_HUMAN 1-589
B | Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit alpha
isoform | 2A5A_HUMAN 1-486
C | Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform |
PP2AA_HUMAN 1-306
Non-standard residues in 6nts #1
---
L2J —
N-[(1R,2R,3S)-2-hydroxy-3-(10H-phenoxazin-10-yl)cyclohexyl]-4-(trifluoromethoxy)benzene-1-sulfonamide
MN — manganese (II) ion
> lighting soft
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> open 3dw8
Summary of feedback from opening 3dw8 fetched from pdb
---
notes | Fetching compressed mmCIF 3dw8 from
http://files.rcsb.org/download/3dw8.cif
Fetching CCD DAL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/DAL/DAL.cif
Fetching CCD ACB from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/B/ACB/ACB.cif
Fetching CCD 1ZN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/1ZN/1ZN.cif
Fetching CCD FGA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/FGA/FGA.cif
Fetching CCD DAM from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/DAM/DAM.cif
3dw8 title:
Structure of a Protein Phosphatase 2A Holoenzyme with B55 subunit [more
info...]
Chain information for 3dw8 #2
---
Chain | Description | UniProt
A D | Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A
alpha isoform | 2AAA_HUMAN 9-589
B E | Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B
alpha isoform | 2ABA_HUMAN 1-447
C F | Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
| PP2AA_HUMAN 1-309
G H | microcystin LR |
Non-standard residues in 3dw8 #2
---
1ZN —
(2S,3S,4E,6E,8S,9S)-3-amino-9-methoxy-2,6,8-trimethyl-10-phenyldeca-4,6-dienoic
acid
DAM — N-methyl-α-β-dehydroalanine
MN — manganese (II) ion
3dw8 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> mmaker #2/C to #1/C
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6nts, chain C (#1) with 3dw8, chain C (#2), sequence alignment
score = 1566.6
RMSD between 288 pruned atom pairs is 0.490 angstroms; (across all 288 pairs:
0.490)
> select /D/E/F
10287 atoms, 10488 bonds, 10 pseudobonds, 1293 residues, 3 models selected
> delete sel
> select /G/H
142 atoms, 144 bonds, 14 residues, 1 model selected
> delete sel
> hide atoms
> show cartoons
> open 4I5L
Summary of feedback from opening 4I5L fetched from pdb
---
notes | Fetching compressed mmCIF 4i5l from
http://files.rcsb.org/download/4i5l.cif
Fetching CCD MAA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/MAA/MAA.cif
Fetching CCD PEG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/PEG/PEG.cif
Fetching CCD CA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/CA/CA.cif
Fetching CCD MLI from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/I/MLI/MLI.cif
4i5l title:
Structural mechanism of trimeric PP2A holoenzyme involving PR70: insight for
Cdc6 dephosphorylation [more info...]
Chain information for 4i5l #3
---
Chain | Description | UniProt
A D | Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A
alpha isoform | 2AAA_HUMAN 9-589
B E | Serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit
beta - Cell division control protein 6 homolog chimeric construct |
P2R3B_HUMAN 122-490, CDC6_HUMAN 512-532
C F | Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform,
PP2A-alpha | PP2AA_HUMAN 1-309
G H | Microcystin-LR (MCLR) bound form |
Non-standard residues in 4i5l #3
---
1ZN —
(2S,3S,4E,6E,8S,9S)-3-amino-9-methoxy-2,6,8-trimethyl-10-phenyldeca-4,6-dienoic
acid
CA — calcium ion
MLI — malonate ion
MN — manganese (II) ion
PEG — di(hydroxyethyl)ether
4i5l mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> mmaker #3/C to #1/C
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6nts, chain C (#1) with 4i5l, chain C (#3), sequence alignment
score = 1592.4
RMSD between 293 pruned atom pairs is 0.359 angstroms; (across all 293 pairs:
0.359)
> select /D/E/F
10080 atoms, 10062 bonds, 26 pseudobonds, 1457 residues, 3 models selected
> delete sel
> select /G/H
146 atoms, 144 bonds, 18 residues, 1 model selected
> delete sel
> hide atoms
> show cartoons
> cd
Current working directory is: /home/wei
> cd /home/wei/Work/PP2A
Current working directory is: /Data/Cloud/AmoyBioX Dropbox/Huang Wei/Work/PP2A
> save Bsubunits.cxs
> open 7K36
Summary of feedback from opening 7K36 fetched from pdb
---
notes | Fetching compressed mmCIF 7k36 from
http://files.rcsb.org/download/7k36.cif
Fetching CCD IHP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/IHP/IHP.cif
7k36 title:
Cryo-EM structure of STRIPAK complex [more info...]
Chain information for 7k36 #4
---
Chain | Description | UniProt
A | Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha
isoform | 2AAA_HUMAN 1-589
B D E F G | Striatin-3 | STRN3_HUMAN 1-713
C | Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform |
PP2AA_HUMAN 1-309
H | MOB-like protein phocein | PHOCN_HUMAN 1-225
I | Striatin-interacting protein 1 | STRP1_HUMAN 1-837
Non-standard residues in 7k36 #4
---
IHP — inositol hexakisphosphate (myo-inositol hexakisphosphate; inositol
1,2,3,4,5,6-hexakisphosphate)
MN — manganese (II) ion
ZN — zinc ion
> mmaker #4/C to #1/C
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6nts, chain C (#1) with 7k36, chain C (#4), sequence alignment
score = 1526.1
RMSD between 289 pruned atom pairs is 0.506 angstroms; (across all 293 pairs:
0.680)
> hide atoms
> show cartoons
> hide #!4 models
> hide #!3 models
> hide #!2 models
> molmap #1/A 15 gridSpacing 1
Opened 6nts map 15 as #5, grid size 149,171,187, pixel 1, shown at level
0.0395, step 1, values float32
> select #5
2 models selected
> color sel pink
> volume #5 level 0.06678
> volume #5 level 0.1
> molmap #1/B 15 gridSpacing 1
Opened 6nts map 15 as #6, grid size 141,177,146, pixel 1, shown at level
0.038, step 1, values float32
> volume #6 level 0.1
> color sel blue
> color sel pink
> select #6
2 models selected
> color sel blue
> molmap #1/C 15 gridSpacing 1
Opened 6nts map 15 as #7, grid size 149,134,151, pixel 1, shown at level
0.0411, step 1, values float32
> select #7
2 models selected
> color sel orange
> volume #7 level 0.1
> select clear
> lighting soft
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> hide #!1 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> show #!2 models
> select #2/A
4535 atoms, 4609 bonds, 582 residues, 1 model selected
> molmap sel 15 gridSpacing 1
Opened 3dw8 map 15 as #8, grid size 167,189,164, pixel 1, shown at level
0.0404, step 1, values float32
> select #2/B
3429 atoms, 3501 bonds, 3 pseudobonds, 421 residues, 2 models selected
> molmap sel 15 gridSpacing 1
Opened 3dw8 map 15 as #9, grid size 150,154,184, pixel 1, shown at level
0.0383, step 1, values float32
> select #2/C
2324 atoms, 2379 bonds, 8 pseudobonds, 290 residues, 2 models selected
> molmap sel 15 gridSpacing 1
Opened 3dw8 map 15 as #10, grid size 132,137,145, pixel 1, shown at level
0.0444, step 1, values float32
> volume #9-11 level 0.1
> volume #8-10 level 0.1
> select #8
2 models selected
> color sel pink
> select #9
2 models selected
> color sel light blue
> select #10
2 models selected
> color sel orange
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!2 models
> show #!3 models
> select #3/A
4714 atoms, 4632 bonds, 738 residues, 1 model selected
> molmap sel 15 gridSpacing 1
Opened 4i5l map 15 as #11, grid size 157,161,178, pixel 1, shown at level
0.0411, step 1, values float32
> select #3/B
3003 atoms, 2991 bonds, 16 pseudobonds, 442 residues, 3 models selected
> molmap sel 15 gridSpacing 1
Opened 4i5l map 15 as #12, grid size 143,163,165, pixel 1, shown at level
0.0378, step 1, values float32
> select #3/C
2483 atoms, 2456 bonds, 9 pseudobonds, 379 residues, 2 models selected
> molmap sel 15 gridSpacing 1
Opened 4i5l map 15 as #13, grid size 140,147,142, pixel 1, shown at level
0.0442, step 1, values float32
> volume #11-13 level 0.1
> select #11
2 models selected
> color sel pink
> select #12
2 models selected
> color sel royal blue
> select #13
2 models selected
> color sel orange
> hide #!3 models
> show #!4 models
> hide #!11 models
> hide #!12 models
> hide #!13 models
> select #4/A
3515 atoms, 3546 bonds, 6 pseudobonds, 554 residues, 2 models selected
> molmap sel 15 gridSpacing 1
Opened 7k36 map 15 as #14, grid size 168,169,180, pixel 1, shown at level
0.0346, step 1, values float32
> select #4/C
2362 atoms, 2417 bonds, 9 pseudobonds, 295 residues, 2 models selected
> molmap sel 15 gridSpacing 1
Opened 7k36 map 15 as #15, grid size 139,143,142, pixel 1, shown at level
0.0435, step 1, values float32
> select #4/B/F/G
3263 atoms, 3346 bonds, 4 pseudobonds, 420 residues, 2 models selected
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.6.dev202302242240 (2023-02-24)
© 2016-2023 Regents of the University of California. All rights reserved.
> open Bsubunits.cxs
Log from Wed Mar 15 10:33:38 2023UCSF ChimeraX version: 1.6.dev202302242240
(2023-02-24)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 6nts
Summary of feedback from opening 6nts fetched from pdb
---
notes | Fetching compressed mmCIF 6nts from
http://files.rcsb.org/download/6nts.cif
Fetching CCD MLL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/MLL/MLL.cif
Fetching CCD L2J from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/J/L2J/L2J.cif
6nts title:
Protein Phosphatase 2A (Aalpha-B56alpha-Calpha) holoenzyme in complex with a
Small Molecule Activator of PP2A (SMAP) [more info...]
Chain information for 6nts #1
---
Chain | Description | UniProt
A | Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha
isoform | 2AAA_HUMAN 1-589
B | Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit alpha
isoform | 2A5A_HUMAN 1-486
C | Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform |
PP2AA_HUMAN 1-306
Non-standard residues in 6nts #1
---
L2J —
N-[(1R,2R,3S)-2-hydroxy-3-(10H-phenoxazin-10-yl)cyclohexyl]-4-(trifluoromethoxy)benzene-1-sulfonamide
MN — manganese (II) ion
> lighting soft
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> open 3dw8
Summary of feedback from opening 3dw8 fetched from pdb
---
notes | Fetching compressed mmCIF 3dw8 from
http://files.rcsb.org/download/3dw8.cif
Fetching CCD DAL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/DAL/DAL.cif
Fetching CCD ACB from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/B/ACB/ACB.cif
Fetching CCD 1ZN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/1ZN/1ZN.cif
Fetching CCD FGA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/FGA/FGA.cif
Fetching CCD DAM from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/DAM/DAM.cif
3dw8 title:
Structure of a Protein Phosphatase 2A Holoenzyme with B55 subunit [more
info...]
Chain information for 3dw8 #2
---
Chain | Description | UniProt
A D | Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A
alpha isoform | 2AAA_HUMAN 9-589
B E | Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B
alpha isoform | 2ABA_HUMAN 1-447
C F | Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
| PP2AA_HUMAN 1-309
G H | microcystin LR |
Non-standard residues in 3dw8 #2
---
1ZN —
(2S,3S,4E,6E,8S,9S)-3-amino-9-methoxy-2,6,8-trimethyl-10-phenyldeca-4,6-dienoic
acid
DAM — N-methyl-α-β-dehydroalanine
MN — manganese (II) ion
3dw8 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> mmaker #2/C to #1/C
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6nts, chain C (#1) with 3dw8, chain C (#2), sequence alignment
score = 1566.6
RMSD between 288 pruned atom pairs is 0.490 angstroms; (across all 288 pairs:
0.490)
> select /D/E/F
10287 atoms, 10488 bonds, 10 pseudobonds, 1293 residues, 3 models selected
> delete sel
> select /G/H
142 atoms, 144 bonds, 14 residues, 1 model selected
> delete sel
> hide atoms
> show cartoons
> open 4I5L
Summary of feedback from opening 4I5L fetched from pdb
---
notes | Fetching compressed mmCIF 4i5l from
http://files.rcsb.org/download/4i5l.cif
Fetching CCD MAA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/MAA/MAA.cif
Fetching CCD PEG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/PEG/PEG.cif
Fetching CCD CA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/CA/CA.cif
Fetching CCD MLI from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/I/MLI/MLI.cif
4i5l title:
Structural mechanism of trimeric PP2A holoenzyme involving PR70: insight for
Cdc6 dephosphorylation [more info...]
Chain information for 4i5l #3
---
Chain | Description | UniProt
A D | Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A
alpha isoform | 2AAA_HUMAN 9-589
B E | Serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit
beta - Cell division control protein 6 homolog chimeric construct |
P2R3B_HUMAN 122-490, CDC6_HUMAN 512-532
C F | Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform,
PP2A-alpha | PP2AA_HUMAN 1-309
G H | Microcystin-LR (MCLR) bound form |
Non-standard residues in 4i5l #3
---
1ZN —
(2S,3S,4E,6E,8S,9S)-3-amino-9-methoxy-2,6,8-trimethyl-10-phenyldeca-4,6-dienoic
acid
CA — calcium ion
MLI — malonate ion
MN — manganese (II) ion
PEG — di(hydroxyethyl)ether
4i5l mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> mmaker #3/C to #1/C
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6nts, chain C (#1) with 4i5l, chain C (#3), sequence alignment
score = 1592.4
RMSD between 293 pruned atom pairs is 0.359 angstroms; (across all 293 pairs:
0.359)
> select /D/E/F
10080 atoms, 10062 bonds, 26 pseudobonds, 1457 residues, 3 models selected
> delete sel
> select /G/H
146 atoms, 144 bonds, 18 residues, 1 model selected
> delete sel
> hide atoms
> show cartoons
> cd
Current working directory is: /home/wei
> cd /home/wei/Work/PP2A
Current working directory is: /Data/Cloud/AmoyBioX Dropbox/Huang Wei/Work/PP2A
> save Bsubunits.cxs
——— End of log from Wed Mar 15 10:33:38 2023 ———
opened ChimeraX session
OpenGL version: 3.3.0 NVIDIA 525.89.02
OpenGL renderer: NVIDIA GeForce GTX 1080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.2
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: ASUS
Model: All Series
OS: Ubuntu 22.10 Kinetic Kudu
Architecture: 64bit ELF
Virtual Machine: none
CPU: 16 Intel(R) Core(TM) i7-5960X CPU @ 3.00GHz
Cache Size: 20480 KB
Memory:
total used free shared buff/cache available
Mem: 62Gi 4.8Gi 51Gi 78Mi 6.5Gi 57Gi
Swap: 1.9Gi 0B 1.9Gi
Graphics:
05:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [GeForce GTX 1080 Ti] [10de:1b06] (rev a1)
Subsystem: ASUSTeK Computer Inc. GP102 [GeForce GTX 1080 Ti] [1043:85e5]
Kernel driver in use: nvidia
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.2.1
Babel: 2.11.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.2
charset-normalizer: 3.0.1
ChimeraX-AddCharge: 1.5.8
ChimeraX-AddH: 2.2.3
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.8
ChimeraX-AtomicLibrary: 10.0.5
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: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.20.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.dev202302242240
ChimeraX-CoreFormats: 1.1
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: 1.1
ChimeraX-DistMonitor: 1.3.3
ChimeraX-DockPrep: 1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-ExperimentalCommands: 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: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.6.dev0
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
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: 2.0.11
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.8
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.6.13
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
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: 1.1.1
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: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
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: 1.10.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.27.2
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.2
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.6
decorator: 5.1.1
distro: 1.7.0
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.0.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.4
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.2.0
jupyterlab-widgets: 3.0.5
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 23.0
pandas: 1.5.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.0.0
prompt-toolkit: 3.0.37
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.2
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.2
python-dateutil: 2.8.2
pytz: 2022.7.1
pyzmq: 25.0.0
qtconsole: 5.4.0
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.0.2
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.9.0
urllib3: 1.26.14
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.5
zipp: 3.15.0
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash in multishadow |
comment:2 by , 3 years ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
ChimeraX crashed in your graphics driver. This is very likely a graphics driver bug. Either updating or downgrading your graphics driver would be the only way to fix it.
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Reported by Wei Huang