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Opened 19 months ago
Closed 19 months ago
#14827 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.4-arm64-arm-64bit
ChimeraX Version: 1.6rc202304202331 (2023-04-20 23:31:10 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 0x00000001e88d1e00 (most recent call first):
File "/Applications/ChimeraX-1.6-rc2023.04.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/serialize.py", line 70 in msgpack_deserialize
File "/Applications/ChimeraX-1.6-rc2023.04.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/session.py", line 708 in restore
File "/Applications/ChimeraX-1.6-rc2023.04.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/session.py", line 1004 in open
File "/Applications/ChimeraX-1.6-rc2023.04.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core_formats/__init__.py", line 26 in open
File "/Applications/ChimeraX-1.6-rc2023.04.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 435 in remember_data_format
File "/Applications/ChimeraX-1.6-rc2023.04.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 465 in collated_open
File "/Applications/ChimeraX-1.6-rc2023.04.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 194 in provider_open
File "/Applications/ChimeraX-1.6-rc2023.04.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
File "/Applications/ChimeraX-1.6-rc2023.04.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 119 in cmd_open
File "/Applications/ChimeraX-1.6-rc2023.04.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
File "/Applications/ChimeraX-1.6-rc2023.04.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 38 in run
File "/Applications/ChimeraX-1.6-rc2023.04.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 1918 in _open_dropped_file
File "/Applications/ChimeraX-1.6-rc2023.04.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 240 in event
File "/Applications/ChimeraX-1.6-rc2023.04.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.6-rc2023.04.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/Applications/ChimeraX-1.6-rc2023.04.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/Applications/ChimeraX-1.6-rc2023.04.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.6-rc2023.04.20.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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"procLaunch" : "2024-03-26 19:11:31.1669 +0100",
"procStartAbsTime" : 4315046266494,
"procExitAbsTime" : 4342585120010,
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"name" : "AE",
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===== Log before crash start =====
UCSF ChimeraX version: 1.6rc202304202331 (2023-04-20)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/jo_air/Dropbox/CBG LAB/Collaborations/Gallego-
> Bartolome/Results/results_MINU_reduced/results_MINUred_ARP4_ARP7_RTT102/results(18)/best_model.pdb"
> format pdb
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> color bychain
> ui tool show "Show Sequence Viewer"
> sequence chain /D
Alignment identifier is 1/D
> select /D:3-12,46-51,123-129
349 atoms, 347 bonds, 23 residues, 1 model selected
> select /D:24-30,58-66,81-83
369 atoms, 376 bonds, 19 residues, 1 model selected
> select /D:88
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /D:1-88
1458 atoms, 1476 bonds, 88 residues, 1 model selected
> select clear
> select /D:110
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /D:110-111
17 atoms, 16 bonds, 2 residues, 1 model selected
> select /D:3-12,46-51,123-129
349 atoms, 347 bonds, 23 residues, 1 model selected
> select /D:51-52
28 atoms, 27 bonds, 2 residues, 1 model selected
> select /D:1-52
828 atoms, 839 bonds, 52 residues, 1 model selected
> select /D:110
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /D:110
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /D:21
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /D:21-71
868 atoms, 881 bonds, 51 residues, 1 model selected
> select /D:109
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /D:109-110
21 atoms, 20 bonds, 2 residues, 1 model selected
> select /D:20
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /D:20-76
971 atoms, 984 bonds, 57 residues, 1 model selected
> select coil
6744 atoms, 6737 bonds, 461 residues, 1 model selected
> close session
> ui tool show AlphaFold
Populating font family aliases took 146 ms. Replace uses of missing font
family "Calibri" with one that exists to avoid this cost.
QCssParser::parseHexColor: Unknown color name '#0C00'
> alphafold predict
> MEALVVDAGSKFLKAGAAIPDQSPAMIIPSQMKRMVDDGSSSADNPTTVFEDVTLDPIERGLIRDWDAMEDLLRYVVYTGLGWEEGNEGNILFTDPLCTPKAIREQLVQLMFETFNVSGFYASEQAVLSLYAVGRISGCTVDIGHGKIDIAPVLEGAVQHIASKRFELGGTELTKLFAQELGKTNPSMNLSMSDVEKLKEQYANCAEDEIAYKKTQNCEIEQHTLPDGQVISIGRERYSVGEALFQPSILGLEEHGIVEQLVRIISTVSSENHRQLLENTVLCGGTTSMTGFESRFQKEANLCSSAIRPTLVKPPEYMPENLGMYSAWVGGAILAKVVFPQNQHVTKADYDETGPSVVHRKCF,MDPQTLITKANKVSYYGNPTSKESWRYDWYQPSKVSSNVQQPQQQLGDMENNLEKYPFRYKTWLRNQEDEKNLQRESCEDILDLKEFDRRILKKSLMTSHTKGDTSKATGAPSANQGDEALSVDDIRGAVGNSEAIPGLSAGVNNDNTKESKDVKMN
AlphaFold Service Broken
## AlphaFold Prediction Requires Newer ChimeraX
Alphafold prediction requires a ChimeraX daily build from March 19, 2024 or
later.
The ChimeraX AlphaFold prediction service was broken by an update on Google
Colab on March 14, 2024.
> ui tool show Updates
> open "/Users/jo_air/Dropbox/CBG LAB/Collaborations/Orzaez/RMSD.cxs" format
> session
opened ChimeraX session
> close session
> open "/Users/jo_air/Dropbox/CBG LAB/Collaborations/Gallego-
> Bartolome/Results/results_MINU_reduced/results_MINUred_ARP4_ARP7_RTT102quimeraBDH1/results(19)/best_model.pdb"
> format pdb
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> color bychain
> open "/Users/jo_air/Dropbox/CBG LAB/Collaborations/Gallego-
> Bartolome/Results/results_MINU_reduced/results_MINUred_ARP4_ARP7_BDH1/best_model.pdb"
Chain information for best_model.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> close session
> open "/Users/jo_air/Dropbox/CBG LAB/Collaborations/Gallego-
> Bartolome/Results/results_MINU_reduced/results_MINUred_ARP4_ARP7_BDH1/best_model.pdb"
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> open "/Users/jo_air/Dropbox/CBG LAB/Collaborations/Gallego-
> Bartolome/Results/Matchmaker_BDH1_ARP7_ARP4_to_ARP7_ARP9_Rtt102_2.cxs"
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.6rc202304202331 (2023-04-20)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/jo_air/Dropbox/CBG LAB/Collaborations/Gallego-
> Bartolome/Results/Matchmaker_BDH1_ARP7_ARP4_to_ARP7_ARP9_Rtt102_2.cxs"
Log from Thu Feb 1 23:40:16 2024UCSF ChimeraX version: 1.6rc202304202331
(2023-04-20)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/jo_air/Desktop/BDH1_ARP7_ARP4.cxs format session
Log from Thu Feb 1 12:01:04 2024UCSF ChimeraX version: 1.6rc202304202331
(2023-04-20)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/jo_air/Downloads/results(3)/best_model.pdb
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
> select /A
6821 atoms, 6889 bonds, 441 residues, 1 model selected
> show sel surfaces
> select /B
5560 atoms, 5612 bonds, 363 residues, 1 model selected
> show sel surfaces
> color (#!1 & sel) light sea green
> select /C
3594 atoms, 3618 bonds, 238 residues, 1 model selected
> show sel surfaces
> color (#!1 & sel) hot pink
> select clear
> lighting simple
> lighting soft
> color bychain
> coulombic
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for best_model.pdb_A SES surface #1.1: minimum, -13.04, mean
-1.66, maximum 15.51
Coulombic values for best_model.pdb_B SES surface #1.2: minimum, -20.82, mean
-3.04, maximum 8.17
Coulombic values for best_model.pdb_C SES surface #1.3: minimum, -15.53, mean
-1.88, maximum 15.76
To also show corresponding color key, enter the above coulombic command and
add key true
> color bychain
> select /C
3594 atoms, 3618 bonds, 238 residues, 1 model selected
> hide sel surfaces
> select clear
> select /B:118@O
1 atom, 1 residue, 1 model selected
> select /C:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
453 atoms, 458 bonds, 29 residues, 2 models selected
> show sel atoms
> color sel byhetero
> show (#!1 & sel-residues & sidechain) target ab
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> style sel stick
Changed 453 atom styles
> select clear
> select /C:23
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
453 atoms, 458 bonds, 29 residues, 2 models selected
> show sel atoms
> hide sel atoms
> show sel atoms
> select H
7903 atoms, 1042 residues, 1 model selected
> hide sel atoms
> select clear
> select /C:27
22 atoms, 21 bonds, 1 residue, 1 model selected
> select up
453 atoms, 458 bonds, 29 residues, 2 models selected
> ui tool show H-Bonds
> hbonds sel interModel false intraMol false intraRes false select true reveal
> true
5 hydrogen bonds found
> hbonds sel interModel false intraMol false intraRes false select true reveal
> true
5 hydrogen bonds found
> show sel atoms
> transparency (#!1 & sel) 30
> transparency (#!1 & sel) 70
> color sel byhetero
> select clear
> select /C:76
22 atoms, 21 bonds, 1 residue, 1 model selected
> select up
91 atoms, 94 bonds, 5 residues, 2 models selected
> show sel atoms
> color sel byhetero
> select H
7903 atoms, 1042 residues, 1 model selected
> hide (#!1 & sel) target a
> select clear
> select /C:77
24 atoms, 25 bonds, 1 residue, 1 model selected
> select up
91 atoms, 94 bonds, 5 residues, 2 models selected
> ui tool show H-Bonds
> hbonds sel interModel false intraMol false intraRes false select true reveal
> true
1 hydrogen bonds found
> hbonds sel interModel false intraMol false intraRes false select true reveal
> true
1 hydrogen bonds found
> transparency (#!1 & sel) 70
> color sel byhetero
> select /C:30
22 atoms, 21 bonds, 1 residue, 1 model selected
> select up
101 atoms, 103 bonds, 5 residues, 2 models selected
> show sel atoms
> color sel byhetero
> select H
7903 atoms, 1042 residues, 1 model selected
> hide (#!1 & sel) target a
> select clear
> select /C:31
22 atoms, 21 bonds, 1 residue, 1 model selected
> select up
101 atoms, 103 bonds, 5 residues, 2 models selected
> ui tool show H-Bonds
> hbonds sel interModel false intraMol false intraRes false select true reveal
> true
2 hydrogen bonds found
> hbonds sel interModel false intraMol false intraRes false select true reveal
> true
2 hydrogen bonds found
> transparency (#!1 & sel) 70
> color sel byhetero
> select clear
> select /C:116
21 atoms, 21 bonds, 1 residue, 1 model selected
> select up
93 atoms, 95 bonds, 5 residues, 2 models selected
> show sel atoms
> color sel byhetero
> select H
7903 atoms, 1042 residues, 1 model selected
> hide (#!1 & sel) target a
> select clear
> select /C:115
22 atoms, 21 bonds, 1 residue, 1 model selected
> select up
93 atoms, 95 bonds, 5 residues, 2 models selected
> ui tool show H-Bonds
> hbonds sel interModel false intraMol false intraRes false select true reveal
> true
5 hydrogen bonds found
> hbonds sel interModel false intraMol false intraRes false select true reveal
> true
5 hydrogen bonds found
> show sel atoms
> transparency (#!1 & sel) 80
> color sel byhetero
> select clear
> view
> save /Users/jo_air/Desktop/BDH-ARP7-ARP4.tif width 1500 height 1266
> supersample 3 transparentBackground true
> save /Users/jo_air/Desktop/BDH-ARP7-ARP4.tif width 2000 height 1688
> supersample 3 transparentBackground true
> save /Users/jo_air/Desktop/BDH-ARP7-ARP4.png width 3000 height 2531
> supersample 3 transparentBackground true
> save /Users/jo_air/Desktop/BDH-ARP7-ARP4.png width 4000 height 3375
> supersample 3 transparentBackground true
Alignment identifier is 1/A
Alignment identifier is 1/B
Alignment identifier is 1/C
> select /A:119@O
1 atom, 1 residue, 1 model selected
> view sel
> select clear
> view
> select /C:30
22 atoms, 21 bonds, 1 residue, 1 model selected
> select up
101 atoms, 103 bonds, 5 residues, 2 models selected
> ui tool show H-Bonds
> hbonds sel interModel false intraMol false intraRes false select true reveal
> true
2 hydrogen bonds found
> hbonds sel interModel false intraMol false intraRes false select true reveal
> true
2 hydrogen bonds found
> select /C:78
10 atoms, 9 bonds, 1 residue, 1 model selected
> select up
91 atoms, 94 bonds, 5 residues, 2 models selected
> ui tool show H-Bonds
> hbonds sel interModel false intraMol false intraRes false select true reveal
> true
1 hydrogen bonds found
> hbonds sel interModel false intraMol false intraRes false select true reveal
> true
1 hydrogen bonds found
> color sel byhetero
> select /C:32
24 atoms, 25 bonds, 1 residue, 1 model selected
> select up
101 atoms, 103 bonds, 5 residues, 2 models selected
> ui tool show H-Bonds
> hbonds sel interModel false intraRes false select true reveal true
8 hydrogen bonds found
> hbonds sel interModel false intraRes false select true reveal true
8 hydrogen bonds found
> select clear
> save /Users/jo_air/Desktop/BDH1_ARP7_ARP4.cxs
> coulombic
Coulombic values for best_model.pdb_A SES surface #1.1: minimum, -13.04, mean
-1.66, maximum 15.51
Coulombic values for best_model.pdb_B SES surface #1.2: minimum, -20.82, mean
-3.04, maximum 8.17
Coulombic values for best_model.pdb_C SES surface #1.3: minimum, -15.53, mean
-1.88, maximum 15.76
To also show corresponding color key, enter the above coulombic command and
add key true
> ui tool show Contacts
> hide surfaces
> show surfaces
> color byhetero
> mlp
Map values for surface "best_model.pdb_A SES surface": minimum -30.64, mean
-5.078, maximum 23.68
Map values for surface "best_model.pdb_B SES surface": minimum -29.42, mean
-4.612, maximum 24.31
Map values for surface "best_model.pdb_C SES surface": minimum -26.88, mean
-5.314, maximum 23.39
To also show corresponding color key, enter the above mlp command and add key
true
> hide surfaces
> show surfaces
> color bypolymer
> color bychain
> color bypolymer
> color bychain
> color bfactor
15975 atoms, 1042 residues, 3 surfaces, atom bfactor range 14.8 to 98.7
> hide surfaces
> color bychain
> show surfaces
> select /C
3594 atoms, 3618 bonds, 6 pseudobonds, 238 residues, 2 models selected
> hide sel surfaces
> color sel byhetero
> select clear
> select /C:10
24 atoms, 23 bonds, 1 residue, 1 model selected
> select up
453 atoms, 458 bonds, 29 residues, 2 models selected
> ui tool show Contacts
> contacts sel intraMol false ignoreHiddenModels true select true reveal true
138 contacts
> contacts sel intraMol false ignoreHiddenModels true select true reveal true
138 contacts
> transparency (#!1 & sel) 80
> color sel byhetero
> select clear
> select /C:17
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
453 atoms, 458 bonds, 29 residues, 2 models selected
> select H
7903 atoms, 11 pseudobonds, 1042 residues, 2 models selected
> hide (#!1 & sel) target a
> select clear
> select solvent
Nothing selected
> select /C:30
22 atoms, 21 bonds, 1 residue, 1 model selected
> select down
22 atoms, 21 bonds, 1 residue, 2 models selected
> select up
101 atoms, 103 bonds, 5 residues, 2 models selected
> select up
3594 atoms, 3618 bonds, 238 residues, 2 models selected
> select down
101 atoms, 103 bonds, 5 residues, 2 models selected
> select up
3594 atoms, 3618 bonds, 238 residues, 2 models selected
> select down
101 atoms, 103 bonds, 5 residues, 2 models selected
> ui tool show Contacts
> contacts sel intraMol false ignoreHiddenModels true select true reveal true
58 contacts
> contacts sel intraMol false ignoreHiddenModels true select true reveal true
81 contacts
> transparency (#!1 & sel) 80
> color sel byhetero
> select /A:23@CE1
1 atom, 1 residue, 1 model selected
> select clear
> save /Users/jo_air/Desktop/BDH1_ARP7_ARP4.cxs
——— End of log from Thu Feb 1 12:01:04 2024 ———
opened ChimeraX session
> open /Users/jo_air/Downloads/5tgc.pdb format pdb
5tgc.pdb title:
Structure of the hetero-trimer of RTT102-ARP7/9 bound to atp [more info...]
Chain information for 5tgc.pdb #2
---
Chain | Description | UniProt
A D | actin-related protein 7 | ARP7_YEAST 1-477
B E | actin-like protein ARP9 | ARP9_YEAST 1-467
C F | regulator of TY1 transposition protein 102 | RT102_YEAST 1-157
Non-standard residues in 5tgc.pdb #2
---
ATP — adenosine-5'-triphosphate
SO4 — sulfate ion
> select #2/B
6327 atoms, 6385 bonds, 4 pseudobonds, 397 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #2/A
6610 atoms, 6680 bonds, 4 pseudobonds, 408 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #2/C
1132 atoms, 1147 bonds, 2 pseudobonds, 67 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #2/D:61@CD
1 atom, 1 residue, 1 model selected
> select add #2
14209 atoms, 14360 bonds, 8 pseudobonds, 883 residues, 2 models selected
> style sel stick
Changed 14209 atom styles
> hide sel atoms
> show sel cartoons
> select clear
> save /Users/jo_air/Desktop/homol.cxs
> ui tool show Matchmaker
> matchmaker #!2 to #1
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 best_model.pdb, chain A (#1) with 5tgc.pdb, chain D (#2), sequence
alignment score = 524.3
RMSD between 227 pruned atom pairs is 1.146 angstroms; (across all 372 pairs:
13.451)
> matchmaker #!2 to #1
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 best_model.pdb, chain A (#1) with 5tgc.pdb, chain D (#2), sequence
alignment score = 524.3
RMSD between 227 pruned atom pairs is 1.146 angstroms; (across all 372 pairs:
13.451)
> select add #1
15975 atoms, 16119 bonds, 89 pseudobonds, 1042 residues, 3 models selected
> hide sel surfaces
> select clear
> save /Users/jo_air/Desktop/Matchmaker_BDH1_ARP7_ARP4_to_ARP7_ARP9_Rtt102.cxs
> save
> /Users/jo_air/Desktop/Matchmaker_BDH1_ARP7_ARP4_to_ARP7_ARP9_Rtt102_1.png
> width 6000 height 3816 supersample 3 transparentBackground true
> select #1/C:77
24 atoms, 25 bonds, 1 residue, 1 model selected
> select up
91 atoms, 94 bonds, 5 residues, 2 models selected
> select up
3594 atoms, 3618 bonds, 238 residues, 2 models selected
> select down
91 atoms, 94 bonds, 5 residues, 2 models selected
> view sel
> select clear
> select #1/C:77
24 atoms, 25 bonds, 1 residue, 1 model selected
> select up
91 atoms, 94 bonds, 5 residues, 2 models selected
> hide sel atoms
> select #1/C:32
24 atoms, 25 bonds, 1 residue, 1 model selected
> select up
101 atoms, 103 bonds, 5 residues, 2 models selected
> hide sel atoms
> select clear
> save
> /Users/jo_air/Desktop/Matchmaker_BDH1_ARP7_ARP4_to_ARP7_ARP9_Rtt102_2.png
> width 6000 height 3816 supersample 3 transparentBackground true
> select clear
> select #1/A
6821 atoms, 6889 bonds, 441 residues, 1 model selected
> show sel surfaces
> select #1/B
5560 atoms, 5612 bonds, 363 residues, 1 model selected
> show sel surfaces
> select #1/C
3594 atoms, 3618 bonds, 6 pseudobonds, 238 residues, 2 models selected
> select #2/E
6270 atoms, 6334 bonds, 3 pseudobonds, 392 residues, 2 models selected
> show sel surfaces
> select #2/D
6895 atoms, 6967 bonds, 3 pseudobonds, 429 residues, 2 models selected
> show sel surfaces
> select clear
[Repeated 1 time(s)]
> view
> select clear
[Repeated 1 time(s)]
> save
> /Users/jo_air/Desktop/Matchmaker_BDH1_ARP7_ARP4_to_ARP7_ARP9_Rtt102_3.png
> width 6000 height 3816 supersample 3 transparentBackground true
> select #2/F:29
24 atoms, 25 bonds, 1 residue, 1 model selected
> select up
126 atoms, 131 bonds, 6 residues, 1 model selected
> select up
588 atoms, 598 bonds, 36 residues, 1 model selected
> select down
126 atoms, 131 bonds, 6 residues, 1 model selected
> view sel
> select clear
[Repeated 1 time(s)]
> transparency 40
> transparency 20
> transparency 0
> save
> /Users/jo_air/Desktop/Matchmaker_BDH1_ARP7_ARP4_to_ARP7_ARP9_Rtt102_4.png
> width 6000 height 3816 supersample 3 transparentBackground true
> save
> /Users/jo_air/Desktop/Matchmaker_BDH1_ARP7_ARP4_to_ARP7_ARP9_Rtt102_2.cxs
——— End of log from Thu Feb 1 23:40:16 2024 ———
opened ChimeraX session
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac14,2
Model Number: Z161000GJY/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 8422.121.1
OS Loader Version: 8422.121.1
Software:
System Software Overview:
System Version: macOS 13.4 (22F66)
Kernel Version: Darwin 22.5.0
Time since boot: 4 days, 1 hour, 54 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9
ChimeraX-AddH: 2.2.4
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
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: 1.2.2
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-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: 1.6rc202304202331
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: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
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: 1.2.1
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: 1.1.4
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: 2.0.12
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: 1.5.9
ChimeraX-ModelPanel: 1.3.7
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-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
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: 1.1
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: 1.10.3
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: 2.2.1
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: 1.28.4
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: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
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
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.2.0
prompt-toolkit: 3.0.38
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
pynrrd: 1.0.0
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: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
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: 2.4.1
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: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (2)
comment:1 by , 19 months ago
| Component: | Unassigned → Core |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 19 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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