![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 19 months ago
Closed 19 months ago
#15190 closed defect (duplicate)
Crash in python_instances_of_class
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.0-arm64-arm-64bit
ChimeraX Version: 1.8.dev202403200605 (2024-03-20 06:05:36 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 0x00000001e6f65300 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 44 in python_instances_of_class
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 2636 in
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/attributes.py", line 256 in
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/attributes.py", line 256 in include_state
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 260 in discovery
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 641 in save
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 917 in save
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py", line 95 in save
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 101 in provider_save
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2904 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 86 in cmd_save
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2904 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 62 in display
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 138 in show_save_file_dialog
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 127 in
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 280 in event_loop
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 60)
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"version" : 2,
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"codeSigningMonitor" : 1,
"incident" : "63CA210F-0FE7-4CFC-A359-427A09634CDE",
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"procLaunch" : "2024-05-13 21:48:13.8265 -0400",
"procStartAbsTime" : 6608712797011,
"procExitAbsTime" : 6638049579233,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
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"crashReporterKey" : "F94F170D-284F-6811-55E1-AB88F552650F",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
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"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRXOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVHg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
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"vmRegionInfo" : "0x158 is not in any region. Bytes before following region: 105553653137064\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO 600020000000-600040000000 [512.0M] rw-\/rwx SM=PRV ",
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"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":93834},
"vmregioninfo" : "0x158 is not in any region. Bytes before following region: 105553653137064\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO 600020000000-600040000000 [512.0M] rw-\/rwx SM=PRV ",
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===== Log before crash start =====
UCSF ChimeraX version: 1.8.dev202403200605 (2024-03-20)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/ukjaelee/Downloads/fold_pd1_vhh_pd1_5038/fold_pd1_vhh_pd1_5038_model_0.cif
Chain information for fold_pd1_vhh_pd1_5038_model_0.cif #1
---
Chain | Description
A | .
B | .
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> select /A:1
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:1-169
1248 atoms, 1267 bonds, 169 residues, 1 model selected
> select /A:121-122
11 atoms, 10 bonds, 2 residues, 1 model selected
> select /A:121-265
1097 atoms, 1124 bonds, 145 residues, 1 model selected
> close session
> open
> /Users/ukjaelee/Downloads/fold_pd1_vhh_pd1_5038-2/fold_pd1_vhh_pd1_5038_model_0.cif
Chain information for fold_pd1_vhh_pd1_5038_model_0.cif #1
---
Chain | Description
A | .
B C | .
> ui tool show "Show Sequence Viewer"
> sequence chain /B /C
Alignment identifier is 1
> select /B-C:2
28 atoms, 30 bonds, 2 residues, 1 model selected
> select /B-C:2-288
4468 atoms, 4598 bonds, 574 residues, 1 model selected
> select /B-C:243-244
26 atoms, 24 bonds, 4 residues, 1 model selected
> select /B-C:1-244
3820 atoms, 3928 bonds, 488 residues, 1 model selected
> select clear
> open
> /Users/ukjaelee/Downloads/fold_pd1_vhh_pd1_5038/fold_pd1_vhh_pd1_5038_model_0.cif
Chain information for fold_pd1_vhh_pd1_5038_model_0.cif #2
---
Chain | Description
A | .
B | .
> 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 fold_pd1_vhh_pd1_5038_model_0.cif, chain C (#1) with
fold_pd1_vhh_pd1_5038_model_0.cif, chain B (#2), sequence alignment score =
1467
RMSD between 9 pruned atom pairs is 1.413 angstroms; (across all 288 pairs:
54.135)
> ui tool show Matchmaker
> matchmaker #1 to #2
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 fold_pd1_vhh_pd1_5038_model_0.cif, chain B (#2) with
fold_pd1_vhh_pd1_5038_model_0.cif, chain C (#1), sequence alignment score =
1467
RMSD between 9 pruned atom pairs is 1.413 angstroms; (across all 288 pairs:
54.135)
> ui tool show Matchmaker
> matchmaker #2 to #1/A pairing bs
Parameters
---
Chain pairing | bs
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 fold_pd1_vhh_pd1_5038_model_0.cif, chain A (#1) with
fold_pd1_vhh_pd1_5038_model_0.cif, chain A (#2), sequence alignment score =
1351.5
RMSD between 99 pruned atom pairs is 0.133 angstroms; (across all 265 pairs:
25.816)
> ui tool show Matchmaker
> matchmaker #2 to #1/B pairing bs
Parameters
---
Chain pairing | bs
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 fold_pd1_vhh_pd1_5038_model_0.cif, chain B (#1) with
fold_pd1_vhh_pd1_5038_model_0.cif, chain B (#2), sequence alignment score =
1459.2
RMSD between 106 pruned atom pairs is 0.332 angstroms; (across all 288 pairs:
64.706)
> ui tool show Matchmaker
> matchmaker #2 to #1/C pairing bs
Parameters
---
Chain pairing | bs
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 fold_pd1_vhh_pd1_5038_model_0.cif, chain C (#1) with
fold_pd1_vhh_pd1_5038_model_0.cif, chain B (#2), sequence alignment score =
1467
RMSD between 9 pruned atom pairs is 1.413 angstroms; (across all 288 pairs:
54.135)
> ui tool show Matchmaker
> matchmaker #1 to #2/A pairing bs
Parameters
---
Chain pairing | bs
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 fold_pd1_vhh_pd1_5038_model_0.cif, chain A (#2) with
fold_pd1_vhh_pd1_5038_model_0.cif, chain A (#1), sequence alignment score =
1351.5
RMSD between 99 pruned atom pairs is 0.133 angstroms; (across all 265 pairs:
25.816)
> select #1/B-C:197-198
28 atoms, 26 bonds, 4 residues, 1 model selected
> select #1/B-C:5-198
3058 atoms, 3148 bonds, 388 residues, 1 model selected
> select #1/B-C:201
10 atoms, 8 bonds, 2 residues, 1 model selected
> select #1/B-C:201-288
1316 atoms, 1350 bonds, 176 residues, 1 model selected
> open "/Users/ukjaelee/Library/CloudStorage/OneDrive-MassGeneralBrigham/0.
> Projects/1. Others/PD1 VHH/3BIK_B.pdb"
Summary of feedback from opening
/Users/ukjaelee/Library/CloudStorage/OneDrive-MassGeneralBrigham/0.
Projects/1. Others/PD1 VHH/3BIK_B.pdb
---
warnings | Cannot find LINK/SSBOND residue CYS (40 )
Cannot find LINK/SSBOND residue CYS (155 )
Cannot find LINK/SSBOND residue CYS (54 )
3BIK_B.pdb title:
Crystal structure of the Pd-1/Pd-L1 complex [more info...]
Chain information for 3BIK_B.pdb #3
---
Chain | Description | UniProt
B | programmed cell death protein 1 | PDCD1_MOUSE 25-157
> close session
> open "/Users/ukjaelee/Library/CloudStorage/OneDrive-MassGeneralBrigham/0.
> Projects/1. Others/PD1 VHH/3BIK_B.pdb"
Summary of feedback from opening
/Users/ukjaelee/Library/CloudStorage/OneDrive-MassGeneralBrigham/0.
Projects/1. Others/PD1 VHH/3BIK_B.pdb
---
warnings | Cannot find LINK/SSBOND residue CYS (40 )
Cannot find LINK/SSBOND residue CYS (155 )
Cannot find LINK/SSBOND residue CYS (54 )
3BIK_B.pdb title:
Crystal structure of the Pd-1/Pd-L1 complex [more info...]
Chain information for 3BIK_B.pdb #1
---
Chain | Description | UniProt
B | programmed cell death protein 1 | PDCD1_MOUSE 25-157
> ui tool show "Show Sequence Viewer"
> sequence chain /B
Alignment identifier is 1/B
> select
> /B:35-38,41-45,50-56,64-70,76-83,86-89,95-99,105-110,119-127,133-136,140-145
523 atoms, 526 bonds, 65 residues, 1 model selected
> select clear
> select /B
920 atoms, 942 bonds, 116 residues, 1 model selected
> select clear
> open
> /Users/ukjaelee/Downloads/fold_csf1r_vhh_csf1r5370/fold_csf1r_vhh_csf1r5370_model_0.cif
Chain information for fold_csf1r_vhh_csf1r5370_model_0.cif #2
---
Chain | Description
A | .
B | .
> close session
> open
> /Users/ukjaelee/Downloads/fold_csf1r_vhh_csf1r5370/fold_csf1r_vhh_csf1r5370_model_0.cif
Chain information for fold_csf1r_vhh_csf1r5370_model_0.cif #1
---
Chain | Description
A | .
B | .
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> select /A:2
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:2-258
1941 atoms, 1985 bonds, 257 residues, 1 model selected
> select /A:1-2
16 atoms, 15 bonds, 2 residues, 1 model selected
> select /A:1-113
883 atoms, 904 bonds, 113 residues, 1 model selected
> select /A:2-52
381 atoms, 388 bonds, 51 residues, 1 model selected
> select /A:2-258
1941 atoms, 1985 bonds, 257 residues, 1 model selected
> close session
> open
> /Users/ukjaelee/Downloads/fold_2024_05_13_21_55/fold_2024_05_13_21_55_model_0.cif
Chain information for fold_2024_05_13_21_55_model_0.cif #1
---
Chain | Description
A B | .
C | .
> close session
> open /Users/ukjaelee/Downloads/fold_w9_dimer/fold_w9_dimer_model_0.cif
Chain information for fold_w9_dimer_model_0.cif #1
---
Chain | Description
A B | .
> ui tool show "Show Sequence Viewer"
> sequence chain /A /B
Alignment identifier is 1
> select /A-B:1-2
34 atoms, 32 bonds, 4 residues, 1 model selected
> select /A-B:1-103
1574 atoms, 1618 bonds, 206 residues, 1 model selected
> select /A-B:73
10 atoms, 8 bonds, 2 residues, 1 model selected
> select /A-B:1-73
1140 atoms, 1168 bonds, 146 residues, 1 model selected
> color sel orange
> select /A-B:74-75
16 atoms, 14 bonds, 4 residues, 1 model selected
> select /A-B:74-198
1952 atoms, 2008 bonds, 250 residues, 1 model selected
> color sel forest green
> select /A-B:200
8 atoms, 6 bonds, 2 residues, 1 model selected
> select /A-B:200-343
2226 atoms, 2268 bonds, 288 residues, 1 model selected
> select /A-B:199
8 atoms, 6 bonds, 2 residues, 1 model selected
> select /A-B:199-367
2652 atoms, 2712 bonds, 338 residues, 1 model selected
> color sel cornflower blue
> select clear
> select /A:96
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
43 atoms, 43 bonds, 5 residues, 1 model selected
> select up
2872 atoms, 2946 bonds, 367 residues, 1 model selected
> select up
5744 atoms, 5892 bonds, 734 residues, 1 model selected
> surface sel
> transparency (#!1 & sel) 70
> select clear
> ui tool show "Color Actions"
> set bgColor white
> select clear
> select /B:364@CE1
1 atom, 1 residue, 1 model selected
> select /A-B:2
18 atoms, 16 bonds, 2 residues, 1 model selected
> select /A-B:2-74
1132 atoms, 1160 bonds, 146 residues, 1 model selected
> select /A-B:73
10 atoms, 8 bonds, 2 residues, 1 model selected
> select /A-B:1-73
1140 atoms, 1168 bonds, 146 residues, 1 model selected
> color (#!1 & sel) orange
> select /A-B:74
8 atoms, 6 bonds, 2 residues, 1 model selected
> select /A-B:74-198
1952 atoms, 2008 bonds, 250 residues, 1 model selected
> color (#!1 & sel) forest green
> select /A-B:199-200
16 atoms, 14 bonds, 4 residues, 1 model selected
> select /A-B:199-367
2652 atoms, 2712 bonds, 338 residues, 1 model selected
> color (#!1 & sel) cornflower blue
> select clear
Drag select of fold_w9_dimer_model_0.cif_A SES surface, 406803 of 407032
triangles, fold_w9_dimer_model_0.cif_B SES surface, 404270 of 405340
triangles, 734 residues
> select clear
> save "/Users/ukjaelee/OneDrive - Mass General Brigham/0. Projects/0.
> Alphafold/fold_w9_dimer/W9 dimer colored.cxs"
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8.dev202403200605 (2024-03-20)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 86
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac14,2
Model Number: Z1610001HKH/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 24 GB
System Firmware Version: 10151.1.1
OS Loader Version: 10151.1.1
Software:
System Software Overview:
System Version: macOS 14.0 (23A344)
Kernel Version: Darwin 23.0.0
Time since boot: 10 days, 23 hours, 39 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:
LG Ultra HD:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.14.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.1.1
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.16
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.3
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.5
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.56
ChimeraX-AtomicLibrary: 14.0.2
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
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: 2.12.1
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: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
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: 1.8.dev202403200605
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4.2
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: 1.1.9
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.13
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.15
ChimeraX-ModelPanel: 1.5
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-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.3
ChimeraX-PDB: 2.7.5
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: 1.1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.3
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-Segmentations: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
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: 1.37.1
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: 0.2.2
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.9
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.1
fonttools: 4.50.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.10.0
html2text: 2024.2.26
idna: 3.6
ihm: 0.43
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.2
jedi: 0.19.1
Jinja2: 3.1.3
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.10
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.1.0
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.3
matplotlib-inline: 0.1.6
msgpack: 1.0.8
ndindex: 1.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.2.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.9.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.3
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.2.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.0
prompt-toolkit: 3.0.43
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.3.0
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3302
pyparsing: 3.1.2
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.2
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.2
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 25.1.2
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.12.0
setuptools: 69.2.0
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.0
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: 0.6.1
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.1
typing-extensions: 4.10.0
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.10
Change History (2)
comment:1 by , 19 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in python_instances_of_class |
comment:2 by , 19 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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