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Opened 21 months ago
Closed 21 months ago
#14523 closed defect (can't reproduce)
Crash in garbage collection
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| 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-12.6.5-x86_64-i386-64bit
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x0000700012375000 (most recent call first):
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001103bf600 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/core/_internal.py", line 255 in __init__
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 333 in pointer
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 251 in set_cvec_pointer
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 133 in __init__
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 1022 in __init__
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 83 in _elements
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 209 in get_prop
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/coulombic.py", line 185 in template_residue_name
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/coulombic.py", line 147 in check_residues
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/coulombic.py", line 41 in assign_charges
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/cmd.py", line 99 in cmd_coulombic
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/Applications/ChimeraX-1.7.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-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 525 in run
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 582 in run_expanded_command
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 72 in func_plus_tip
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 339 in run
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 420 in run_shortcut
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 402 in try_shortcut
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 1376 in run_provider
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/__init__.py", line 66 in run_provider
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 1302 in run_provider
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 397 in run_provider
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/toolbar/tool.py", line 205 in callback
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.7.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-1.7.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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.surface._surface, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, 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, chimerax.mlp._mlp, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp (total: 56)
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{
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"procPath" : "\/Applications\/ChimeraX-1.7.app\/Contents\/MacOS\/ChimeraX",
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"exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
"ktriageinfo" : "VM - Compressor failed a blocking pager_get\n",
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 140737486724951\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n VM_ALLOCATE 7fffffe72000-7fffffe73000 [ 4K] r-x\/r-x SM=ALI ",
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"uuid" : "f02d178c-7914-3fc4-b9f4-9881945b3165",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2113.60.148"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4341067776,
"CFBundleShortVersionString" : "1.7.0",
"CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
"size" : 16384,
"uuid" : "194a3167-3db5-3029-8d22-1d742b826bb9",
"path" : "\/Applications\/ChimeraX-1.7.app\/Contents\/MacOS\/ChimeraX",
"name" : "ChimeraX",
"CFBundleVersion" : "1.7.0.0"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4566806528,
"size" : 442368,
"uuid" : "6376ba16-20f7-3c31-a5c5-a10648ae7b56",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4470448128,
"size" : 64094208,
"uuid" : "9d768904-ac4b-327d-8126-cec11a08b966",
"path" : "\/Applications\/ChimeraX-1.7.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
"name" : "libopenblas64_.0.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4933640192,
"size" : 165052416,
"uuid" : "4aa1de3e-464c-340c-ab61-bcd39bfc7658",
"path" : "\/Applications\/ChimeraX-1.7.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
"name" : "QtWebEngineCore"
}
],
"sharedCache" : {
"base" : 140703288619008,
"size" : 19331678208,
"uuid" : "e0be2d6e-28ef-33ab-8499-8d9d42337be7"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=1.7G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.7G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 512K 4 \nActivity Tracing 256K 1 \nCG backing stores 2160K 4 \nCG image 240K 25 \nColorSync 232K 28 \nCoreAnimation 148K 14 \nCoreGraphics 12K 2 \nCoreUI image data 5116K 36 \nFoundation 36K 2 \nKernel Alloc Once 8K 1 \nMALLOC 1.1G 494 \nMALLOC guard page 32K 7 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)\nMach message 16K 2 \nObjC additional data 15K 1 \nOpenGL GLSL 384K 4 \nSTACK GUARD 100K 25 \nStack 171.2M 26 \nStack Guard 56.0M 1 \nVM_ALLOCATE 237.5M 258 \n__CTF 756 1 \n__DATA 46.7M 673 \n__DATA_CONST 32.5M 340 \n__DATA_DIRTY 1641K 212 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 677.3M 153 \n__TEXT 816.0M 677 \n__UNICODE 592K 1 \ndyld private memory 1184K 3 \nmapped file 182.3M 46 \nshared memory 3104K 26 \n=========== ======= ======= \nTOTAL 3.5G 3071 \nTOTAL, minus reserved VM space 3.3G 3071 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "61af99aeda72d16a4beb7756",
"factorPackIds" : {
"SIRI_DIALOG_ASSETS" : "629fe54ebc762c0b6f758b6b"
},
"deploymentId" : 240000409
},
{
"rolloutId" : "607844aa04477260f58a8077",
"factorPackIds" : {
"SIRI_MORPHUN_ASSETS" : "6103050cbfe6dc472e1c982a"
},
"deploymentId" : 240000066
}
],
"experiments" : [
]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 2GTL format mmcif fromDatabase pdb
2gtl title:
Lumbricus Erythrocruorin at 3.5A resolution [more info...]
Chain information for 2gtl #1
---
Chain | Description | UniProt
A E I | Extracellular globin 4 | GLB4_LUMTE 1-151
B F J | Extracellular globin 2 | GLB2_LUMTE 1-145
C G K | Extracellular globin-3 | GLB3_LUMTE 1-153
D H L | Hemoglobin chain d1 | O61233_LUMTE 8-147
M | Hemoglobin linker chain L1 | Q9GV76_LUMTE 9-225
N | Extracellular hemoglobin linker L2 subunit | Q2I743_LUMTE 10-229
O | Extracellular hemoglobin linker L3 subunit | Q2I742_LUMTE 8-222
Non-standard residues in 2gtl #1
---
CA — calcium ion
CMO — carbon monoxide
HEM — protoporphyrin IX containing Fe (HEME)
ZN — zinc ion
2gtl mmCIF Assemblies
---
1| complete point assembly
2| point asymmetric unit
3| point asymmetric unit, std point frame
4| crystal asymmetric unit
> select /M /N /O
5095 atoms, 5210 bonds, 19 pseudobonds, 657 residues, 2 models selected
> select ~sel & ##selected
14553 atoms, 14925 bonds, 88 pseudobonds, 1767 residues, 2 models selected
> hide sel atoms
> select ~sel & ##selected
5095 atoms, 5210 bonds, 19 pseudobonds, 657 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> mlp sel
Map values for surface "2gtl_M SES surface": minimum -27.51, mean -4.23,
maximum 21.91
Map values for surface "2gtl_N SES surface": minimum -28.72, mean -4.949,
maximum 21.91
Map values for surface "2gtl_O SES surface": minimum -29, mean -5.716, maximum
22.98
To also show corresponding color key, enter the above mlp command and add key
true
> hide sel surfaces
> select clear
> select add /M:26
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add /N:24
13 atoms, 11 bonds, 2 residues, 2 models selected
> select add /O:27
19 atoms, 16 bonds, 3 residues, 3 models selected
> select up
597 atoms, 600 bonds, 79 residues, 4 models selected
> show sel atoms
> style sel stick
Changed 597 atom styles
> color sel byhetero
> coulombic sel
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
/M LEU 13
/M LYS 15
/M ASP 22
/M LYS 26
/M LYS 27
/M ASP 30
/M LYS 37
/M ASP 43
/M LYS 44
/M LYS 45
/M GLU 59
/M GLU 64
/M SER 187
/N PHE 19
/N ARG 23
/N ARG 26
/N GLU 39
/N ASP 186
/N HIS 228
/N ASP 229
/O GLN 8
/O SER 9
/O HIS 10
/O ASP 11
/O GLU 12
/O ILE 13
/O ILE 14
/O ASP 15
/O LYS 16
/O LEU 17
/O ILE 18
/O GLU 19
/O LYS 23
/O LYS 221
/O LYS 222
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 2gtl_M SES surface #1.2: minimum, -25.60, mean -4.72,
maximum 12.62
Coulombic values for 2gtl_N SES surface #1.3: minimum, -23.87, mean -3.44,
maximum 16.59
Coulombic values for 2gtl_O SES surface #1.4: minimum, -45.36, mean -7.97,
maximum 10.68
To also show corresponding color key, enter the above coulombic command and
add key true
> undo
> hide sel surfaces
> style sel stick
Changed 597 atom styles
> color sel byhetero
> select clear
> lighting soft
> lighting simple
> lighting full
> set bgColor black
> set bgColor white
> lighting simple
> lighting soft
> set bgColor black
> mlp
Map values for surface "2gtl_A SES surface": minimum -27.35, mean -3.46,
maximum 25.63
Map values for surface "2gtl_B SES surface": minimum -24.43, mean -4.748,
maximum 23.49
Map values for surface "2gtl_C SES surface": minimum -29.2, mean -4.082,
maximum 25.1
Map values for surface "2gtl_D SES surface": minimum -27.96, mean -3.691,
maximum 23.3
Map values for surface "2gtl_E SES surface": minimum -27.49, mean -3.405,
maximum 25.96
Map values for surface "2gtl_F SES surface": minimum -25.45, mean -4.776,
maximum 24.49
Map values for surface "2gtl_G SES surface": minimum -28.11, mean -4.069,
maximum 24.69
Map values for surface "2gtl_H SES surface": minimum -28.09, mean -3.677,
maximum 23.35
Map values for surface "2gtl_I SES surface": minimum -27.61, mean -3.48,
maximum 26.12
Map values for surface "2gtl_J SES surface": minimum -25.38, mean -4.745,
maximum 24.81
Map values for surface "2gtl_K SES surface": minimum -30.19, mean -4.019,
maximum 24.42
Map values for surface "2gtl_L SES surface": minimum -29.02, mean -3.7,
maximum 22.67
Map values for surface "2gtl_M SES surface": minimum -27.51, mean -4.23,
maximum 21.91
Map values for surface "2gtl_N SES surface": minimum -28.72, mean -4.949,
maximum 21.91
Map values for surface "2gtl_O SES surface": minimum -29, mean -5.716, maximum
22.98
To also show corresponding color key, enter the above mlp command and add key
true
> color byhetero
> hide surfaces
> select /A:5-151
1209 atoms, 1238 bonds, 147 residues, 1 model selected
> select :HEM
516 atoms, 552 bonds, 48 pseudobonds, 12 residues, 2 models selected
> show sel atoms
> select clear
> select /G:160@FE
1 atom, 1 residue, 1 model selected
> select up
43 atoms, 46 bonds, 1 residue, 1 model selected
> select up
1230 atoms, 1257 bonds, 151 residues, 1 model selected
> show sel cartoons
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
43 atoms, 46 bonds, 1 residue, 1 model selected
> select up
1193 atoms, 1224 bonds, 147 residues, 1 model selected
> show sel cartoons
> save /Users/annahorton/Desktop/image1.png supersample 3
> mlp sel
Map values for surface "2gtl_F SES surface": minimum -25.45, mean -4.776,
maximum 24.49
To also show corresponding color key, enter the above mlp command and add key
true
> mlp sel
Map values for surface "2gtl_F SES surface": minimum -25.45, mean -4.776,
maximum 24.49
To also show corresponding color key, enter the above mlp command and add key
true
> show sel surfaces
> mlp sel
Map values for surface "2gtl_F SES surface": minimum -25.45, mean -4.776,
maximum 24.49
To also show corresponding color key, enter the above mlp command and add key
true
> close session
> open 2GTL format mmcif fromDatabase pdb
2gtl title:
Lumbricus Erythrocruorin at 3.5A resolution [more info...]
Chain information for 2gtl #1
---
Chain | Description | UniProt
A E I | Extracellular globin 4 | GLB4_LUMTE 1-151
B F J | Extracellular globin 2 | GLB2_LUMTE 1-145
C G K | Extracellular globin-3 | GLB3_LUMTE 1-153
D H L | Hemoglobin chain d1 | O61233_LUMTE 8-147
M | Hemoglobin linker chain L1 | Q9GV76_LUMTE 9-225
N | Extracellular hemoglobin linker L2 subunit | Q2I743_LUMTE 10-229
O | Extracellular hemoglobin linker L3 subunit | Q2I742_LUMTE 8-222
Non-standard residues in 2gtl #1
---
CA — calcium ion
CMO — carbon monoxide
HEM — protoporphyrin IX containing Fe (HEME)
ZN — zinc ion
2gtl mmCIF Assemblies
---
1| complete point assembly
2| point asymmetric unit
3| point asymmetric unit, std point frame
4| crystal asymmetric unit
> select /M:9-225
1705 atoms, 1750 bonds, 217 residues, 1 model selected
> select /M /N /O
5095 atoms, 5210 bonds, 19 pseudobonds, 657 residues, 2 models selected
> select ~sel & ##selected
14553 atoms, 14925 bonds, 88 pseudobonds, 1767 residues, 2 models selected
> select /M:9-225
1705 atoms, 1750 bonds, 217 residues, 1 model selected
> select /M /N /O
5095 atoms, 5210 bonds, 19 pseudobonds, 657 residues, 2 models selected
> select ~sel & ##selected
14553 atoms, 14925 bonds, 88 pseudobonds, 1767 residues, 2 models selected
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> select /M:9-225
1705 atoms, 1750 bonds, 217 residues, 1 model selected
> select /N:10-229
1722 atoms, 1757 bonds, 220 residues, 1 model selected
> select /M:9-225
1705 atoms, 1750 bonds, 217 residues, 1 model selected
> select /M /N /O
5095 atoms, 5210 bonds, 19 pseudobonds, 657 residues, 2 models selected
> style sel stick
Changed 5095 atom styles
> style sel ball
Changed 5095 atom styles
> style sel stick
Changed 5095 atom styles
> show sel cartoons
> mlp sel
Map values for surface "2gtl_M SES surface": minimum -27.51, mean -4.23,
maximum 21.91
Map values for surface "2gtl_N SES surface": minimum -28.72, mean -4.949,
maximum 21.91
Map values for surface "2gtl_O SES surface": minimum -29, mean -5.716, maximum
22.98
To also show corresponding color key, enter the above mlp command and add key
true
> select clear
> hide surfaces
> coulombic
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-18.8.6
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine (1x6x8 (fused) LP
OpenGL vendor: Intel Inc.
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: MacBookAir9,1
Processor Name: Dual-Core Intel Core i3
Processor Speed: 1.1 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 512 KB
L3 Cache: 4 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 1968.100.17.0.0 (iBridge: 20.16.4252.0.0,0)
OS Loader Version: 540.120.3~22
Software:
System Software Overview:
System Version: macOS 12.6.5 (21G531)
Kernel Version: Darwin 21.6.0
Time since boot: 25 days 5:35
Graphics/Displays:
Intel Iris Plus Graphics:
Chipset Model: Intel Iris Plus Graphics
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x8a5c
Revision ID: 0x0007
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.1
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.13
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.3
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.3
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: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.2
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: 0.2.0
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.0
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.5.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.8
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
Pillow: 10.0.1
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.3
urllib3: 2.1.0
wcwidth: 0.2.12
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 21 months ago
| Cc: | added |
|---|---|
| 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 , 21 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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