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Opened 4 months ago
Closed 4 months ago
#18308 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-12.6.5-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 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 0x0000000111429600 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 161 in
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 161 in __iter__
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 907 in atomspec_atoms
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 627 in _add_model_parts
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 476 in _check
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 490 in _check
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 470 in find_matches
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 612 in find_matches
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 455 in find_matches
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 1004 in find_matches
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 1001 in evaluate
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 1091 in evaluate
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/args.py", line 36 in parse
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/args.py", line 71 in parse
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2499 in _parse_arg
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2640 in _process_positional_arguments
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2864 in run
File "/Applications/ChimeraX-1.7.1.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-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/match_maker/tool.py", line 303 in run_matchmaker
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/match_maker/tool.py", line 171 in
File "/Applications/ChimeraX-1.7.1.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-1.7.1.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-1.7.1.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.pdb_lib._load_libs, chimerax.surface._surface, chimerax.map._map, 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.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 (total: 54)
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{
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"procLaunch" : "2025-07-29 12:01:04.4375 +0100",
"procRole" : "Foreground",
"version" : 2,
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"deployVersion" : 210,
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"captureTime" : "2025-07-29 12:24:36.1925 +0100",
"incident" : "9AC52D6B-ADD0-43AA-BF86-B7506BC27AA4",
"bug_type" : "309",
"pid" : 1693,
"procExitAbsTime" : 11566013422622,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.1","CFBundleVersion":"1.7.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"sip" : "enabled",
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"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
"ktriageinfo" : "VM - Fault hit memory shortage\nVM - Fault hit memory shortage\nVM - Fault hit memory shortage\nVM - Fault hit memory shortage\nVM - Fault hit memory shortage\n",
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 140737488232279\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n VM_ALLOCATE 7ffffffe2000-7ffffffe3000 [ 4K] r-x\/r-x SM=ALI ",
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"uuid" : "6376ba16-20f7-3c31-a5c5-a10648ae7b56",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4496728064,
"size" : 64094208,
"uuid" : "9d768904-ac4b-327d-8126-cec11a08b966",
"path" : "\/Applications\/ChimeraX-1.7.1.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" : 4907184128,
"size" : 165052416,
"uuid" : "4aa1de3e-464c-340c-ab61-bcd39bfc7658",
"path" : "\/Applications\/ChimeraX-1.7.1.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" : 140703627681792,
"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=2.7G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.7G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG backing stores 2160K 4 \nCG image 3640K 35 \nCG raster data 432K 1 \nColorSync 232K 28 \nCoreAnimation 15.3M 42 \nCoreGraphics 12K 2 \nCoreUI image data 3592K 27 \nFoundation 36K 2 \nKernel Alloc Once 8K 1 \nMALLOC 2.1G 468 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 256K 1 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)\nMach message 16K 3 \nObjC additional data 15K 1 \nOpenGL GLSL 384K 4 \nSTACK GUARD 108K 27 \nStack 164.2M 28 \nStack Guard 56.0M 1 \nVM_ALLOCATE 262.2M 237 \nVM_ALLOCATE (reserved) 32.0M 1 reserved VM address space (unallocated)\n__CTF 756 1 \n__DATA 46.7M 675 \n__DATA_CONST 32.5M 340 \n__DATA_DIRTY 1641K 213 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 677.2M 154 \n__TEXT 815.2M 678 \n__UNICODE 592K 1 \ndyld private memory 1184K 3 \nmapped file 492.7M 70 \nshared memory 2984K 27 \n=========== ======= ======= \nTOTAL 4.8G 3090 \nTOTAL, minus reserved VM space 4.7G 3090 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "6112e14f37f5d11121dcd519",
"factorPackIds" : {
"SIRI_TEXT_TO_SPEECH" : "634710168e8be655c1316aaa"
},
"deploymentId" : 240000231
},
{
"rolloutId" : "61301e3a61217b3110231469",
"factorPackIds" : {
"SIRI_FIND_MY_CONFIGURATION_FILES" : "652886aa2c02f032beae8316"
},
"deploymentId" : 240000028
}
],
"experiments" : [
]
}
}
===== Log before crash start =====
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/miguelberbeirasantana/Desktop/setbp1_structure/DALI
> hits/7ml0.cif" format mmcif
7ml0.cif title:
RNA polymerase II pre-initiation complex (PIC1) [more info...]
Chain information for 7ml0.cif #1
---
Chain | Description | UniProt
0 | General transcription and DNA repair factor IIH helicase subunit XPD |
A0A6A5Q1C1_YEASX 1-778
1 | DNA-directed RNA polymerase subunit |
2 | RNA polymerase II transcription factor B subunit 2 | A0A6A5Q2X3_YEASX
1-513
3 | BJ4_G0050160.mRNA.1.CDS.1 | A0A7I9BTI9_YEASX 1-321
4 | DNA-directed RNA polymerase II subunit RPB4 |
5 | General transcription and DNA repair factor IIH subunit TFB5 | TFB5_YEAST
1-72
6 | General transcription and DNA repair factor IIH subunit SSL1 |
7 | General transcription and DNA repair factor IIH helicase subunit XPB |
RAD25_YEAST 1-843
A | DNA-directed RNA polymerase subunit | A0A6A5Q1P2_YEASX 1-1733
B | DNA-directed RNA polymerase subunit beta | A0A6A5Q4H2_YEASX 1-1224
C | DNA-directed RNA polymerase II subunit RPB3 | A0A6A5Q0Z3_YEASX 1-318
D | DNA-directed RNA polymerase II subunit RPB4 | A0A6A5PTI6_YEASX 1-221
E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 |
A0A6A5Q456_YEASX 1-215
F | DNA-directed RNA polymerases I,II,and III subunit RPABC2 |
A0A6L0ZRI7_YEASX 1-155
G | DNA-directed RNA polymerase II subunit RPB7 | A0A6A5Q270_YEASX 1-171
H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 |
A0A6A5Q8C2_YEASX 1-146
I | DNA-directed RNA polymerase II subunit RPB9 | A0A7I9EWC2_YEASX 1-122
J | DNA-directed RNA polymerases II subunit RPABC5 | A0A6A5Q7Q6_YEASX 1-70
K | DNA-directed RNA polymerase II subunit RPB11 | A0A6A5Q7A1_YEASX 1-120
L | DNA-directed RNA polymerases II subunit RPABC4 | A0A6A5PY05_YEASX 1-70
M | Transcription initiation factor IIB | TF2B_YEAST 1-345
N | non-template strand DNA |
O | TATA-box-binding protein | TBP_YEAST 1-240
Q | Transcription initiation factor IIF subunit alpha | T2FA_YEAST 1-735
R | Transcription initiation factor IIF subunit beta | A0A6A5PZ00_YEASX 1-400
T | template strand DNA |
W | Transcription initiation factor IIE subunit alpha | A0A6A5PTU5_YEASX 1-482
X | Transcription initiation factor IIE subunit beta | A0A6A5PS93_YEASX 1-328
Non-standard residues in 7ml0.cif #1
---
MG — magnesium ion
SF4 — iron/sulfur cluster
ZN — zinc ion
> split #1
Split 7ml0.cif (#1) into 28 models
Chain information for 7ml0.cif 0 #1.1
---
Chain | Description
0 | No description available
Chain information for 7ml0.cif 1 #1.2
---
Chain | Description
1 | No description available
Chain information for 7ml0.cif 2 #1.3
---
Chain | Description
2 | No description available
Chain information for 7ml0.cif 3 #1.4
---
Chain | Description
3 | No description available
Chain information for 7ml0.cif 4 #1.5
---
Chain | Description
4 | No description available
Chain information for 7ml0.cif 5 #1.6
---
Chain | Description
5 | No description available
Chain information for 7ml0.cif 6 #1.7
---
Chain | Description
6 | No description available
Chain information for 7ml0.cif 7 #1.8
---
Chain | Description
7 | No description available
Chain information for 7ml0.cif A #1.9
---
Chain | Description
A | No description available
Chain information for 7ml0.cif B #1.10
---
Chain | Description
B | No description available
Chain information for 7ml0.cif C #1.11
---
Chain | Description
C | No description available
Chain information for 7ml0.cif D #1.12
---
Chain | Description
D | No description available
Chain information for 7ml0.cif E #1.13
---
Chain | Description
E | No description available
Chain information for 7ml0.cif F #1.14
---
Chain | Description
F | No description available
Chain information for 7ml0.cif G #1.15
---
Chain | Description
G | No description available
Chain information for 7ml0.cif H #1.16
---
Chain | Description
H | No description available
Chain information for 7ml0.cif I #1.17
---
Chain | Description
I | No description available
Chain information for 7ml0.cif J #1.18
---
Chain | Description
J | No description available
Chain information for 7ml0.cif K #1.19
---
Chain | Description
K | No description available
Chain information for 7ml0.cif L #1.20
---
Chain | Description
L | No description available
Chain information for 7ml0.cif M #1.21
---
Chain | Description
M | No description available
Chain information for 7ml0.cif N #1.22
---
Chain | Description
N | No description available
Chain information for 7ml0.cif O #1.23
---
Chain | Description
O | No description available
Chain information for 7ml0.cif Q #1.24
---
Chain | Description
Q | No description available
Chain information for 7ml0.cif R #1.25
---
Chain | Description
R | No description available
Chain information for 7ml0.cif T #1.26
---
Chain | Description
T | No description available
Chain information for 7ml0.cif W #1.27
---
Chain | Description
W | No description available
Chain information for 7ml0.cif X #1.28
---
Chain | Description
X | No description available
> show cartoons
> hide atoms
> select add #1.2
2415 atoms, 2448 bonds, 1 pseudobond, 367 residues, 2 models selected
> ui tool show "Show Sequence Viewer"
> select add #1.1
8522 atoms, 8676 bonds, 7 pseudobonds, 1121 residues, 5 models selected
> select subtract #1.2
6107 atoms, 6228 bonds, 6 pseudobonds, 754 residues, 3 models selected
> select subtract #1.1
Nothing selected
> select add #1.2
2415 atoms, 2448 bonds, 1 pseudobond, 367 residues, 2 models selected
> ui tool show "Show Sequence Viewer"
> sequence chain #1.2/1
Alignment identifier is 1.2/1
> select #1.2/1:639
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1.2/1
2415 atoms, 2448 bonds, 1 pseudobond, 367 residues, 2 models selected
> select add #1
64214 atoms, 65571 bonds, 108 pseudobonds, 8257 residues, 54 models selected
> hide #!1.1 models
> select subtract #1
Nothing selected
> hide #!1.3 models
> hide #!1.4 models
> hide #!1.5 models
> hide #1.6 models
> hide #!1.7 models
> hide #!1.8 models
> hide #!1.9 models
> hide #!1.11 models
> select #1.2/1:281
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1.2/1:281-289
85 atoms, 90 bonds, 9 residues, 1 model selected
> select #1.2/1:541
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1.2/1:541-553
79 atoms, 78 bonds, 13 residues, 1 model selected
> select #1.2/1:540
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1.2/1:540-639
585 atoms, 591 bonds, 1 pseudobond, 95 residues, 2 models selected
> select #1.2/1:591-639
288 atoms, 290 bonds, 49 residues, 1 model selected
> select #1.2/1:537-639
600 atoms, 606 bonds, 1 pseudobond, 98 residues, 2 models selected
> close #1.11
> open "/Users/miguelberbeirasantana/Desktop/setbp1_structure/DALI
> hits/2q8g.cif"
2q8g.cif title:
Structure of pyruvate dehydrogenase kinase isoform 1 in complex with glucose-
lowering drug AZD7545 [more info...]
Chain information for 2q8g.cif #2
---
Chain | Description | UniProt
A | [Pyruvate dehydrogenase [lipoamide]] kinase isozyme 1 | PDK1_HUMAN 30-436
Non-standard residues in 2q8g.cif #2
---
AZX —
4-[(3-chloro-4-{[(2R)-3,3,3-trifluoro-2-hydroxy-2-methylpropanoyl]amino}phenyl)sulfonyl]-N,N-dimethylbenzamide
K — potassium ion
2q8g.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
> close #1.9
> close
> open "/Users/miguelberbeirasantana/Desktop/setbp1_structure/DALI
> hits/2q8g.cif"
2q8g.cif title:
Structure of pyruvate dehydrogenase kinase isoform 1 in complex with glucose-
lowering drug AZD7545 [more info...]
Chain information for 2q8g.cif #1
---
Chain | Description | UniProt
A | [Pyruvate dehydrogenase [lipoamide]] kinase isozyme 1 | PDK1_HUMAN 30-436
Non-standard residues in 2q8g.cif #1
---
AZX —
4-[(3-chloro-4-{[(2R)-3,3,3-trifluoro-2-hydroxy-2-methylpropanoyl]amino}phenyl)sulfonyl]-N,N-dimethylbenzamide
K — potassium ion
2q8g.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> select /A:41
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:41-197
1268 atoms, 1294 bonds, 1 pseudobond, 155 residues, 2 models selected
> select
> /A:41-51,58-68,71-95,98-123,131-149,151-203,225-245,269-292,324-333,357-369,404-412
1840 atoms, 1876 bonds, 1 pseudobond, 220 residues, 2 models selected
> select clear
> select /A:41-246
1583 atoms, 1615 bonds, 2 pseudobonds, 194 residues, 2 models selected
> select clear
> select /A:41-203
1315 atoms, 1343 bonds, 1 pseudobond, 161 residues, 2 models selected
> close
> open "/Users/miguelberbeirasantana/Desktop/setbp1_structure/SETBP1
> truncating variants by
> themselves/fold_setbp1_201_transcript_1_p_ala75glyfsx3/fold_setbp1_201_transcript_1_p_ala75glyfsx3_model_0.cif"
Chain information for fold_setbp1_201_transcript_1_p_ala75glyfsx3_model_0.cif
#1
---
Chain | Description
A | .
> open "/Users/miguelberbeirasantana/Desktop/setbp1_structure/SETBP1
> truncating variants by
> themselves/fold_setbp1_201_transcript_1_p_gly15argfsx47/fold_setbp1_201_transcript_1_p_gly15argfsx47_model_0.cif"
Chain information for fold_setbp1_201_transcript_1_p_gly15argfsx47_model_0.cif
#2
---
Chain | Description
A | .
> open "/Users/miguelberbeirasantana/Desktop/setbp1_structure/SETBP1
> truncating variants by
> themselves/fold_setbp1_201_transcript_1_p_ile822tyrfs_13/fold_setbp1_201_transcript_1_p_ile822tyrfs_13_model_0.cif"
Chain information for
fold_setbp1_201_transcript_1_p_ile822tyrfs_13_model_0.cif #3
---
Chain | Description
A | .
> open "/Users/miguelberbeirasantana/Desktop/setbp1_structure/SETBP1
> truncating variants by
> themselves/fold_setbp1_201_transcript_1_p_lys693profs_86/fold_setbp1_201_transcript_1_p_lys693profs_86_model_0.cif"
Chain information for
fold_setbp1_201_transcript_1_p_lys693profs_86_model_0.cif #4
---
Chain | Description
A | .
> ui tool show Matchmaker
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 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
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 Pro
Model Identifier: MacBookPro16,2
Processor Name: Quad-Core Intel Core i5
Processor Speed: 2 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 512 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 16 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: 3:45
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: 0x8a53
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: No
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
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: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
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: 2.0.4
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: 1.7.1
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: 2.6.1
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: 1.5.14
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: 1.0.4
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: 1.12.4
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: 1.33.3
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: 0.2.1
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: 4.47.2
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: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
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: 10.2.0
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: 1.0.8
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: 0.5.0
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: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 4 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 , 4 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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