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Opened 6 weeks ago
Closed 6 weeks ago
#18881 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-15.5-arm64-arm-64bit
ChimeraX Version: 1.7.dev202309272145 (2023-09-27 21:45:56 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00000003682c7000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000034619b000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x000000020b659f00 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 1602 in remove_deleted_pointers
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 123 in __init__
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 796 in __init__
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 86 in _atoms_pair
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 198 in get_prop
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 2211 in _bond_intercept
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/pbgroup.py", line 281 in first_intercept
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 725 in _position_intercepts
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 692 in first_intercept
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1075 in first_intercept_children
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1058 in first_intercept
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/models.py", line 131 in first_intercept
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 852 in picked_object_on_segment
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 820 in picked_object
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 801 in _front_center_point
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 792 in _front_center_cofr
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 724 in _compute_center_of_rotation
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 697 in _get_cofr
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 1016 in rotate
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mouse_modes/std_modes.py", line 392 in _rotate
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mouse_modes/std_modes.py", line 354 in touchpad_two_finger_trans
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mouse_modes/mousemodes.py", line 599 in _dispatch_touch_event
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mouse_modes/trackpad.py", line 130 in _collapse_touch_events
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mouse_modes/trackpad.py", line 63 in
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 138 in invoke
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 237 in _activate
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 206 in activate
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 382 in activate_trigger
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 54 in draw_new_frame
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 139 in _redraw_timer_callback
File "/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 912 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 1063 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.surface._surface, chimerax.pdb_lib._load_libs, chimerax.map._map, 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.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 (total: 50)
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"procLaunch" : "2025-09-26 08:54:16.0833 +0200",
"procStartAbsTime" : 4673358929676,
"procExitAbsTime" : 4781124434915,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
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"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
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"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/mmcif.cpython-311-darwin.so",
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"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/_mmcif.cpython-311-darwin.so",
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"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic\/_ribbons.cpython-311-darwin.so",
"name" : "_ribbons.cpython-311-darwin.so"
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"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/graphics\/_graphics.cpython-311-darwin.so",
"name" : "_graphics.cpython-311-darwin.so"
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"uuid" : "7707b367-c0b6-320e-94e2-a9f03c216a52",
"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/pdb\/_pdbio.cpython-311-darwin.so",
"name" : "_pdbio.cpython-311-darwin.so"
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"uuid" : "3e80d0a7-ec7b-369f-a494-de94afe5ae02",
"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_multiprocessing.cpython-311-darwin.so",
"name" : "_multiprocessing.cpython-311-darwin.so"
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"uuid" : "60485b6f-67e5-38c1-aec9-efd6031ff166",
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"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
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"name" : "libsystem_c.dylib"
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.8G resident=0K(0%) swapped_out_or_unallocated=1.8G(100%)\nWritable regions: Total=3.1G written=60.3M(2%) resident=1847K(0%) swapped_out=58.5M(2%) unallocated=3.1G(98%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 128K 1 \nActivity Tracing 256K 1 \nCG image 2112K 32 \nColorSync 720K 37 \nCoreAnimation 2160K 115 \nCoreGraphics 64K 4 \nCoreUI image data 5120K 40 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 2.5G 106 \nMALLOC guard page 288K 18 \nMach message 64K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 592K 37 \nStack 193.4M 38 \nStack Guard 56.0M 1 \nVM_ALLOCATE 248.0M 204 \nVM_ALLOCATE (reserved) 224.0M 6 reserved VM address space (unallocated)\n__AUTH 5927K 715 \n__AUTH_CONST 79.4M 963 \n__CTF 824 1 \n__DATA 36.9M 1091 \n__DATA_CONST 36.5M 1113 \n__DATA_DIRTY 2778K 343 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 646.3M 144 \n__OBJC_RO 61.4M 1 \n__OBJC_RW 2396K 1 \n__TEXT 1.2G 1112 \n__TEXT (graphics) 150.1M 21 \n__TPRO_CONST 128K 2 \ndyld private memory 2320K 20 \nmapped file 571.2M 88 \npage table in kernel 1847K 1 \nshared memory 3232K 27 \n=========== ======= ======= \nTOTAL 5.9G 6295 \nTOTAL, minus reserved VM space 5.7G 6295 \n",
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===== Log before crash start =====
Startup Messages
---
warnings | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
Registration file '/Users/svearikeoeverdieck/Library/Application
Support/ChimeraX/registration' has expired
UCSF ChimeraX version: 1.7.dev202309272145 (2023-09-27)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 9mia
9mia title:
206-3G08 Fab in complex with HIV-1 GT1.1 v4.1 SOSIP Env trimer and RM20A3 Fab
[more info...]
Chain information for 9mia #1
---
Chain | Description | UniProt
A C E | GT1.1 v4.1 SOSIP gp120 |
B D F | Envelope glycoprotein gp160 | Q2N0S6_9HIV1 512-664
G J O | RM20A3 heavy chain Fv |
H K P | 206-3G08 heavy chain Fv |
I M Q | RM20A3 light chain Fv |
L N R | 206-3G08 lambda chain Fv |
Non-standard residues in 9mia #1
---
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> show cartoons
> hide atoms
Drag select of 98 residues
> select up
1095 atoms, 1116 bonds, 145 residues, 1 model selected
> select up
1712 atoms, 1759 bonds, 224 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
Drag select of 99 residues
> select up
2762 atoms, 2834 bonds, 360 residues, 1 model selected
> select up
3424 atoms, 3518 bonds, 448 residues, 1 model selected
> hide sel cartoons
Drag select of 187 residues
> select up
5468 atoms, 5600 bonds, 720 residues, 1 model selected
> select up
6904 atoms, 7080 bonds, 910 residues, 1 model selected
> hide sel cartoons
Drag select of 123 residues
> select up
8122 atoms, 8320 bonds, 1075 residues, 1 model selected
> select up
8644 atoms, 8861 bonds, 1141 residues, 1 model selected
> hide sel cartoons
> color #1 #aaaca5ff
> ui tool show "Show Sequence Viewer"
> sequence chain /A /C /E
Alignment identifier is 1
> select /A,C,E:69
42 atoms, 45 bonds, 3 residues, 1 model selected
> select /A,C,E:69-70
57 atoms, 60 bonds, 6 residues, 1 model selected
> select /A,C,E:69
42 atoms, 45 bonds, 3 residues, 1 model selected
> select /A,C,E:69
42 atoms, 45 bonds, 3 residues, 1 model selected
> color sel purple
> show sel atoms
> style sel stick
Changed 42 atom styles
> select sel @ select up
351 atoms, 348 bonds, 42 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 351 atom styles
> color sel byhetero
> select clear
> open 9mia
9mia title:
206-3G08 Fab in complex with HIV-1 GT1.1 v4.1 SOSIP Env trimer and RM20A3 Fab
[more info...]
Chain information for 9mia #2
---
Chain | Description | UniProt
A C E | GT1.1 v4.1 SOSIP gp120 |
B D F | Envelope glycoprotein gp160 | Q2N0S6_9HIV1 512-664
G J O | RM20A3 heavy chain Fv |
H K P | 206-3G08 heavy chain Fv |
I M Q | RM20A3 light chain Fv |
L N R | 206-3G08 lambda chain Fv |
Non-standard residues in 9mia #2
---
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> hide #!2 models
> select #1/C:253
7 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
Populating font family aliases took 149 ms. Replace uses of missing font
family "Times" with one that exists to avoid this cost.
> swapaa interactive sel TRP rotLib Richardson.mode
9mia #1/C PRO 253: phi -77.8, psi 71.1 trans
Changed 91 bond radii
> select #1/C:67
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel TRP rotLib Richardson.mode
9mia #1/C ASN 67: phi -125.2, psi 149.6 trans
Changed 91 bond radii
> select #1/C:69
14 atoms, 15 bonds, 1 residue, 1 model selected
> select sel @ select #1/A,C,E:249
30 atoms, 30 bonds, 3 residues, 1 model selected
> select #1/A,C,E:249
30 atoms, 30 bonds, 3 residues, 1 model selected
> select #1/A,C,E:100
24 atoms, 21 bonds, 3 residues, 1 model selected
> select #1/A,C,E:100
24 atoms, 21 bonds, 3 residues, 1 model selected
> select #1/A,C,E:99
24 atoms, 21 bonds, 3 residues, 1 model selected
> select #1/A,C,E:99
24 atoms, 21 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 24 atom styles
> select #1/A,C,E:185
24 atoms, 21 bonds, 3 residues, 1 model selected
> select #1/A,C,E:185-186
51 atoms, 48 bonds, 6 residues, 1 model selected
> select #1/A,C,E:186
27 atoms, 24 bonds, 3 residues, 1 model selected
> select #1/A,C,E:186-186A
51 atoms, 48 bonds, 6 residues, 1 model selected
> select #1/A,C,E:186
27 atoms, 24 bonds, 3 residues, 1 model selected
> select #1/A,C,E:186
27 atoms, 24 bonds, 3 residues, 1 model selected
> select #1/A,C,E:234
24 atoms, 21 bonds, 3 residues, 1 model selected
> select #1/A,C,E:234
24 atoms, 21 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 24 atom styles
> color sel light sea green
> select sel @ show sel & #!1 atoms
> style sel & #!1 stick
Changed 156 atom styles
> select clear
> select #1/A,C,E:267
27 atoms, 24 bonds, 3 residues, 1 model selected
> select #1/A,C,E:267-268
54 atoms, 51 bonds, 6 residues, 1 model selected
> select #1/A,C,E:267
27 atoms, 24 bonds, 3 residues, 1 model selected
> select #1/A,C,E:267
27 atoms, 24 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 27 atom styles
> color sel forest green
> select sel @ show sel & #!1 atoms
> style sel & #!1 stick
Changed 108 atom styles
> color (#!1 & sel) byhetero
> select up
516 atoms, 498 bonds, 60 residues, 2 models selected
> show sel & #!1 atoms
> style sel & #!1 stick
Changed 258 atom styles
> select clear
> select #1/A,C,E:283
24 atoms, 21 bonds, 3 residues, 1 model selected
> select #1/A,C,E:283
24 atoms, 21 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 24 atom styles
> color sel cornflower blue
> select sel @ show sel & #!1 atoms
> style sel & #!1 stick
Changed 165 atom styles
> color (#!1 & sel) byhetero
> select up
786 atoms, 762 bonds, 96 residues, 2 models selected
> show sel & #!1 atoms
> style sel & #!1 stick
Changed 393 atom styles
> select clear
> select #1/P:33@OH
1 atom, 1 residue, 1 model selected
> select add #1/E:283@ND2
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance #1/P:33@OH #1/E:283@ND2
Distance between 9mia #1/P TYR 33 OH and /E ASN 283 ND2: 4.915Å
> select #1/E:283@OD1
1 atom, 1 residue, 1 model selected
> select add #1/E:477@OD2
2 atoms, 2 residues, 1 model selected
> distance #1/E:283@OD1 #1/E:477@OD2
Distance between 9mia #1/E ASN 283 OD1 and ASP 477 OD2: 3.368Å
> select #1/A,C,E:283
24 atoms, 21 bonds, 3 residues, 1 model selected
> select #1/A,C,E:283
24 atoms, 21 bonds, 3 residues, 1 model selected
> select #1/A,C,E:324
12 atoms, 9 bonds, 3 residues, 1 model selected
> select #1/A,C,E:324-330
165 atoms, 165 bonds, 21 residues, 1 model selected
> select #1/A,C,E:325
24 atoms, 21 bonds, 3 residues, 1 model selected
> select #1/A,C,E:325
24 atoms, 21 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 24 atom styles
> color sel purple
> select sel @ show sel & #!1 atoms
> select up
378 atoms, 360 bonds, 48 residues, 2 models selected
> show sel & #!1 atoms
> style sel & #!1 stick
Changed 189 atom styles
> select up
1476 atoms, 1476 bonds, 186 residues, 2 models selected
> select down
378 atoms, 360 bonds, 48 residues, 2 models selected
> select #1/A,C,E:329
15 atoms, 12 bonds, 3 residues, 1 model selected
> select #1/A,C,E:329
15 atoms, 12 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 15 atom styles
> select #1/A,C,E:397
18 atoms, 15 bonds, 3 residues, 1 model selected
> select #1/A,C,E:397
18 atoms, 15 bonds, 3 residues, 1 model selected
> style sel stick
Changed 18 atom styles
> show sel atoms
> select #1/A,C,E:426
24 atoms, 21 bonds, 3 residues, 1 model selected
> select #1/A,C,E:426
24 atoms, 21 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 24 atom styles
> color sel magenta
> select sel @ show sel & #!1 atoms
> select up
540 atoms, 546 bonds, 54 residues, 2 models selected
> select up
2334 atoms, 2370 bonds, 282 residues, 2 models selected
> select down
540 atoms, 546 bonds, 54 residues, 2 models selected
> show sel & #!1 atoms
> style sel & #!1 stick
Changed 270 atom styles
> color (#!1 & sel) byhetero
> select #1/A,C,E:463-464
39 atoms, 36 bonds, 6 residues, 1 model selected
> select #1/A,C,E:463-464
39 atoms, 36 bonds, 6 residues, 1 model selected
> select #1/A,C,E:463
18 atoms, 15 bonds, 3 residues, 1 model selected
> select #1/A,C,E:463
18 atoms, 15 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 18 atom styles
> ui tool show "Show Sequence Viewer"
> sequence chain #1/B #1/D #1/F #2/B #2/D #2/F
Alignment identifier is 1
> close #2
> ui tool show "Show Sequence Viewer"
> sequence chain /B /D /F
Alignment identifier is 1
> select /B,D,F:543-544
48 atoms, 45 bonds, 6 residues, 1 model selected
> select /B,D,F:543-545
72 atoms, 69 bonds, 9 residues, 1 model selected
> select /B,D,F:546
18 atoms, 15 bonds, 3 residues, 1 model selected
> select /B,D,F:546
18 atoms, 15 bonds, 3 residues, 1 model selected
> select /B,D,F:545
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /B,D,F:545
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /B,D,F:598
18 atoms, 15 bonds, 3 residues, 1 model selected
> select /B,D,F:598
18 atoms, 15 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 18 atom styles
===== Log before crash end =====
Log:
Startup Messages
---
warnings | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
Registration file '/Users/svearikeoeverdieck/Library/Application
Support/ChimeraX/registration' has expired
UCSF ChimeraX version: 1.7.dev202309272145 (2023-09-27)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple
Python: 3.11.2
Locale: en_US.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: Mac14,9
Model Number: Z17G002THN/A
Chip: Apple M2 Pro
Total Number of Cores: 10 (6 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.121.1
OS Loader Version: 11881.121.1
Software:
System Software Overview:
System Version: macOS 15.5 (24F74)
Kernel Version: Darwin 24.5.0
Time since boot: 8 days, 21 hours, 1 minute
Graphics/Displays:
Apple M2 Pro:
Chipset Model: Apple M2 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
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: 2.4.0
Babel: 2.12.1
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: 1.6.2
charset-normalizer: 3.2.0
ChimeraX-AddCharge: 1.5.11
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.11.1
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.48
ChimeraX-AtomicLibrary: 10.1
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: 1.0.3
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: 1.5.4
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.dev202309272145
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: 1.1.2
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: 1.2.1
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: 1.5.12
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: 1.11
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0.1
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: 1.1.2
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: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.10
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: 1.12.2
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: 1.32.2
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.1
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: 1.1.2
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.4
contourpy: 1.1.1
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.42.1
funcparserlib: 1.0.1
glfw: 2.6.2
grako: 3.16.5
h5py: 3.9.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.38
imagecodecs: 2023.7.10
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: 5.3.2
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: 2.8.7
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 10.0.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.10.0
prompt-toolkit: 3.0.39
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: 25.1.1
qtconsole: 5.4.3
QtPy: 2.4.0
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: 0.6.2
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: 6.3.3
traitlets: 5.9.0
typing-extensions: 4.8.0
tzdata: 2023.3
urllib3: 2.0.5
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 6 weeks 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 , 6 weeks ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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