![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 9 months ago
Closed 9 months ago
#16776 closed defect (can't reproduce)
Crash in event loop
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard, Greg Couch | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.1-x86_64-i386-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 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 0x00007ff84e997b40 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 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, chimerax.surface._surface, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, 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, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.alignment_algs._nw, chimerax.morph._morph (total: 61)
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{
"uptime" : 200000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 504,
"deployVersion" : 210,
"modelCode" : "Macmini8,1",
"coalitionID" : 13600,
"osVersion" : {
"train" : "macOS 15.1",
"build" : "24B83",
"releaseType" : "User"
},
"captureTime" : "2025-02-03 14:19:25.8274 -0800",
"codeSigningMonitor" : 0,
"incident" : "EF2B7324-A4A5-4935-98B2-B7BDC9A542A2",
"pid" : 14880,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-02-03 13:08:03.7161 -0800",
"procStartAbsTime" : 203976596389428,
"procExitAbsTime" : 208258711298586,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"72F5BE26-D4F3-56D4-A641-50D41F3BD97D","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "85C55B7C-3B71-960C-DE44-2BC20A8921CD",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"bootSessionUUID" : "86CFB0F9-25E5-4157-9DE9-C59CFCE81D03",
"wakeTime" : 4547,
"bridgeVersion" : {"build":"22P1072","train":"9.1"},
"sleepWakeUUID" : "A4E779D5-2EC4-445C-981F-EA49A1426E5C",
"sip" : "enabled",
"vmRegionInfo" : "0x5d50c80ffd40 is not in any region. Bytes after previous region: 102595638467905 Bytes before following region: 2951581008576\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n CoreServices 15f726000-15f79e000 [ 480K] rw-\/rwx SM=PRV \n---> GAP OF 0x5ffea0862000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x00005d50c80ffd40","rawCodes":[1,102601535257920],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00005d50c80ffd40"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":14880},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0x5d50c80ffd40 is not in any region. Bytes after previous region: 102595638467905 Bytes before following region: 2951581008576\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n CoreServices 15f726000-15f79e000 [ 480K] rw-\/rwx SM=PRV \n---> GAP OF 0x5ffea0862000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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"uuid" : "cd27fd2a-b8c4-32fa-b3fa-7c4a8f467dfc",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtOpenGLWidgets.abi3.so",
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"name" : "_ribbons.cpython-311-darwin.so"
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"uuid" : "65c46829-28f8-3e3d-8cdc-c208915d68a9",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/graphics\/_graphics.cpython-311-darwin.so",
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"path" : "\/Applications\/ChimeraX-1.9.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-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/etree.cpython-311-darwin.so",
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/_elementpath.cpython-311-darwin.so",
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}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/zachpilon/Desktop/ZackPilon W25/Hemoglobin red blue all parts
> move no hem.cxs"
opened ChimeraX session
> set bgColor color white
Invalid "bgColor" argument: Invalid color name or specifier
> set bgColor white
> select add #1.1
26 pseudobonds, 1 model selected
> show #!1 models
> hide #!3 models
> hide #1.1 models
> select subtract #1.1
Nothing selected
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!3 models
> show sel
> hide #3.1 models
> select subtract #3.1
Nothing selected
> ui tool show Log
> morph #2,1,2 frames 150 hideModels false hideResidues false
Expected a keyword
> morph #2,1,2 frames 150 hideModels false
Computed 151 frame morph #4
> coordset #4 1,151
Called accessibilityLabel on invalid object: 2148138997
> hide #!3 models
> close #4
> show #!3 models
> morph #1,2 frames 80 hideModels false :morph #2,1 frames 80 hideModels false
Expected a keyword
> morph #1,2 frames 80 hideModels false:morph #2,1 frames 80 hideModels false
Invalid "hideModels" argument: Expected true or false (or 1 or 0)
> morph #1,2 frames 80 hideModels false : morph #2,1 frames 80 hideModels
> false
Expected a keyword
> morph #1,2 frames 80 hideModels false
Computed 81 frame morph #4
> coordset #4 1,81
> morph #2,1 frames 80 hideModels false
Computed 81 frame morph #5
> coordset #5 1,81
> hide #!3 models
> close #4
> close #5
> show #!3 models
> hide #!3 models
> show #!2 models
> show #!1 models
> hide #!2 models
> select add #1
5222 atoms, 4677 bonds, 26 pseudobonds, 1245 residues, 2 models selected
> select subtract #1/B:147@FE
5221 atoms, 4677 bonds, 19 pseudobonds, 1245 residues, 2 models selected
> select subtract #1/B:147@ND
5220 atoms, 4675 bonds, 19 pseudobonds, 1245 residues, 2 models selected
> select subtract #1/B:147@C4D
5219 atoms, 4673 bonds, 19 pseudobonds, 1245 residues, 2 models selected
> select subtract #1/B:147@O1D
5218 atoms, 4670 bonds, 19 pseudobonds, 1245 residues, 2 models selected
> select #1/B:91
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:147@FE
1 atom, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
43 atoms, 46 bonds, 1 residue, 1 model selected
> select up
1356 atoms, 1195 bonds, 338 residues, 1 model selected
> select up
5222 atoms, 4677 bonds, 1245 residues, 1 model selected
> select up
14168 atoms, 13805 bonds, 2453 residues, 3 models selected
> select up
14168 atoms, 13805 bonds, 2453 residues, 3 models selected
> select up
14168 atoms, 13805 bonds, 2453 residues, 3 models selected
> select up
14168 atoms, 13805 bonds, 2453 residues, 3 models selected
> select up
14168 atoms, 13805 bonds, 2453 residues, 3 models selected
> hide sel
> show sel
> hide sel & #!1 atoms
> show sel & #!1 atoms
> select #1/B:52
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
45 atoms, 45 bonds, 7 residues, 1 model selected
> select up
1121 atoms, 1148 bonds, 146 residues, 1 model selected
> select up
1356 atoms, 1195 bonds, 338 residues, 1 model selected
> select up
5222 atoms, 4677 bonds, 1245 residues, 1 model selected
> hide sel atoms
> show sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
43 atoms, 46 bonds, 1 residue, 1 model selected
> select up
1356 atoms, 1195 bonds, 338 residues, 1 model selected
> select up
5222 atoms, 4677 bonds, 1245 residues, 1 model selected
> select down
1356 atoms, 1195 bonds, 338 residues, 1 model selected
> select down
43 atoms, 46 bonds, 1 residue, 1 model selected
> select up
45 atoms, 47 bonds, 2 residues, 1 model selected
> select up
86 atoms, 92 bonds, 2 residues, 1 model selected
> select up
88 atoms, 93 bonds, 3 residues, 1 model selected
> select up
129 atoms, 138 bonds, 3 residues, 1 model selected
> select up
131 atoms, 139 bonds, 4 residues, 1 model selected
> select up
172 atoms, 184 bonds, 4 residues, 1 model selected
> select ~sel & ##selected
5050 atoms, 4493 bonds, 10 pseudobonds, 1241 residues, 2 models selected
> select ~sel
9118 atoms, 9312 bonds, 36 pseudobonds, 1212 residues, 5 models selected
> select ~sel
5050 atoms, 4493 bonds, 1241 residues, 1 model selected
> hide sel atoms
> select ~sel
9118 atoms, 9312 bonds, 36 pseudobonds, 1212 residues, 5 models selected
> combine sel
Remapping chain ID 'A' in T Deoxy Hemoglobin.pdb #2 to 'E'
Remapping chain ID 'B' in T Deoxy Hemoglobin.pdb #2 to 'F'
Remapping chain ID 'C' in T Deoxy Hemoglobin.pdb #2 to 'G'
Remapping chain ID 'D' in T Deoxy Hemoglobin.pdb #2 to 'H'
Remapping chain ID 'A' in Morph - R OXY Hemoglobin.pdb #3 to 'I'
Remapping chain ID 'B' in Morph - R OXY Hemoglobin.pdb #3 to 'J'
Remapping chain ID 'C' in Morph - R OXY Hemoglobin.pdb #3 to 'K'
Remapping chain ID 'D' in Morph - R OXY Hemoglobin.pdb #3 to 'L'
> close #4
> select ~sel
13996 atoms, 13621 bonds, 20 pseudobonds, 2449 residues, 4 models selected
> hide sel & #!1 atoms
> select ~sel
172 atoms, 184 bonds, 16 pseudobonds, 4 residues, 2 models selected
> combine sel
> hide #!1 models
> select add #1
5222 atoms, 4677 bonds, 26 pseudobonds, 1245 residues, 2 models selected
> show #!2 models
> select subtract #1
Nothing selected
> select add #2
4612 atoms, 4684 bonds, 20 pseudobonds, 634 residues, 2 models selected
> hide #!4 models
> style sel stick
Changed 4612 atom styles
> style sel stick
Changed 4612 atom styles
> style sel sphere
Changed 4612 atom styles
> style sel stick
Changed 4612 atom styles
> show sel atoms
> morph #4,2 hideModels false frames 124 rate sinusoidal
Computed 125 frame morph #5
> coordset #5 1,125
> hide #!2 models
> select subtract #2
Nothing selected
> show #!4 models
> hide #!4 models
> select add #5
4334 atoms, 4444 bonds, 574 residues, 1 model selected
> select ~sel
19390 atoms, 18482 bonds, 72 pseudobonds, 3698 residues, 7 models selected
> select subtract #1
14168 atoms, 13805 bonds, 46 pseudobonds, 2453 residues, 5 models selected
> select subtract #2
9556 atoms, 9121 bonds, 26 pseudobonds, 1819 residues, 3 models selected
> select subtract #3
5222 atoms, 4677 bonds, 26 pseudobonds, 1245 residues, 2 models selected
> select subtract #4
Nothing selected
> select #5/D:132
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #5/D:132
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
136 atoms, 137 bonds, 20 residues, 1 model selected
> select up
1102 atoms, 1129 bonds, 146 residues, 1 model selected
> select up
4334 atoms, 4444 bonds, 574 residues, 1 model selected
> select up
23724 atoms, 22926 bonds, 4272 residues, 5 models selected
> show #!4 models
> hide #!4 models
> select add #4
23724 atoms, 22926 bonds, 26 pseudobonds, 4272 residues, 6 models selected
> select subtract #3
19390 atoms, 18482 bonds, 26 pseudobonds, 3698 residues, 5 models selected
> select subtract #4
14168 atoms, 13805 bonds, 2453 residues, 3 models selected
> select add #2
14168 atoms, 13805 bonds, 20 pseudobonds, 2453 residues, 4 models selected
> select add #1
14168 atoms, 13805 bonds, 46 pseudobonds, 2453 residues, 5 models selected
> select subtract #2
9556 atoms, 9121 bonds, 26 pseudobonds, 1819 residues, 3 models selected
> select subtract #1
4334 atoms, 4444 bonds, 574 residues, 1 model selected
> show sel atoms
> hide sel atoms
> select ::name="HEM"
516 atoms, 552 bonds, 48 pseudobonds, 12 residues, 6 models selected
> select add #4
5566 atoms, 5045 bonds, 58 pseudobonds, 1253 residues, 6 models selected
> select subtract #4
344 atoms, 368 bonds, 32 pseudobonds, 8 residues, 4 models selected
> hide #!5 models
> select add #2
4784 atoms, 4868 bonds, 36 pseudobonds, 638 residues, 4 models selected
> select subtract #2
172 atoms, 184 bonds, 16 pseudobonds, 4 residues, 2 models selected
> select add #1
5222 atoms, 4677 bonds, 26 pseudobonds, 1245 residues, 2 models selected
> select subtract #1
Nothing selected
> show #!1 models
> hide #!1 models
> show #!2 models
> select #2/C:61
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
137 atoms, 137 bonds, 20 residues, 1 model selected
> select up
1069 atoms, 1097 bonds, 141 residues, 1 model selected
> select up
1113 atoms, 1143 bonds, 143 residues, 1 model selected
> select up
4612 atoms, 4684 bonds, 634 residues, 1 model selected
> select up
8946 atoms, 9128 bonds, 1208 residues, 2 models selected
> hide sel & #!2 atoms
> show sel & #!2 atoms
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
43 atoms, 46 bonds, 1 residue, 1 model selected
> select up
45 atoms, 47 bonds, 2 residues, 1 model selected
> select up
86 atoms, 92 bonds, 2 residues, 1 model selected
> select up
88 atoms, 93 bonds, 3 residues, 1 model selected
> select up
129 atoms, 138 bonds, 3 residues, 1 model selected
> select up
131 atoms, 139 bonds, 4 residues, 1 model selected
> select up
172 atoms, 184 bonds, 4 residues, 1 model selected
> select ~sel & ##selected
4440 atoms, 4500 bonds, 4 pseudobonds, 630 residues, 2 models selected
> hide sel atoms
> select ~sel & ##selected
172 atoms, 184 bonds, 16 pseudobonds, 4 residues, 2 models selected
> combine sel
> select add #2
4612 atoms, 4684 bonds, 20 pseudobonds, 634 residues, 2 models selected
> select subtract #2
Nothing selected
Cell requested for row 3 is out of bounds for table with 7 rows! Resizing
table model.
> hide #!6 models
> hide #!2 models
> show #!6 models
> show #!5 models
> hide #!6 models
> close #5
> rename #6 id #5
> morph #4,5 hideModels false frames 124 rate sinusoidal
Computed 125 frame morph #6
> coordset #6 1,125
> defattr r HEM
Missing or invalid "fileName" argument: File 'r' does not exist
> setattr r HEM color red
Expected a keyword
> setattr r HEM color blue
Expected a keyword
> setattr r HEM color
Assigning HEM attribute to 4906 items
Not creating attribute 'HEM'; use 'create true' to override
> hide #!6 models
> hide #!5 models
> show #!6 models
> show #!5 models
> show #!4 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> show #!4 models
> show #!5 models
> hide #!5 models
> hide #!4 models
> show #!6 models
> select #6/C:78
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
36 atoms, 36 bonds, 5 residues, 1 model selected
> select up
1069 atoms, 1097 bonds, 141 residues, 1 model selected
> select up
4334 atoms, 4444 bonds, 574 residues, 1 model selected
> select ~sel & ##selected
Nothing selected
> hide #!6 atoms
> show #!6 atoms
> hide #!6 atoms
> color #6 red
> undo
> select
28336 atoms, 27610 bonds, 92 pseudobonds, 4906 residues, 10 models selected
> select clear
> select ::name="HEM"
688 atoms, 736 bonds, 64 pseudobonds, 16 residues, 8 models selected
> view sel
> nucleotides #6 fill
> select ::name="HEM"
688 atoms, 736 bonds, 64 pseudobonds, 16 residues, 8 models selected
> hide #!6 models
> show #!5 models
> select up
19668 atoms, 18722 bonds, 64 pseudobonds, 3758 residues, 8 models selected
> select add #4
19668 atoms, 18722 bonds, 74 pseudobonds, 3758 residues, 8 models selected
> select subtract #4
14446 atoms, 14045 bonds, 48 pseudobonds, 2513 residues, 6 models selected
> combine sel
Remapping chain ID 'A' in T Deoxy Hemoglobin.pdb #2 to 'E'
Remapping chain ID 'B' in T Deoxy Hemoglobin.pdb #2 to 'F'
Remapping chain ID 'C' in T Deoxy Hemoglobin.pdb #2 to 'G'
Remapping chain ID 'D' in T Deoxy Hemoglobin.pdb #2 to 'H'
Remapping chain ID 'A' in copy of T Deoxy Hemoglobin.pdb #5 to 'I'
Remapping chain ID 'B' in copy of T Deoxy Hemoglobin.pdb #5 to 'J'
Remapping chain ID 'C' in copy of T Deoxy Hemoglobin.pdb #5 to 'K'
Remapping chain ID 'D' in copy of T Deoxy Hemoglobin.pdb #5 to 'L'
Called accessibilityLabel on invalid object: 2157867720
> hide #!5 models
> select add #5
14446 atoms, 14045 bonds, 52 pseudobonds, 2513 residues, 6 models selected
> select subtract #5
9834 atoms, 9361 bonds, 32 pseudobonds, 1879 residues, 4 models selected
> hide #!7 models
> show #!7 models
> undo
> close #7
> select add #2
9834 atoms, 9361 bonds, 36 pseudobonds, 1879 residues, 4 models selected
> select add #1
9834 atoms, 9361 bonds, 46 pseudobonds, 1879 residues, 4 models selected
> select subtract #2
5222 atoms, 4677 bonds, 26 pseudobonds, 1245 residues, 2 models selected
> select subtract #1
Nothing selected
> show #!5 models
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
43 atoms, 46 bonds, 1 residue, 1 model selected
> select up
1167 atoms, 1199 bonds, 148 residues, 1 model selected
> select up
4612 atoms, 4684 bonds, 634 residues, 1 model selected
> select up
28336 atoms, 27610 bonds, 4906 residues, 6 models selected
> select down
4612 atoms, 4684 bonds, 634 residues, 1 model selected
> select up
4612 atoms, 4684 bonds, 634 residues, 1 model selected
> select up
28336 atoms, 27610 bonds, 4906 residues, 6 models selected
> select down
4612 atoms, 4684 bonds, 634 residues, 1 model selected
> select up
4612 atoms, 4684 bonds, 634 residues, 1 model selected
Drag select of 21 residues
> select subtract #5/A:82
157 atoms, 20 residues, 1 model selected
> select up
533 atoms, 542 bonds, 70 residues, 1 model selected
> select up
2192 atoms, 2250 bonds, 287 residues, 1 model selected
> select up
2309 atoms, 2342 bonds, 320 residues, 1 model selected
> select up
4612 atoms, 4684 bonds, 634 residues, 1 model selected
> select up
4612 atoms, 4684 bonds, 634 residues, 1 model selected
> select up
4612 atoms, 4684 bonds, 634 residues, 1 model selected
> combine sel
> hide #!7 models
> hide #!5 models
> show #!7 models
> select add #5
4612 atoms, 4684 bonds, 20 pseudobonds, 634 residues, 2 models selected
> select subtract #5
Nothing selected
> show #!3 models
> hide #!7 models
> hide #!3 models
> show #!6 models
> hide #!6 models
> show #!4 models
> select #4/D:87
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
89 atoms, 90 bonds, 11 residues, 1 model selected
> select up
1124 atoms, 1151 bonds, 146 residues, 1 model selected
> select up
1366 atoms, 1198 bonds, 345 residues, 1 model selected
> select up
5222 atoms, 4677 bonds, 1245 residues, 1 model selected
> select up
32948 atoms, 32294 bonds, 5540 residues, 7 models selected
> select down
5222 atoms, 4677 bonds, 1245 residues, 1 model selected
> select up
5222 atoms, 4677 bonds, 1245 residues, 1 model selected
> combine sel
> hide #!4 models
> select add #4
5222 atoms, 4677 bonds, 26 pseudobonds, 1245 residues, 2 models selected
> select subtract #4
Nothing selected
> show #!7 models
> hide #!7 models
> hide #!8 models
> morph #7,8 hideModels false frames 124 rate sinusoidal
Computed 125 frame morph #9
> coordset #9 1,125
> close #9
> show #!3 models
> hide #!3 models
> show #!3 models
> select #3/B:34
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
99 atoms, 99 bonds, 14 residues, 1 model selected
> select up
1098 atoms, 1125 bonds, 146 residues, 1 model selected
> select up
4334 atoms, 4444 bonds, 574 residues, 1 model selected
> select up
38170 atoms, 36971 bonds, 6785 residues, 8 models selected
> select down
4334 atoms, 4444 bonds, 574 residues, 1 model selected
> hide sel atoms
> hide #!3 models
> select subtract #3
Nothing selected
> save "/Users/zachpilon/Desktop/ZackPilon W25/Hemoglobin red blue all parts
> move no hem.cxs"
> show #!8 models
> show #!7 models
> hide #!7 models
> show #!7 models
> ui tool show "Render/Select by Attribute"
> toolshed show
> select ::name="HEM"
1032 atoms, 1104 bonds, 96 pseudobonds, 24 residues, 12 models selected
> select add #5
5472 atoms, 5604 bonds, 100 pseudobonds, 654 residues, 12 models selected
> select subtract #5
860 atoms, 920 bonds, 80 pseudobonds, 20 residues, 10 models selected
> select add #4
5910 atoms, 5413 bonds, 90 pseudobonds, 1261 residues, 10 models selected
> select subtract #4
688 atoms, 736 bonds, 64 pseudobonds, 16 residues, 8 models selected
> select add #2
5128 atoms, 5236 bonds, 68 pseudobonds, 646 residues, 8 models selected
> select subtract #2
516 atoms, 552 bonds, 48 pseudobonds, 12 residues, 6 models selected
> select add #1
5566 atoms, 5045 bonds, 58 pseudobonds, 1253 residues, 6 models selected
> select subtract #1
344 atoms, 368 bonds, 32 pseudobonds, 8 residues, 4 models selected
> show #!4 models
> show #!5 models
> hide #!7 models
> hide #!8 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> close #7
> close #8
> show #!3 models
> hide #!3 models
> show #!5 models
> hide #!5 models
> hide #!4 models
> show #!6 models
> morph #4,5 frames 124 rate sinusoidal
Computed 125 frame morph #7
> coordset #7 1,125
> hide #!6 models
> hide #!7 models
> save "/Users/zachpilon/Desktop/ZackPilon W25/Hemoglobin red blue all parts
> move no hem.cxs"
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-23.0.22
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac mini
Model Identifier: Macmini8,1
Processor Name: 6-Core Intel Core i5
Processor Speed: 3 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 9 MB
Memory: 8 GB
System Firmware Version: 2069.40.2.0.0 (iBridge: 22.16.11072.0.0,0)
OS Loader Version: 582~2132
Software:
System Software Overview:
System Version: macOS 15.1 (24B83)
Kernel Version: Darwin 24.1.0
Time since boot: 5 days, 4 hours, 36 minutes
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0000
Metal Support: Metal 3
Displays:
VG270:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: TEGAA003851S
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Adapter Type: DVI or HDMI
Adapter Firmware Version: 2.19
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
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: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
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: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
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-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
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: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
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: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
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: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 9 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in event loop |
comment:2 by , 9 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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