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Opened 19 months ago
Closed 19 months ago
#14954 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-14.4.1-arm64-arm-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: Bus error
Thread 0x000000017a567000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000177543000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000016f063000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001ff60fac0 (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/grako/ast.py", line 59 in update
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/ast.py", line 19 in __init__
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/ast.py", line 90 in copy
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 642 in _try
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py", line 137 in __enter__
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 665 in _option
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py", line 137 in __enter__
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 168 in _model_
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
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 157 in block0
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 787 in _positive_closure
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 159 in _model_list_
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
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 136 in _as_term_
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
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 89 in _atom_specifier_
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 206 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/atomspec.py", line 192 in _parse_unquoted
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 121 in parse
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/defattr.py", line 180 in defattr
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/add_charge/charge.py", line 81 in add_standard_charges
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/add_charge/charge.py", line 34 in add_charges
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/coulombic.py", line 110 in assign_charges
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/cmd.py", line 99 in cmd_coulombic
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3468 in __call__
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 2929 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/core/scripting.py", line 184 in _run_commands
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/runscript.py", line 61 in run_command_script
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/runscript.py", line 51 in runscript
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 2908 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319 in execute
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
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.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.surface._surface, lxml._elementpath, lxml.etree, chimerax.pdb_lib._load_libs, PIL._imagingmath, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, chimerax.mlp._mlp (total: 59)
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{
"uptime" : 260000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,2",
"coalitionID" : 8844,
"osVersion" : {
"train" : "macOS 14.4.1",
"build" : "23E224",
"releaseType" : "User"
},
"captureTime" : "2024-04-11 00:36:59.3079 -0600",
"codeSigningMonitor" : 1,
"incident" : "6981FB8A-3CAC-49E7-8A38-5ED5115D00D1",
"pid" : 34688,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-04-11 00:33:24.6755 -0600",
"procStartAbsTime" : 6256344369203,
"procExitAbsTime" : 6261495080843,
"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"},
"storeInfo" : {"deviceIdentifierForVendor":"54EDB63B-59DA-5473-BF40-1A458E1F4283","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "3FE89ED7-3137-4E81-0724-502C8964939F",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRW+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 4792,
"sleepWakeUUID" : "1E2D91F6-0AFE-439C-9DD3-DDA48B79E181",
"sip" : "enabled",
"vmRegionInfo" : "0x6c75646f6d27 is not in any region. Bytes after previous region: 118770415660328 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> \n UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000101, 0x27656c75646f6d27","rawCodes":[257,2838794391578963239],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"UNKNOWN_0x101 at 0x27656c75646f6d27 -> 0x00006c75646f6d27 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"ChimeraX","byPid":34688},
"vmregioninfo" : "0x6c75646f6d27 is not in any region. Bytes after previous region: 118770415660328 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> \n UNUSED SPACE AT END",
"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,
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===== 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
> runscript /Users/neyrinck/Dropbox/notebook/proteins/makepictures.cxc
> alias picmovie view orient ; save "/Users/neyrinck/Google Drive/My
> Drive/$1/$2/$2_$3.jpg" supersample 2 ; movie record ; turn y 2 180 ; wait
> 180 ; movie encode "/Users/neyrinck/Google Drive/My
> Drive/$1/$2/$2_$3_rot.mp4"
> alias makepicture close ; set bgColor white ; windowsize 480 480 ;open
> "/Users/neyrinck/Google Drive/My Drive/$1/$2/best_model.pdb" ; alphafold pae
> #1 file "/Users/neyrinck/Google Drive/My Drive/$1/$2/best_model_pae.json" ;
> view orient ; sequence chain #1/A ; sequence chain #1/B ;color bychain ;
> color /A indianred ; color /B royalblue ; alphafold contacts /A to /B
> palette paegreen ; hbonds /A reveal true restrict /B color fuchsia radius
> 0.8 dashes 2 ; picmovie $1 $2 contacts_hbonds ; style sphere ; show atoms ;
> picmovie $1 $2 sphere ; style nucleic stick ; hide atoms ; coulombic key
> true ; picmovie $1 $2 coulombic ; style nucleic stick ; hide atoms ; mlp key
> true ; picmovie $1 $2 hydrophobic
> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults T114
> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T114/best_model.pdb"
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
Alignment identifier is 1/A
Alignment identifier is 1/B
2 hydrogen bonds found
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T114/T114_contacts_hbonds.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../T114/T114_contacts_hbonds_rot.mp4
Changed 1591 atom styles
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T114/T114_sphere.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../T114/T114_sphere_rot.mp4
Changed 0 atom styles
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -19.23, mean
-4.14, maximum 10.47
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -10.42, mean
-0.28, maximum 10.68
> key red-white-blue :-10 :0 :10 showTool true
> ui mousemode right "color key"
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T114/T114_coulombic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../T114/T114_coulombic_rot.mp4
Changed 0 atom styles
Map values for surface "best_model.pdb_A SES surface": minimum -33.89, mean
-5.556, maximum 25.37
Map values for surface "best_model.pdb_B SES surface": minimum -28.27, mean
-4.359, maximum 25.61
> key lipophilicity :-20 :0 :20 showTool true
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T114/T114_hydrophobic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../T114/T114_hydrophobic_rot.mp4
> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults T115
> ui mousemode right translate
> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T115/best_model.pdb"
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
Alignment identifier is 1/A
Alignment identifier is 1/B
Exception ignored in tp_clear of:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/grako/ast.py", line 63, in update
for d in args:
TypeError: NoneType takes no arguments
13 hydrogen bonds found
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T115/T115_contacts_hbonds.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../T115/T115_contacts_hbonds_rot.mp4
Changed 1967 atom styles
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T115/T115_sphere.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../T115/T115_sphere_rot.mp4
Changed 0 atom styles
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -21.97, mean
-4.44, maximum 11.92
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -16.18, mean
-0.12, maximum 14.03
> key red-white-blue :-10 :0 :10 showTool true
> ui mousemode right "color key"
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T115/T115_coulombic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../T115/T115_coulombic_rot.mp4
Changed 0 atom styles
Map values for surface "best_model.pdb_A SES surface": minimum -27.82, mean
-5.541, maximum 26.28
Map values for surface "best_model.pdb_B SES surface": minimum -26.13, mean
-3.721, maximum 22.6
> key lipophilicity :-20 :0 :20 showTool true
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T115/T115_hydrophobic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../T115/T115_hydrophobic_rot.mp4
> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults T116
> ui mousemode right translate
> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T116/best_model.pdb"
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
Alignment identifier is 1/A
Alignment identifier is 1/B
2 hydrogen bonds found
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T116/T116_contacts_hbonds.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../T116/T116_contacts_hbonds_rot.mp4
Changed 1963 atom styles
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T116/T116_sphere.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../T116/T116_sphere_rot.mp4
Changed 0 atom styles
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -20.69, mean
-4.04, maximum 11.91
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -18.26, mean
-1.14, maximum 10.07
> key red-white-blue :-10 :0 :10 showTool true
> ui mousemode right "color key"
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T116/T116_coulombic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../T116/T116_coulombic_rot.mp4
Changed 0 atom styles
Map values for surface "best_model.pdb_A SES surface": minimum -25.18, mean
-5.076, maximum 23.22
Map values for surface "best_model.pdb_B SES surface": minimum -24.51, mean
-0.2534, maximum 23.12
> key lipophilicity :-20 :0 :20 showTool true
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T116/T116_hydrophobic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../T116/T116_hydrophobic_rot.mp4
> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults T117
> ui mousemode right translate
> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T117/best_model.pdb"
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
Alignment identifier is 1/A
Alignment identifier is 1/B
7 hydrogen bonds found
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T117/T117_contacts_hbonds.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../T117/T117_contacts_hbonds_rot.mp4
Changed 2188 atom styles
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T117/T117_sphere.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../T117/T117_sphere_rot.mp4
Changed 0 atom styles
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -21.97, mean
-5.18, maximum 11.74
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -11.49, mean
-0.01, maximum 12.92
> key red-white-blue :-10 :0 :10 showTool true
> ui mousemode right "color key"
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T117/T117_coulombic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../T117/T117_coulombic_rot.mp4
Changed 0 atom styles
Map values for surface "best_model.pdb_A SES surface": minimum -24.83, mean
-4.713, maximum 23.71
Map values for surface "best_model.pdb_B SES surface": minimum -26.96, mean
-3.615, maximum 22.23
> key lipophilicity :-20 :0 :20 showTool true
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T117/T117_hydrophobic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../T117/T117_hydrophobic_rot.mp4
> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults T118
> ui mousemode right translate
> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T118/best_model.pdb"
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
Alignment identifier is 1/A
Alignment identifier is 1/B
2 hydrogen bonds found
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T118/T118_contacts_hbonds.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../T118/T118_contacts_hbonds_rot.mp4
Changed 2432 atom styles
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T118/T118_sphere.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../T118/T118_sphere_rot.mp4
Changed 0 atom styles
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -19.25, mean
-3.88, maximum 12.91
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -20.78, mean
-1.43, maximum 12.45
> key red-white-blue :-10 :0 :10 showTool true
> ui mousemode right "color key"
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T118/T118_coulombic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../T118/T118_coulombic_rot.mp4
Changed 0 atom styles
Map values for surface "best_model.pdb_A SES surface": minimum -28.85, mean
-5.105, maximum 24.32
Map values for surface "best_model.pdb_B SES surface": minimum -26.97, mean
-2.082, maximum 26.52
> key lipophilicity :-20 :0 :20 showTool true
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T118/T118_hydrophobic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../T118/T118_hydrophobic_rot.mp4
> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults T119
> ui mousemode right translate
> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T119/best_model.pdb"
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
Alignment identifier is 1/A
Alignment identifier is 1/B
2 hydrogen bonds found
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T119/T119_contacts_hbonds.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../T119/T119_contacts_hbonds_rot.mp4
Changed 2455 atom styles
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T119/T119_sphere.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../T119/T119_sphere_rot.mp4
Changed 0 atom styles
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -23.33, mean
-4.23, maximum 12.18
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -14.27, mean
-1.20, maximum 13.12
> key red-white-blue :-10 :0 :10 showTool true
> ui mousemode right "color key"
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T119/T119_coulombic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../T119/T119_coulombic_rot.mp4
Changed 0 atom styles
Map values for surface "best_model.pdb_A SES surface": minimum -25.72, mean
-5.308, maximum 25.88
Map values for surface "best_model.pdb_B SES surface": minimum -27.73, mean
-4.331, maximum 22.87
> key lipophilicity :-20 :0 :20 showTool true
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T119/T119_hydrophobic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../T119/T119_hydrophobic_rot.mp4
> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults T120
> ui mousemode right translate
> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T120/best_model.pdb"
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
Alignment identifier is 1/A
Alignment identifier is 1/B
8 hydrogen bonds found
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T120/T120_contacts_hbonds.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../T120/T120_contacts_hbonds_rot.mp4
Changed 2482 atom styles
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T120/T120_sphere.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../T120/T120_sphere_rot.mp4
Changed 0 atom styles
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -20.23, mean
-4.49, maximum 11.32
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -17.03, mean
-2.50, maximum 13.02
> key red-white-blue :-10 :0 :10 showTool true
> ui mousemode right "color key"
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T120/T120_coulombic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../T120/T120_coulombic_rot.mp4
Changed 0 atom styles
Map values for surface "best_model.pdb_A SES surface": minimum -29.42, mean
-5.278, maximum 21.3
Map values for surface "best_model.pdb_B SES surface": minimum -25.55, mean
-3.796, maximum 25.68
> key lipophilicity :-20 :0 :20 showTool true
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T120/T120_hydrophobic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../T120/T120_hydrophobic_rot.mp4
> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults T121
> ui mousemode right translate
> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T121/best_model.pdb"
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
Alignment identifier is 1/A
Alignment identifier is 1/B
1 hydrogen bonds found
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T121/T121_contacts_hbonds.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../T121/T121_contacts_hbonds_rot.mp4
Changed 3082 atom styles
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T121/T121_sphere.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../T121/T121_sphere_rot.mp4
Changed 0 atom styles
Exception ignored in tp_clear of:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/grako/ast.py", line 59, in update
def upairs(d):
TypeError: NoneType takes no arguments
===== 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 Metal - 88
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple
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: MacBookPro18,2
Model Number: Z14W00106LL/A
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 32 GB
System Firmware Version: 10151.101.3
OS Loader Version: 10151.101.3
Software:
System Software Overview:
System Version: macOS 14.4.1 (23E224)
Kernel Version: Darwin 23.4.0
Time since boot: 9 days, 13 hours, 20 minutes
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 24
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
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 , 19 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 , 19 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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