![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 18 months ago
Closed 18 months ago
#15066 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.6.5-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00007000179f4000 (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 0x00007ff85edcb7c0 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mouse_modes/mousemodes.py", line 526 in _cursor_position
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mouse_modes/mousemodes.py", line 483 in mouse_pause_tracking
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 151 in _redraw_timer_callback
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, chimerax.pdb_lib._load_libs, 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, PIL._imagingmath, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite, lxml._elementpath, lxml.etree, pandas._libs.tslibs.ccalendar, pandas._libs.tslibs.np_datetime, pandas._libs.tslibs.dtypes, pandas._libs.tslibs.base, pandas._libs.tslibs.nattype, pandas._libs.tslibs.timezones, pandas._libs.tslibs.fields, pandas._libs.tslibs.timedeltas, pandas._libs.tslibs.tzconversion, pandas._libs.tslibs.timestamps, pandas._libs.properties, pandas._libs.tslibs.offsets, pandas._libs.tslibs.strptime, pandas._libs.tslibs.parsing, pandas._libs.tslibs.conversion, pandas._libs.tslibs.period, pandas._libs.tslibs.vectorized, pandas._libs.ops_dispatch, pandas._libs.missing, pandas._libs.hashtable, pandas._libs.algos, pandas._libs.interval, pandas._libs.lib, pandas._libs.ops, numexpr.interpreter, pandas._libs.hashing, pandas._libs.arrays, pandas._libs.tslib, pandas._libs.sparse, pandas._libs.internals, pandas._libs.indexing, pandas._libs.index, pandas._libs.writers, pandas._libs.join, pandas._libs.window.aggregations, pandas._libs.window.indexers, pandas._libs.reshape, pandas._libs.groupby, pandas._libs.json, pandas._libs.parsers, pandas._libs.testing, scipy._lib._ccallback_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._isolve._iterative, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.linalg._flinalg, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._minpack2, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize.__nnls, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, scipy.ndimage._nd_image, _ni_label, scipy.ndimage._ni_label, scipy.integrate._odepack, scipy.integrate._quadpack, scipy.integrate._vode, scipy.integrate._dop, scipy.integrate._lsoda, scipy.special.cython_special, scipy.stats._stats, scipy.stats.beta_ufunc, scipy.stats._boost.beta_ufunc, scipy.stats.binom_ufunc, scipy.stats._boost.binom_ufunc, scipy.stats.nbinom_ufunc, scipy.stats._boost.nbinom_ufunc, scipy.stats.hypergeom_ufunc, scipy.stats._boost.hypergeom_ufunc, scipy.stats.ncf_ufunc, scipy.stats._boost.ncf_ufunc, scipy.stats.ncx2_ufunc, scipy.stats._boost.ncx2_ufunc, scipy.stats.nct_ufunc, scipy.stats._boost.nct_ufunc, scipy.stats.skewnorm_ufunc, scipy.stats._boost.skewnorm_ufunc, scipy.stats.invgauss_ufunc, scipy.stats._boost.invgauss_ufunc, scipy.interpolate._fitpack, scipy.interpolate.dfitpack, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, scipy.stats._biasedurn, scipy.stats._levy_stable.levyst, scipy.stats._stats_pythran, scipy._lib._uarray._uarray, scipy.stats._statlib, scipy.stats._sobol, scipy.stats._qmc_cy, scipy.stats._mvn, scipy.stats._rcont.rcont, scipy.cluster._vq, scipy.cluster._hierarchy, scipy.cluster._optimal_leaf_ordering (total: 205)
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{
"uptime" : 19000,
"procRole" : "Background",
"version" : 2,
"userID" : 2122167388,
"deployVersion" : 210,
"modelCode" : "iMac18,1",
"coalitionID" : 1428,
"osVersion" : {
"train" : "macOS 13.6.5",
"build" : "22G621",
"releaseType" : "User"
},
"captureTime" : "2024-04-29 15:45:20.1260 +0200",
"incident" : "B46B12CE-0E6F-4F35-9B85-AD728299083C",
"pid" : 10159,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-04-29 11:56:03.1149 +0200",
"procStartAbsTime" : 5658251786768,
"procExitAbsTime" : 19415204111818,
"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":"AE8AD2DB-D36A-5002-815D-2039C5F04D91","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "77D1A10D-75DB-DEAE-3308-F078D9BDDCE8",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"sip" : "enabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 140737487245143\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffef1000-7fffffef2000 [ 4K] r-x\/r-x SM=SHM ",
"exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":10159},
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 140737487245143\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffef1000-7fffffef2000 [ 4K] r-x\/r-x SM=SHM ",
"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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"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703589044224,
"size" : 40944,
"uuid" : "982c4eec-b380-3c37-ab95-14150e14dd61",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
},
{
"size" : 0,
"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
},
{
"source" : "P",
"arch" : "x86_64h",
"base" : 140703589261312,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 4837360,
"uuid" : "46af372c-e1f2-33b3-a032-d5ac06f50c80",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "1979.102"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703751598080,
"CFBundleShortVersionString" : "2.1.1",
"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 3112954,
"uuid" : "1afba695-4d4c-3b3e-9911-92f50c585ba4",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703640489984,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 16814080,
"uuid" : "d6809150-c4c5-3370-b0eb-87b0611cde58",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2299.77.138"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703585329152,
"size" : 624112,
"uuid" : "022fb827-a638-3286-a672-588c661526e0",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
}
],
"sharedCache" : {
"base" : 140703584706560,
"size" : 21474836480,
"uuid" : "bf87914a-b30e-39fd-b5da-b0f495dca399"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.2G resident=0K(0%) swapped_out_or_unallocated=1.2G(100%)\nWritable regions: Total=2.9G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.9G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG backing stores 1440K 8 \nCG image 460K 51 \nColorSync 264K 30 \nCoreAnimation 796K 110 \nCoreGraphics 16K 3 \nCoreUI image data 2996K 45 \nFoundation 36K 2 \nKernel Alloc Once 8K 1 \nMALLOC 2.4G 798 \nMALLOC guard page 32K 7 \nMALLOC_LARGE (reserved) 256K 1 reserved VM address space (unallocated)\nMach message 16K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 116K 29 \nStack 173.2M 30 \nStack Guard 56.0M 1 \nVM_ALLOCATE 275.7M 243 \nVM_ALLOCATE (reserved) 32.0M 1 reserved VM address space (unallocated)\n__CTF 824 1 \n__DATA 54.4M 948 \n__DATA_CONST 41.5M 406 \n__DATA_DIRTY 1812K 230 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 217.5M 301 \n__OBJC_RO 66.3M 1 \n__OBJC_RW 2013K 2 \n__TEXT 1.0G 930 \ndyld private memory 420K 4 \nmapped file 267.4M 72 \nshared memory 3020K 34 \n=========== ======= ======= \nTOTAL 4.6G 4303 \nTOTAL, minus reserved VM space 4.6G 4303 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "19bca3c7d47bc551d1c31d3bceab6d665dbab763",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "5fb4245a1bbfe8005e33a1e1",
"factorPackIds" : {
},
"deploymentId" : 240000021
},
{
"rolloutId" : "5ffde50ce2aacd000d47a95f",
"factorPackIds" : {
},
"deploymentId" : 240000372
}
],
"experiments" : [
]
}
}
===== Log before crash start =====
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/j.govers/Downloads/cryosparc_P3_J751_mesh_pdb.pdb
> open /Users/j.govers/Downloads/cryosparc_P3_J751_map(1).mrc
Opened cryosparc_P3_J751_map(1).mrc as #2, grid size 160,160,160, pixel 3.18,
shown at level 0.118, step 1, values float32
> color #2 #b2b2b290 models
> set bgColor white
> color #2 #bfa59d90 models
> color #2 #bfa59d8f models
> volume #2 level 0.2531
> open /Users/j.govers/Downloads/XL-MS_mapping.cxs
> To restore session:
>
> * install XMAS bundle version 1.1.3 or newer
>
Unable to restore session: need to install missing bundle
Downloading bundle ChimeraX_XMAS-1.1.3-py3-none-any.whl
Installed ChimeraX-XMAS (1.1.3)
> open /Users/j.govers/Downloads/XL-MS_mapping.cxs
opened ChimeraX session
> hide #10 models
> show #15 models
> hide #15 models
> show #15 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/D #1/E #2/D #2/E
Alignment identifier is 1
> select #1/D-E:12 #2/D-E:12
48 atoms, 44 bonds, 4 residues, 2 models selected
> select #1/D-E:12 #2/D-E:12
48 atoms, 44 bonds, 4 residues, 2 models selected
1 [ID: 1] region 4 chains [12] RMSD: 0.000
> select #1/D-E:16 #2/D-E:16
88 atoms, 84 bonds, 4 residues, 2 models selected
> select #1/D-E:16 #2/D-E:16
88 atoms, 84 bonds, 4 residues, 2 models selected
1 [ID: 1] region 4 chains [16] RMSD: 0.000
> select #1/E:16-23
140 atoms, 141 bonds, 8 residues, 1 model selected
> hide #15 models
> close #14
> close
> open "/Users/j.govers/Documents/ChimeraX/ranked_0 (1).pdb"
Chain information for ranked_0 (1).pdb #1
---
Chain | Description
A B C | No description available
D E | No description available
F G | No description available
H I | No description available
J K | No description available
L M | No description available
> hide atoms
> show cartoons
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting full
> graphics silhouettes false
> color /A-C #004387ff
> hide cartoons
> select /A-C
12213 atoms, 12303 bonds, 774 residues, 1 model selected
> show sel cartoons
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain /A /B /C
Alignment identifier is 1
> select /A-C:13
66 atoms, 63 bonds, 3 residues, 1 model selected
> show sel atoms
> color sel red
> select clear
> select /D
9884 atoms, 9960 bonds, 606 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select /B:13@CA
1 atom, 1 residue, 1 model selected
> select clear
> shape sphere radius 5
> close #2
> shape sphere radius 1
> select add #2
1 model selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,4.5167,0,1,0,-5.8787,0,0,1,13.454
> view matrix models #2,1,0,0,42.156,0,1,0,0.1678,0,0,1,3.6096
> select /A-C:13
66 atoms, 63 bonds, 3 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> select clear
> shape cylinder radius 40 height 10
> select add #3
1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.061653,0.74918,-0.65949,0,-0.070281,-0.65584,-0.75162,0,-0.99562,0.092688,0.012219,0
> view matrix models
> #3,-0.29771,0.47549,-0.82781,0,-0.48547,-0.82205,-0.29759,0,-0.822,0.31328,0.47557,0
> color #3 #ca473eff
> view matrix models
> #3,0.16443,-0.30588,0.93776,0,-0.97425,-0.19907,0.1059,0,0.15429,-0.93103,-0.33073,0
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.16443,-0.30588,0.93776,8.8014,-0.97425,-0.19907,0.1059,-6.8525,0.15429,-0.93103,-0.33073,16.097
> view matrix models
> #3,0.16443,-0.30588,0.93776,9.4838,-0.97425,-0.19907,0.1059,-6.4146,0.15429,-0.93103,-0.33073,17.969
> view matrix models
> #3,0.16443,-0.30588,0.93776,41.434,-0.97425,-0.19907,0.1059,-1.5535,0.15429,-0.93103,-0.33073,8.0621
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 0 maps.
> view matrix models
> #3,0.16443,-0.30588,0.93776,39.273,-0.97425,-0.19907,0.1059,0.056249,0.15429,-0.93103,-0.33073,3.7536
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.23986,-0.26199,0.93479,39.273,-0.96159,-0.19647,0.19168,0.056249,0.13344,-0.94486,-0.29905,3.7536
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.23986,-0.26199,0.93479,40.411,-0.96159,-0.19647,0.19168,0.20636,0.13344,-0.94486,-0.29905,3.3763
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> select /D]
Nothing selected
> select /D
9884 atoms, 9960 bonds, 606 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> ui mousemode right "tape measure"
> marker segment #4 position 45.4,-6.507,22.33 toPosition 48.07,-8.983,19.87
> color yellow radius 0.1 label 4.392 labelHeight 0.4392 labelColor yellow
> select add #3
9884 atoms, 9960 bonds, 606 residues, 2 models selected
> select subtract #3
9884 atoms, 9960 bonds, 606 residues, 1 model selected
> show #3 models
> hide #3 models
> shape cylinder radius 40 height 1
> color #5 #caab91ff
> color #5 #ca635dff
> color #5 #ca7c7cff
> close #3
> close #4
> select add #5
9884 atoms, 9960 bonds, 606 residues, 2 models selected
> select add #1
67123 atoms, 67729 bonds, 4242 residues, 2 models selected
> select subtract #1
1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.44955,-0.83691,-0.31222,0,0.6459,0.546,-0.53357,0,0.61702,0.038203,0.78602,0
> view matrix models
> #5,0.18412,-0.40109,-0.89735,0,0.56918,0.78781,-0.23534,0,0.80133,-0.46742,0.37334,0
> view matrix models
> #5,0.19866,-0.35908,-0.91192,0,0.49995,0.83742,-0.22083,0,0.84296,-0.41205,0.34589,0
> turn
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.19866,-0.35908,-0.91192,4.8533,0.49995,0.83742,-0.22083,-5.7019,0.84296,-0.41205,0.34589,14.547
> view matrix models
> #5,0.19866,-0.35908,-0.91192,4.5633,0.49995,0.83742,-0.22083,-5.0082,0.84296,-0.41205,0.34589,13.882
> turn
> view matrix models
> #5,0.16213,-0.30163,-0.93954,4.5633,0.50899,0.84126,-0.18225,-5.0082,0.84537,-0.44867,0.28992,13.882
> turn
> view matrix models
> #5,0.19866,-0.35908,-0.91192,5.527,0.49995,0.83742,-0.22083,-6.3588,0.84296,-0.41205,0.34589,15.891
> view matrix models
> #5,0.19866,-0.35908,-0.91192,5.1206,0.49995,0.83742,-0.22083,-5.7366,0.84296,-0.41205,0.34589,15.02
> turn
> view matrix models
> #5,0.19866,-0.35908,-0.91192,41.916,0.49995,0.83742,-0.22083,-0.33779,0.84296,-0.41205,0.34589,1.8386
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.15393,-0.29245,-0.94381,41.916,0.50957,0.84187,-0.17775,-0.33779,0.84655,-0.45358,0.27862,1.8386
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.15393,-0.29245,-0.94381,42.183,0.50957,0.84187,-0.17775,0.47707,0.84655,-0.45358,0.27862,2.2423
> hide #5 models
> show #5 models
> view matrix models
> #5,0.15393,-0.29245,-0.94381,41.754,0.50957,0.84187,-0.17775,0.16902,0.84655,-0.45358,0.27862,2.2283
> select clear
> turn
> select add #5
1 model selected
> ui mousemode right "rotate selected models"
> select subtract #5
Nothing selected
> turn
> select add #5
1 model selected
> view matrix models
> #5,0.16033,-0.28906,-0.94379,41.754,0.5108,0.84247,-0.17126,0.16902,0.84462,-0.45463,0.28272,2.2283
> view matrix models
> #5,0.17756,-0.28539,-0.94182,41.754,0.5137,0.84317,-0.15865,0.16902,0.83939,-0.45565,0.29632,2.2283
> turn
> ui mousemode right "translate selected models"
> hide #2 models
> show #2 models
> hide #2 models
> select subtract #5
Nothing selected
> ui mousemode right distance
> ui mousemode right "pick blobs"
> ui mousemode right "tape measure"
> marker segment #3 position 33.94,20.3,1.792 toPosition 37.83,20.98,0.5472
> color yellow radius 0.1 label 4.134 labelHeight 0.4134 labelColor yellow
> select /A-C:125
60 atoms, 60 bonds, 3 residues, 1 model selected
> color sel hot pink
> marker segment #3 position 38.98,36.09,-15.17 toPosition 31.28,34.69,-12.73
> color yellow radius 0.1 label 8.206 labelHeight 0.8206 labelColor yellow
> select up
840 atoms, 843 bonds, 51 residues, 1 model selected
> select up
12213 atoms, 12303 bonds, 774 residues, 1 model selected
> select down
840 atoms, 843 bonds, 51 residues, 1 model selected
> select down
60 atoms, 60 bonds, 3 residues, 1 model selected
> select /D
9884 atoms, 9960 bonds, 606 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select up
67123 atoms, 67729 bonds, 4242 residues, 1 model selected
> select down
9884 atoms, 9960 bonds, 606 residues, 1 model selected
> select /A-C:135
33 atoms, 30 bonds, 3 residues, 1 model selected
> color sel lime
> marker segment #3 position 24.77,17.61,-28.4 toPosition 28.43,18.26,-29.55
> color yellow radius 0.1 label 3.883 labelHeight 0.3883 labelColor yellow
> marker segment #3 position 24.77,17.61,-28.4 toPosition 28.45,18.27,-29.56
> color yellow radius 0.1 label 3.905 labelHeight 0.3905 labelColor yellow
> select /A-C:154
57 atoms, 54 bonds, 3 residues, 1 model selected
> color sel cyan
> marker segment #3 position 43.17,0.668,-21.39 toPosition 35.4,-0.9303,-19.14
> color yellow radius 0.1 label 8.245 labelHeight 0.8245 labelColor yellow
> marker segment #3 position 55.72,-17.09,12.47 toPosition 49.37,-18.23,14.5
> color yellow radius 0.1 label 6.764 labelHeight 0.6764 labelColor yellow
> marker segment #3 position 48.52,23.05,11.43 toPosition 41.97,22.01,13.59
> color yellow radius 0.1 label 6.976 labelHeight 0.6976 labelColor yellow
> marker segment #3 position 43.17,0.668,-21.39 toPosition
> 35.82,-0.8546,-19.23 color yellow radius 0.1 label 7.813 labelHeight 0.7813
> labelColor yellow
> marker segment #3 position 49.63,-31.23,-19.01 toPosition
> 41.37,-32.82,-16.68 color yellow radius 0.1 label 8.728 labelHeight 0.8728
> labelColor yellow
> select /A-C:204
36 atoms, 33 bonds, 3 residues, 1 model selected
> color sel yellow
> marker segment #3 position 32.91,12.62,-32.5 toPosition 29.24,11.61,-31.69
> color yellow radius 0.1 label 3.895 labelHeight 0.3895 labelColor yellow
> marker segment #3 position 32.91,12.62,-32.5 toPosition 29.38,11.72,-31.61
> color yellow radius 0.1 label 3.754 labelHeight 0.3754 labelColor yellow
> marker segment #3 position 32.91,12.62,-32.5 toPosition 29.61,14.57,-32.54
> color yellow radius 0.1 label 3.838 labelHeight 0.3838 labelColor yellow
> undo
> color sel yellow
> marker segment #3 position 52.12,-35.79,9.394 toPosition 49.93,-36.53,9.782
> color yellow radius 0.1 label 2.348 labelHeight 0.2348 labelColor yellow
> marker segment #3 position 32.91,12.62,-32.5 toPosition 29.4,12.22,-31.24
> color yellow radius 0.1 label 3.749 labelHeight 0.3749 labelColor yellow
> marker segment #3 position 32.97,20.36,-32.72 toPosition 52.12,-10.04,15.86
> color yellow radius 0.1 label 60.42 labelHeight 6.042 labelColor yellow
> select /A-C:204
36 atoms, 33 bonds, 3 residues, 1 model selected
> select /A-C:225
48 atoms, 45 bonds, 3 residues, 1 model selected
> close #3
> ui mousemode right "tape measure"
> color sel magenta
> marker segment #3 position 26.1,15.13,-14.68 toPosition 32.95,16.13,-16.92
> color yellow radius 0.1 label 7.279 labelHeight 0.7279 labelColor yellow
> hide #5 models
> close #5
> select /A-C:204
36 atoms, 33 bonds, 3 residues, 1 model selected
> select clear
> color A-C:225 lime
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color /A-C:225 lime
> color /A-C:225 magenta
> color /A-C:13 red
> color /A-C #004387ff
> select /D /F /H
23552 atoms, 23788 bonds, 1495 residues, 1 model selected
> show sel cartoons
> color sel light gray
> select clear
> color /D:137
> color /D:137 #95BCFF
> show cartoons
> undo
> color /D:137 #95BCFF
> select /D:137
22 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select clear
> show atoms
> undo
> select /D:137
22 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> color /D:271 #FD333B show
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color /D:271 #FD333B
> select /D:271 color sel #FD333B show sel
Expected a keyword
> select /D:271 color sel #FD333B show sel atoms
Expected a keyword
> select /D:271 color sel #FD333B
Expected a keyword
> select /D:271
19 atoms, 18 bonds, 1 residue, 1 model selected
> color sel #FD333B
> show sel atoms
> select clear
> select /D:31 /D:152 /D:34 /D:493 /D:236 /D:1 /D:237 /D:38 color sel #FD333B
> show sel atoms
Expected a keyword
> select /D:31 /D:152 /D:34 /D:493 /D:236 /D:1 /D:237 /D:38
130 atoms, 124 bonds, 8 residues, 1 model selected
> color sel #FD333B show sel atoms
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> show sel atoms
> select clear
> close #3
> select /D:31 /D:152 /D:34 /D:493 /D:236 /D:1 /D:237 /D:38
130 atoms, 124 bonds, 8 residues, 1 model selected
> color sel #FD333B
> select clear
> select /D:436 /D:574 /D:137
45 atoms, 42 bonds, 3 residues, 1 model selected
> color sel #95BCFF
> show sel atoms
> select clear
> select /D:236 /D:436 /D:271
53 atoms, 50 bonds, 3 residues, 1 model selected
> color sel #A4C5FF
> show sel atoms
> select clear
> select /D:236 /D:436 /D:271
53 atoms, 50 bonds, 3 residues, 1 model selected
> select clear
> select /D:236 /D:436 /D:271
53 atoms, 50 bonds, 3 residues, 1 model selected
> select clear
> select /D:218
19 atoms, 18 bonds, 1 residue, 1 model selected
> color sel #FF525A
> show sel atoms
> select clear
> select /D:436 /D:574 /D:137
45 atoms, 42 bonds, 3 residues, 1 model selected
> color sel #95BCFF
> show sel atoms
> select /D:31 /D:152 /D:34 /D:493 /D:236 /D:1 /D:237 /D:38
130 atoms, 124 bonds, 8 residues, 1 model selected
> color sel #FD333B
> show sel atoms
> select clear
> select /D:436 /D:574 /D:137
45 atoms, 42 bonds, 3 residues, 1 model selected
> select clear
> select /D:236 /D:436 /D:271
53 atoms, 50 bonds, 3 residues, 1 model selected
> color sel #A4C5FF
> show sel atoms
> select /D:218
19 atoms, 18 bonds, 1 residue, 1 model selected
> color sel #FF525A
> show sel atoms
> select clear
> select /D:282 /D:493 /D:38 /D:436 /D:34 /D:31
94 atoms, 89 bonds, 6 residues, 1 model selected
> color sel #FFA3A8
> undo
> color sel #FFA3A8
> show sel atoms
> select /D:574
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel # #4E8EFF
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel #4E8EFF
> show sel atoms
> select /D:436 /D:574 /D:137
45 atoms, 42 bonds, 3 residues, 1 model selected
> color sel #95BCFF
> select clear
> select /D:31 /D:152 /D:34 /D:493 /D:236 /D:1 /D:237 /D:38
130 atoms, 124 bonds, 8 residues, 1 model selected
> color sel #FD333B
> select clear
> select /D:574
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> select /D:218
19 atoms, 18 bonds, 1 residue, 1 model selected
> color sel #FF525A
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-20.7.2
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640
OpenGL vendor: Intel Inc.
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac18,1
Processor Name: Dual-Core Intel Core i5
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 4 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 526.0.0.0.0
OS Loader Version: 577.140.2~22
SMC Version (system): 2.39f40
Software:
System Software Overview:
System Version: macOS 13.6.5 (22G621)
Kernel Version: Darwin 22.6.0
Time since boot: 5 hours, 24 minutes
Graphics/Displays:
Intel Iris Plus Graphics 640:
Chipset Model: Intel Iris Plus Graphics 640
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x5926
Revision ID: 0x0006
Metal Support: Metal 3
Displays:
iMac:
Display Type: LCD
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
HP E23 G4:
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: CN42370YGF
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: DVI or HDMI
Adapter Firmware Version: b.74
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-XMAS: 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
et-xmlfile: 1.1.0
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
openpyxl: 3.1.2
openvr: 1.23.701
packaging: 21.3
pandas: 2.2.2
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
QtRangeSlider: 0.1.5
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
seaborn: 0.13.2
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 , 18 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 18 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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