![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 months ago
Closed 7 months ago
#17347 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.3.2-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x00000001edb2c840 (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, 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.surface._surface, 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, psutil._psutil_osx, psutil._psutil_posix, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, PIL._webp, chimerax.dssp._dssp (total: 62)
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"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac14,9",
"coalitionID" : 14651,
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"build" : "24D81",
"releaseType" : "User"
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"codeSigningMonitor" : 1,
"incident" : "3A491082-9E7F-4F51-87F0-1EAF998DB013",
"pid" : 90952,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-04-09 15:35:41.0770 +0100",
"procStartAbsTime" : 17199854042709,
"procExitAbsTime" : 17461955413249,
"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":"710CC797-3D63-5E95-911A-5391B7D6613D","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "8082133D-FF55-A5C9-9B39-07ADD6399E0D",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
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"wakeTime" : 118256,
"sleepWakeUUID" : "6F9C8067-83C2-423F-8E8A-14E5AE58EB76",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4309860352\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100e34000-100e38000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":90952},
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4309860352\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100e34000-100e38000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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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/omallen/OneDrive - The Francis Crick Institute/PhD/Paper
> work/chimerasessions/ApoandPIP_HBCcomparison.cxs" format session
Opened Apo_Emready.mrc as #1, grid size 440,440,440, pixel 0.65, shown at
level 5.06, step 1, values float32
Opened PIP_Emready.mrc as #4, grid size 440,440,440, pixel 0.65, shown at
level 4.03, step 1, values float32
opened ChimeraX session
> show #!1 models
> show #!2 models
> hide #!2 models
> hide #!3 models
> hide #!1 models
> hide #!4 models
> open /Users/omallen/Library/CloudStorage/OneDrive-
> TheFrancisCrickInstitute/PhD/Apo/cryosparc_P256_J1166_008_volume_map_sharp.mrc
Opened cryosparc_P256_J1166_008_volume_map_sharp.mrc as #5, grid size
440,440,440, pixel 0.65, shown at level 0.0436, step 2, values float32
> volume #5 step 1
> volume #5 level 0.08382
> volume #5 level 0.09052
> show #!2 models
> ui tool show Toolbar
> select add #2
9206 atoms, 9444 bonds, 36 pseudobonds, 1222 residues, 4 models selected
> show sel & #!2 cartoons
> ui tool show "Fit in Map"
> fitmap #2 inMap #5
Fit molecule
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb (#2)
to map cryosparc_P256_J1166_008_volume_map_sharp.mrc (#5) using 8726 atoms
average map value = 0.3494, steps = 120
shifted from previous position = 4.18
rotated from previous position = 7.05 degrees
atoms outside contour = 1481, contour level = 0.090521
Position of
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb (#2)
relative to cryosparc_P256_J1166_008_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.99997494 0.00707934 0.00002711 -1.01256812
-0.00707933 0.99997493 -0.00017045 1.03163649
-0.00002831 0.00017025 0.99999999 0.78746983
Axis 0.02405541 0.00391298 -0.99970297
Axis point 145.67275394 140.80305016 0.00000000
Rotation angle (degrees) 0.40573999
Shift along axis -0.80755690
> select clear
> surface dust #5 size 6.5
> volume #5 style mesh
> hide #!5 models
> show #!5 models
> volume #5 level 0.1205
> select #2/A:50
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:55
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/A:53
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/A:53-70
147 atoms, 153 bonds, 18 residues, 1 model selected
> select #2/A:53-75
192 atoms, 201 bonds, 23 residues, 1 model selected
> select #2/A:53-77
211 atoms, 221 bonds, 25 residues, 1 model selected
> select #2/A:53-80
233 atoms, 243 bonds, 28 residues, 1 model selected
> select #2/A:53-82
249 atoms, 259 bonds, 30 residues, 1 model selected
> ui tool show "Surface Zone"
> surface zone #5 nearAtoms #2 distance 3.9
> surface zone #5 nearAtoms #2 distance 4.1
> surface zone #5 nearAtoms #2 distance 1.77
> surface zone #5 nearAtoms sel distance 1.78
> surface zone #5 nearAtoms sel distance 1.86
> surface zone #5 nearAtoms sel distance 2.29
> select add #2
8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select #2/A:53-82
249 atoms, 259 bonds, 30 residues, 1 model selected
> show sel cartoons
> show sel atoms
> volume #5 style surface
> fitmap #2 inMap #5
Fit molecule
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb (#2)
to map cryosparc_P256_J1166_008_volume_map_sharp.mrc (#5) using 8726 atoms
average map value = 0.3494, steps = 40
shifted from previous position = 0.00559
rotated from previous position = 0.0109 degrees
atoms outside contour = 2074, contour level = 0.12055
Position of
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb (#2)
relative to cryosparc_P256_J1166_008_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.99997481 0.00709769 -0.00004926 -1.00538528
-0.00709769 0.99997481 0.00000200 1.01711711
0.00004927 -0.00000165 1.00000000 0.80377550
Axis -0.00025765 -0.00694035 -0.99997588
Axis point 142.00535630 142.18303541 0.00000000
Rotation angle (degrees) 0.40668096
Shift along axis -0.81055623
> color #5 #d6d6d6ff models
> color #5 #d6d6d600 models
> color #5 #d6d6d634 models
> color #5 #d6d6d633 models
> color sel byhetero
> select clear
> volume #5 level 0.09427
No atoms selected for zoning
> select #2/A:53-82
249 atoms, 259 bonds, 30 residues, 1 model selected
> surface zone #5 nearAtoms sel distance 2.76
> surface zone #5 nearAtoms sel distance 1.4
> select clear
> select #2/A:53-82
249 atoms, 259 bonds, 30 residues, 1 model selected
> surface zone #5 nearAtoms sel distance 1.4
> surface zone #5 nearAtoms sel distance 1.5
> surface zone #5 nearAtoms sel distance 1.6
> surface zone #5 nearAtoms sel distance 1.7
> surface zone #5 nearAtoms sel distance 1.8
> volume #5 level 0.1243
> volume #5 level 0.1506
> volume #5 level 0.09803
> show #!1 models
> resample #1 onGrid #5
Unknown command: resample #1 onGrid #5
> vop resample #1 onGrid #5
Opened Apo_Emready.mrc resampled as #6, grid size 440,440,440, pixel 0.65,
shown at step 1, values float32
> surface zone #1 nearAtoms sel distance 5.78
> surface zone #1 nearAtoms sel distance 5.71
> surface zone #1 nearAtoms sel distance 0.98
> surface zone #6 nearAtoms sel distance 3.9
> surface zone #6 nearAtoms sel distance 4.03
> surface zone #6 nearAtoms sel distance 1.54
> volume #6 color #d6d6d6
> volume #6 color #d6d6d633
> surface zone #6 nearAtoms sel distance 1.52
> surface zone #6 nearAtoms sel distance 1.9
> volume #6 level 1.359
> volume #6 level 7.281
> volume #6 level 4.038
> volume #6 level 2.117
> surface dust #5 size 6.5
> surface zone #6 nearAtoms sel distance 1.9
> surface zone #5 nearAtoms sel distance 3.9
> surface zone #5 nearAtoms sel distance 3.8
> surface zone #5 nearAtoms sel distance 3.7
> surface zone #5 nearAtoms sel distance 3.6
> surface zone #5 nearAtoms sel distance 3.5
> surface zone #5 nearAtoms sel distance 3.4
> surface zone #5 nearAtoms sel distance 3.3
> surface zone #5 nearAtoms sel distance 3.2
> surface zone #5 nearAtoms sel distance 3.1
> surface zone #5 nearAtoms sel distance 3
> surface zone #5 nearAtoms sel distance 2.9
> surface zone #5 nearAtoms sel distance 2.8
> surface zone #5 nearAtoms sel distance 2.7
> surface zone #5 nearAtoms sel distance 2.6
> surface zone #5 nearAtoms sel distance 2.5
> surface zone #5 nearAtoms sel distance 2.4
> surface zone #5 nearAtoms sel distance 2.3
> surface zone #5 nearAtoms sel distance 2.2
> surface zone #5 nearAtoms sel distance 2.1
> surface zone #5 nearAtoms sel distance 2
> surface zone #5 nearAtoms sel distance 1.9
> surface zone #5 nearAtoms sel distance 1.8
> surface zone #5 nearAtoms sel distance 1.7
> surface zone #5 nearAtoms sel distance 1.6
> surface zone #5 nearAtoms sel distance 1.5
> vop zone #5 near #2 range 5
> vop resample
> volume resample
Missing or invalid "volumes" argument: empty atom specifier
> surface
> hide #!2 models
> show #!2 models
> undo
> hide #!2 surfaces
> show #!2 cartoons
> select #2/A:53-82
249 atoms, 259 bonds, 30 residues, 1 model selected
> surface zone #5 nearAtoms sel distance 1.5
> select add #2
8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 3 models selected
> hide sel cartoons
> hide sel atoms
> select #2/A:53-82
249 atoms, 259 bonds, 30 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> show sel atoms
> ui tool show "Side View"
> surface zone #5 nearAtoms sel distance 1.43
> surface zone #5 nearAtoms sel distance 1.83
> surface zone #5 nearAtoms sel distance 1.84
> surface zone #5 nearAtoms sel distance 1.93
> volume #5 level 0.1281
> volume #5 style mesh
> select clear
> graphics silhouettes false
> volume #5 level 0.2031
> volume #5 style surface
> volume #5 level 0.09427
> select #2/A:53-82
249 atoms, 259 bonds, 30 residues, 1 model selected
> color zone #5 near sel [dist 3]
Expected a keyword
> color zone #5 near sel [dist ]
Expected a keyword
> color zone #5 near sel [dist ]
Expected a keyword
> color zone #5 near sel
> color #2 #d6d6d6ff
> color #2 #d6d6d61b
> hide #!5 models
> show #!5 models
> select add #2
8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 3 models selected
> hide #!2 models
> show #!2 models
> select add #5
8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 8 models selected
> show sel surfaces
> color #5 silver models
> color #5 #d6d6d6ff models
> color #2 #d6d6d61c
> select subtract #5
8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 6 models selected
> ui tool show "Color Actions"
> color sel orchid
> color #5 #d6d6d620 models
> color #5 #d6d6d621 models
> hide sel surfaces
> show sel cartoons
> hide #!5 models
> show #!5 models
> color #2 orchid
> surface unzone #5
> select up
8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 6 models selected
> select up
17969 atoms, 18445 bonds, 8 pseudobonds, 2358 residues, 15 models selected
> select down
8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 10 models selected
> select down
8 pseudobonds, 5 models selected
> select #2/A:53-82
249 atoms, 259 bonds, 30 residues, 1 model selected
> color zone #5 near sel
> hide #!5 models
> show #!5 models
> undo
> show #!5 models
> color #5 #d6d6d6ff models
> color #5 #d6d6d629 models
> color #5 #d6d6d631 models
> color #5 #d6d6d634 models
> color #5 #d6d6d633 models
> surface zone #5 nearAtoms sel distance 1.93
> select add #2
8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 3 models selected
> hide sel cartoons
> hide sel atoms
> select #2/A:53-82
249 atoms, 259 bonds, 30 residues, 1 model selected
> show sel cartoons
> show sel atoms
> select clear
> select #2/A:53-82
249 atoms, 259 bonds, 30 residues, 1 model selected
> surface zone #5 nearAtoms sel distance 1.93
> surface zone #5 nearAtoms sel distance 1.94
> surface zone #5 nearAtoms sel distance 1.95
> surface zone #5 nearAtoms sel distance 1.96
> surface zone #5 nearAtoms sel distance 1.95
> surface zone #5 nearAtoms sel distance 1.94
> surface zone #5 nearAtoms sel distance 1.93
> surface zone #5 nearAtoms sel distance 1.92
> surface zone #5 nearAtoms sel distance 1.93
> ui tool show "Volume Viewer"
> volume #5 style mesh
> select clear
> select #2/A:53-82
249 atoms, 259 bonds, 30 residues, 1 model selected
> color (#!2 & sel) byhetero
> select clear
> select #2/A:53-85
269 atoms, 279 bonds, 33 residues, 1 model selected
> show sel cartoons
> show sel atoms
> surface zone #5 nearAtoms sel distance 1.93
> color (#!2 & sel) byhetero
> select clear
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting full
> lighting flat
> lighting simple
> lighting soft
> lighting full
> undo
> redo
> graphics silhouettes false
> lighting shadows false
> lighting simple
> lighting full
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting simple
> lighting soft
> lighting simple
> lighting full
> lighting simple
> volume #1 step 1
> volume #5 step 1
> volume #5 level 0.09427
> volume #5 transparency 0.5
> set raytracing true
Expected a keyword
> graphics silhouettes true
> set silhouetteWidth 2
> select ~sel & ##selected
Nothing selected
> 1
Unknown command: 1
> set silhouetteWidth 1
> set silhouetteWidth 0.5
> set silhouetteWidth 0.75
> graphics silhouettes true
> set silhouetteWidth 1
> select ~sel & ##selected
Nothing selected
> set silhouetteWidth 2
> set silhouetteWidth 4
> set silhouetteWidth 0
> set silhouetteWidth 0.5
> set silhouetteWidth 0.9
> set silhouetteWidth 1
> set silhouetteWidth 0
> volume #5 transparency 0.5
> volume #5 transparency 1
> volume #5 transparency 0.2
> volume #5 transparency 0.3
> volume #5 transparency 0.4
> volume #5 transparency 0.7
> volume #5 transparency 0
> volume #5 transparency 0.5
> volume #5 transparency 0.1
> ui tool show "Side View"
> graphics silhouettes false
> graphics silhouettes true
> select add #2
8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 2 models selected
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> set silhouetteWidth 1
> select clear
> save "/Users/omallen/Library/CloudStorage/OneDrive-
> TheFrancisCrickInstitute/PhD/Paper
> work/Revision_Figures/Apo_density_TM1.cxs"
> save "/Users/omallen/Library/CloudStorage/OneDrive-
> TheFrancisCrickInstitute/PhD/Paper
> work/Revision_Figures/Apo_density_TM1.tif" width 3000 height 2775
> supersample 3 transparentBackground true
> save "/Users/omallen/Library/CloudStorage/OneDrive-
> TheFrancisCrickInstitute/PhD/Paper
> work/Revision_Figures/Apo_density_TM1_opaque.tif" width 3000 height 2775
> supersample 3
> select #2/A:86-90
36 atoms, 36 bonds, 5 residues, 1 model selected
> select add #2
8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 3 models selected
> hide sel cartoons
> hide sel atoms
> select #2/A:86-90
36 atoms, 36 bonds, 5 residues, 1 model selected
> show sel cartoons
> select #2/A:86-95
72 atoms, 74 bonds, 10 residues, 1 model selected
> show sel cartoons
> select #2/A:86-100
110 atoms, 113 bonds, 15 residues, 1 model selected
> show sel cartoons
> select #2/A:86-110
191 atoms, 197 bonds, 25 residues, 1 model selected
> show sel cartoons
> select #2/A:86-104
146 atoms, 150 bonds, 19 residues, 1 model selected
> select add #2
8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 3 models selected
> hide sel cartoons
> select #2/A:86-104
146 atoms, 150 bonds, 19 residues, 1 model selected
> show sel cartoons
> surface zone #5 nearAtoms sel distance 1.93
> show sel atoms
> color (#!2 & sel) byhetero
> select clear
No atoms selected for zoning
> select #2/A:86-104
146 atoms, 150 bonds, 19 residues, 1 model selected
> surface zone #5 nearAtoms sel distance 1.65
> surface zone #5 nearAtoms sel distance 1.89
> surface zone #5 nearAtoms sel distance 1.9
> surface zone #5 nearAtoms sel distance 2.33
> surface dust #5 size 6.5
> surface zone #5 nearAtoms sel distance 2.33
> select clear
> select add #2
8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 2 models selected
> show sel cartoons
> hide sel cartoons
> select #2/A:86-104
146 atoms, 150 bonds, 19 residues, 1 model selected
> show sel cartoons
> select clear
> volume #5 level 0.1543
> undo
> volume #5 level 0.09427
> select clear
> select #2/A:86-103
139 atoms, 143 bonds, 18 residues, 1 model selected
> select add #2
8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 3 models selected
> hide sel cartoons
> hide sel atoms
> select #2/A:86-103
139 atoms, 143 bonds, 18 residues, 1 model selected
> show sel cartoons
> show sel atoms
> surface zone #5 nearAtoms sel distance 2.33
> select add #2
8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 3 models selected
> hide sel cartoons
> hide sel atoms
> select #2/A:87-103
134 atoms, 138 bonds, 17 residues, 1 model selected
> show sel cartoons
> show sel atoms
> surface zone #5 nearAtoms sel distance 2.33
> select clear
> save "/Users/omallen/Library/CloudStorage/OneDrive-
> TheFrancisCrickInstitute/PhD/Paper
> work/Revision_Figures/Apo_density_Turret.tif" width 3000 height 2775
> supersample 3
> save "/Users/omallen/Library/CloudStorage/OneDrive-
> TheFrancisCrickInstitute/PhD/Paper
> work/Revision_Figures/Apo_density_Turret.cxs"
> save "/Users/omallen/Library/CloudStorage/OneDrive-
> TheFrancisCrickInstitute/PhD/Paper
> work/Revision_Figures/Apo_density_Turretotherside.tif" width 3000 height
> 2775 supersample 3
> volume #5 level 0.1243
> volume #5 level 0.1281
> surface unzone #5
> volume #5 level 0.09427
> hide #!5 models
> select add #2
8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> hide sel cartoons
> select #2/A:87-125-160
Nothing selected
> show #!2 cartoons
> select #2/A:87-125-160
Nothing selected
> select add #2
8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 2 models selected
> hide sel cartoons
> select #2/A:125-160
260 atoms, 264 bonds, 36 residues, 1 model selected
> show sel cartoons
> show sel atoms
> hide sel cartoons
> hide sel atoms
> select #2/A:130-163
247 atoms, 250 bonds, 34 residues, 1 model selected
> show sel cartoons
> show sel atoms
> surface zone #5 nearAtoms sel distance 2.33
> show #!5 models
> surface zone #5 nearAtoms sel distance 2.33
> color (#!2 & sel) byhetero
> select clear
No atoms selected for zoning
> select #2/A:130-163
247 atoms, 250 bonds, 34 residues, 1 model selected
> surface zone #5 nearAtoms sel distance 0.94
> surface zone #5 nearAtoms sel distance 2.17
> select clear
> save "/Users/omallen/Library/CloudStorage/OneDrive-
> TheFrancisCrickInstitute/PhD/Paper
> work/Revision_Figures/Apo_density_TM2.tif" width 3000 height 2775
> supersample 3
> save "/Users/omallen/Library/CloudStorage/OneDrive-
> TheFrancisCrickInstitute/PhD/Paper
> work/Revision_Figures/Apo_density_TM2.cxs"
> select add #2
8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select #2/A:170-185
115 atoms, 117 bonds, 16 residues, 1 model selected
> show sel cartoons
> select #2/A:170-190
159 atoms, 162 bonds, 21 residues, 1 model selected
> show sel cartoons
> surface zone #5 nearAtoms sel distance 2.17
> select add #2
8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 3 models selected
> show sel cartoons
> select #2/A:272-283
80 atoms, 79 bonds, 12 residues, 1 model selected
> select add #2
8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 3 models selected
> hide sel cartoons
> hide sel atoms
> select #2/A:272-283
80 atoms, 79 bonds, 12 residues, 1 model selected
> show sel cartoons
> show sel atoms
> surface zone #5 nearAtoms sel distance 2.17
> color (#!2 & sel) byhetero
> surface zone #5 nearAtoms sel distance 2.2
> surface zone #5 nearAtoms sel distance 1.78
> select clear
> save "/Users/omallen/Library/CloudStorage/OneDrive-
> TheFrancisCrickInstitute/PhD/Paper
> work/Revision_Figures/Apo_density_Gloop.tif" width 3000 height 2775
> supersample 3
> save "/Users/omallen/Library/CloudStorage/OneDrive-
> TheFrancisCrickInstitute/PhD/Paper
> work/Revision_Figures/Apo_density_Gloop.cxs"
> volume #5 style surface
> color #5 #d6d6d62d models
> color #5 #d6d6d64b models
> color #5 #d6d6d632 models
> color #5 #d6d6d633 models
> color #5 #ebebebff models
> color #5 #ebebeb1d models
> hide #!2 models
> show #!2 models
> surface unzone #5
No atoms selected for zoning
> select #2/A:272-283
80 atoms, 79 bonds, 12 residues, 1 model selected
> surface zone #5 nearAtoms sel distance 1.78
> select add #2
8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 3 models selected
> select subtract #2
4 models selected
> color #5 #ebebeb1c models
> color #5 #ebebebff models
> hide #!5 models
> hide #!2 models
> open /Users/omallen/Library/CloudStorage/OneDrive-
> TheFrancisCrickInstitute/PhD/R162W/25041/Map_deposted_R162W.mrc
Opened Map_deposted_R162W.mrc as #7, grid size 200,200,200, pixel 1.3, shown
at level 0.147, step 1, values float32
> open /Users/omallen/Library/CloudStorage/OneDrive-
> TheFrancisCrickInstitute/PhD/R162W/PreparePDBDeposition_9/R162WFINAL_real_space_refined_004-coot-0_real_space_refined_008.deposit_000.cif
Summary of feedback from opening /Users/omallen/Library/CloudStorage/OneDrive-
TheFrancisCrickInstitute/PhD/R162W/PreparePDBDeposition_9/R162WFINAL_real_space_refined_004-coot-0_real_space_refined_008.deposit_000.cif
---
warnings | Skipping chem_comp category: Missing column 'type' on line 590
Skipping entity category: Missing column 'type' on line 17346
Missing entity information. Treating each chain as a separate entity.
Bad residue range for struct_conf "6" on line 140
Invalid residue range for struct_conf "7": invalid entity "B", on line 141
Invalid residue range for struct_conf "8": invalid entity "B", on line 142
Invalid residue range for struct_conf "9": invalid entity "B", on line 143
Invalid residue range for struct_conf "10": invalid entity "B", on line 144
Invalid residue range for struct_conf "11": invalid entity "B", on line 145
7 messages similar to the above omitted
Bad residue range for struct_conf "24" on line 159
Invalid sheet range for struct_sheet_range "15 1" on line 542
Invalid sheet range for struct_sheet_range "16 1": invalid entity "B", on line
543
Invalid sheet range for struct_sheet_range "17 1": invalid entity "B", on line
544
Invalid sheet range for struct_sheet_range "18 1": invalid entity "B", on line
545
Invalid sheet range for struct_sheet_range "19 1": invalid entity "B", on line
546
27 messages similar to the above omitted
Missing or incomplete sequence information. Inferred polymer connectivity.
Skipping chem_comp category: Missing column 'type' on line 17807
Chain information for
R162WFINAL_real_space_refined_004-coot-0_real_space_refined_008.deposit_000.cif
#8
---
Chain | Description
A B C D | No description available
> dssp
Computing secondary structure
> color #8 #76d6ffff
> vop resample #8 onGrid #7
> ui mousemode right "move picked models"
> view matrix models #7,1,0,0,8.596,0,1,0,14.611,0,0,1,11.771
> volume #7 color #d6d6d6
> volume #7 color #d6d6d62a
> volume #7 color #d6d6d62b
> volume #7 level 0.3069
> volume #7 color #d6d6d67d
> ui tool show "Fit in Map"
> fitmap #8 inMap #7
Fit molecule
R162WFINAL_real_space_refined_004-coot-0_real_space_refined_008.deposit_000.cif
(#8) to map Map_deposted_R162W.mrc (#7) using 16710 atoms
average map value = 0.1643, steps = 56
shifted from previous position = 1.65
rotated from previous position = 2.59 degrees
atoms outside contour = 12511, contour level = 0.30691
Position of
R162WFINAL_real_space_refined_004-coot-0_real_space_refined_008.deposit_000.cif
(#8) relative to Map_deposted_R162W.mrc (#7) coordinates:
Matrix rotation and translation
0.99904039 0.04364511 0.00365979 -16.07766265
-0.04368355 0.99898289 0.01117760 -10.04576712
-0.00316822 -0.01132675 0.99993083 -8.28604144
Axis -0.24883231 0.07549772 -0.96559959
Axis point -256.35165071 298.63577796 0.00000000
Rotation angle (degrees) 2.59179413
Shift along axis 11.24320770
> view matrix models #7,1,0,0,8.5273,0,1,0,14.028,0,0,1,13.751
> fitmap #8 inMap #7
Fit molecule
R162WFINAL_real_space_refined_004-coot-0_real_space_refined_008.deposit_000.cif
(#8) to map Map_deposted_R162W.mrc (#7) using 16710 atoms
average map value = 0.1643, steps = 64
shifted from previous position = 2.07
rotated from previous position = 0.0113 degrees
atoms outside contour = 12512, contour level = 0.30691
Position of
R162WFINAL_real_space_refined_004-coot-0_real_space_refined_008.deposit_000.cif
(#8) relative to Map_deposted_R162W.mrc (#7) coordinates:
Matrix rotation and translation
0.99904562 0.04353748 0.00351236 -16.03551677
-0.04357403 0.99898849 0.01110417 -10.05050367
-0.00302536 -0.01124662 0.99993218 -8.31277280
Axis -0.24787267 0.07250403 -0.96607572
Axis point -256.34646527 298.49329793 0.00000000
Rotation angle (degrees) 2.58406990
Shift along axis 11.27683237
> fitmap #8 inMap #7
Fit molecule
R162WFINAL_real_space_refined_004-coot-0_real_space_refined_008.deposit_000.cif
(#8) to map Map_deposted_R162W.mrc (#7) using 16710 atoms
average map value = 0.1643, steps = 48
shifted from previous position = 0.00116
rotated from previous position = 0.00158 degrees
atoms outside contour = 12512, contour level = 0.30691
Position of
R162WFINAL_real_space_refined_004-coot-0_real_space_refined_008.deposit_000.cif
(#8) relative to Map_deposted_R162W.mrc (#7) coordinates:
Matrix rotation and translation
0.99904494 0.04355420 0.00349802 -16.03495196
-0.04359064 0.99898758 0.01112082 -10.05091747
-0.00301012 -0.01126268 0.99993204 -8.31191031
Axis -0.24813042 0.07214536 -0.96603641
Axis point -256.17698253 298.26223636 0.00000000
Rotation angle (degrees) 2.58516437
Shift along axis 11.28324034
> view matrix models
> #8,0.96041,-0.26456,0.087263,29.605,0.26449,0.96431,0.012559,-34.45,-0.087471,0.011019,0.99611,12.072
> fitmap #8 inMap #7
Fit molecule
R162WFINAL_real_space_refined_004-coot-0_real_space_refined_008.deposit_000.cif
(#8) to map Map_deposted_R162W.mrc (#7) using 16710 atoms
average map value = 0.4305, steps = 116
shifted from previous position = 3.55
rotated from previous position = 16.7 degrees
atoms outside contour = 7787, contour level = 0.30691
Position of
R162WFINAL_real_space_refined_004-coot-0_real_space_refined_008.deposit_000.cif
(#8) relative to Map_deposted_R162W.mrc (#7) coordinates:
Matrix rotation and translation
0.99995381 0.00960961 0.00017168 -14.39763100
-0.00960963 0.99995382 0.00013001 -11.64595909
-0.00017042 -0.00013166 0.99999998 -14.00600694
Axis -0.01361154 0.01779507 -0.99974900
Axis point -1244.88982642 1472.45187575 0.00000000
Rotation angle (degrees) 0.55073751
Shift along axis 13.99122468
> save /Users/omallen/Library/CloudStorage/OneDrive-
> TheFrancisCrickInstitute/PhD/R162W/25041/Map_deposited_R162W_inlinewithmodel.mrc
> models #7
> color #7-8 byhetero
> hide #8.1 models
> hide #8.2 models
> select add #8
16710 atoms, 16948 bonds, 272 pseudobonds, 1134 residues, 3 models selected
> hide sel atoms
> hide sel cartoons
> select #8/A:53-82
522 atoms, 534 bonds, 24 pseudobonds, 30 residues, 2 models selected
> show sel cartoons
> show sel atoms
> delete H
> surface zone #7 nearAtoms sel distance 7.8
> volume #7 style mesh
> surface zone #7 nearAtoms sel distance 7.59
> surface zone #7 nearAtoms sel distance 2.99
> select clear
No atoms selected for zoning
> select #8/A:53-82
264 atoms, 276 bonds, 24 pseudobonds, 30 residues, 2 models selected
> surface zone #7 nearAtoms sel distance 2.92
> surface zone #7 nearAtoms sel distance 2.59
> select clear
> save "/Users/omallen/Library/CloudStorage/OneDrive-
> TheFrancisCrickInstitute/PhD/Paper
> work/Revision_Figures/Mut_density_TM1.tif" width 3000 height 2951
> supersample 3
> save "/Users/omallen/Library/CloudStorage/OneDrive-
> TheFrancisCrickInstitute/PhD/Paper
> work/Revision_Figures/Mut_density_TM1.cxs"
> select add #8
8578 atoms, 8816 bonds, 272 pseudobonds, 1134 residues, 3 models selected
> hide sel cartoons
> hide sel atoms
> select #8/A:87-103
137 atoms, 141 bonds, 17 residues, 1 model selected
> show sel cartoons
> show sel atoms
> surface zone #7 nearAtoms sel distance 2.59
> select clear
> save "/Users/omallen/Library/CloudStorage/OneDrive-
> TheFrancisCrickInstitute/PhD/Paper
> work/Revision_Figures/Mut_density_Turret.cxs"
> save "/Users/omallen/Library/CloudStorage/OneDrive-
> TheFrancisCrickInstitute/PhD/Paper
> work/Revision_Figures/Mut_density_Turret.tif" width 3000 height 2951
> supersample 3
> select add #8
8578 atoms, 8816 bonds, 272 pseudobonds, 1134 residues, 3 models selected
> hide sel cartoons
> hide sel atoms
> select #8/A:130-163
250 atoms, 255 bonds, 27 pseudobonds, 34 residues, 2 models selected
> show sel atoms
> show sel cartoons
> surface zone #7 nearAtoms sel distance 2.59
> select clear
> save "/Users/omallen/Library/CloudStorage/OneDrive-
> TheFrancisCrickInstitute/PhD/Paper
> work/Revision_Figures/Mut_density_TM2.tif" width 3000 height 2951
> supersample 3
===== 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 Metal - 89.3
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple
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: MacBook Pro
Model Identifier: Mac14,9
Model Number: MPHE3B/A
Chip: Apple M2 Pro
Total Number of Cores: 10 (6 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.81.4
OS Loader Version: 11881.81.4
Software:
System Software Overview:
System Version: macOS 15.3.2 (24D81)
Kernel Version: Darwin 24.3.0
Time since boot: 20 days, 23 hours, 4 minutes
Graphics/Displays:
Apple M2 Pro:
Chipset Model: Apple M2 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL U2419H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
DELL U2419H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
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 , 7 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 7 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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