![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 months ago
Closed 7 months ago
#17168 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-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00007ff8481e7b00 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 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.pdb_lib._load_libs, chimerax.map._map, lxml._elementpath, lxml.etree, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, PIL._webp, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 65)
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{
"uptime" : 190000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,1",
"coalitionID" : 1003,
"osVersion" : {
"train" : "macOS 15.3.2",
"build" : "24D81",
"releaseType" : "User"
},
"captureTime" : "2025-03-23 11:35:00.5490 +0100",
"codeSigningMonitor" : 0,
"incident" : "8C72A77A-A8C1-4810-9439-D1C230E20C83",
"pid" : 96897,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-03-22 18:09:40.5100 +0100",
"procStartAbsTime" : 176106179299406,
"procExitAbsTime" : 194033668501771,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"C4027B15-248B-5659-BACC-6FB29543A4B7","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "8D528D7E-5C72-169F-357F-E09EC31F9564",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"bootSessionUUID" : "ECAC3F3E-CD7E-4414-A068-42C10232CC05",
"wakeTime" : 21,
"bridgeVersion" : {"build":"22P3060","train":"9.3"},
"sleepWakeUUID" : "31E31D81-CADF-4270-A3D9-455E8608087B",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4359725056\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 103dc2000-103dc6000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.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":96897},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4359725056\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 103dc2000-103dc6000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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"uuid" : "904783ad-6f16-31e9-b1a8-65089262f743",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/.dylibs\/libwebpmux.3.dylib",
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"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/.dylibs\/libwebpdemux.2.dylib",
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"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/.dylibs\/libsharpyuv.0.dylib",
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/zxc755/Desktop/structure_presentation.cxs
Opened J804_006_volume_map_apo_HNH_center.mrc as #11, grid size 420,420,420,
pixel 0.725, shown at level 0.06, step 1, values float32
Opened J811_006_volume_map_apo_HNH_in.mrc as #12, grid size 420,420,420, pixel
0.725, shown at level 0.06, step 1, values float32
Opened J813_005_volume_map_HNH_outwards.mrc as #13, grid size 420,420,420,
pixel 0.725, shown at level 0.065, step 1, values float32
Opened J653_005_volume_map_TS_in_HNH.mrc as #14, grid size 420,420,420, pixel
0.725, shown at level 0.07, step 1, values float32
Opened J635_005_volume_map_2p4Å.mrc as #15, grid size 420,420,420, pixel
0.725, shown at level 0.065, step 1, values float32
Opened J652_006_volume_map_HNH_in.mrc as #16, grid size 420,420,420, pixel
0.725, shown at level 0.07, step 2, values float32
Opened J651_005_volume_map_HNH_out.mrc as #17, grid size 420,420,420, pixel
0.725, shown at level 0.07, step 2, values float32
Opened J343_006_volume_map.mrc as #18, grid size 420,420,420, pixel 0.725,
shown at level 0.065, step 1, values float32
Opened J788_006_volume_map_HNH_in.mrc as #19, grid size 420,420,420, pixel
0.725, shown at level 0.06, step 2, values float32
Opened J348_008_volume_map.mrc as #20, grid size 420,420,420, pixel 0.725,
shown at level 0.06, step 2, values float32
opened ChimeraX session
> show #!1 models
> hide #!1 models
> show #!11 models
> hide #!8 models
> hide #!5 models
> hide #!3 models
> show #!12 models
> hide #!12 models
> show #!15 models
> show #!18 models
> color zone #11 near #1 distance 5
> color zone #11 near #1 distance 10
> color zone #15 near #5 distance 10
> color zone #18 near #8 distance 10
> hide #!18 models
> hide #!15 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/apo_center_side.tif" width 1984 height
> 1210 supersample 3 transparentBackground true
> show #!15 models
> hide #!11 models
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting soft
> show #!18 models
> hide #!15 models
> hide #!18 models
> show #!11 models
> turn x 90
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/apo_center_top.tif" width 1984 height
> 1210 supersample 3 transparentBackground true
> hide #!11 models
> show #!12 models
> color zone #12 near #2 distance 5
> color zone #12 near #2 distance 10
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/apo_in_top.tif" width 1984 height 1210
> supersample 3 transparentBackground true
> hide #!12 models
> show #!16 models
> color zone #16 near #6 distance 10
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/halfcleaved_in_top.tif" width 1984
> height 1210 supersample 3 transparentBackground true
> hide #!16 models
> show #!18 models
> hide #!18 models
> show #!19 models
> color zone #19 near #9 distance 10
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/post_in_top.tif" width 1984 height 1210
> supersample 3
> volume #19 step 1
> volume #20 step 1
> volume #17 step 1
> volume #16 step 1
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/post_in_top.tif" width 1984 height 1210
> supersample 3 transparentBackground true
> show #!16 models
> hide #!19 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/halfcleaved_in_top.tif" width 1984
> height 1210 supersample 3 transparentBackground true
> hide #!16 models
> show #!12 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/apo_in_top.tif" width 1984 height 1210
> supersample 3 transparentBackground true
> turn x -90
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/apo_in_side.tif" width 1984 height 1210
> supersample 3 transparentBackground true
> hide #!12 models
> show #!16 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/halfcleaved_in_side.tif" width 1984
> height 1210 supersample 3 transparentBackground true
> hide #!16 models
> show #!19 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/post_in_side.tif" width 1984 height
> 1210 supersample 3 transparentBackground true
> hide #!19 models
> show #!20 models
> color zone #20 near #10 distance 10
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/post_out_side.tif" width 1984 height
> 1210 supersample 3 transparentBackground true
> show #!17 models
> hide #!20 models
> color zone #17 near #7 distance 10
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/halfcleaved_out_side.tif" width 1984
> height 1210 supersample 3
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/halfcleaved_out_side.tif" width 1984
> height 1210 supersample 3 transparentBackground true
> show #!13 models
> hide #!17 models
> color zone #13 near #3 distance 10
> hide #!13 models
> turn x 90
> show #!16 models
> show #!17 models
> hide #!16 models
> show #!16 models
> hide #!17 models
> show #!17 models
> hide #!16 models
> show #!16 models
> hide #!17 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!17 models
> hide #!17 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!16 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/halfcleaved_out_top.tif" width 1984
> height 1210 supersample 3 transparentBackground true
> show #!20 models
> hide #!17 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/post_out_top.tif" width 1984 height
> 1210 supersample 3 transparentBackground true
> hide #!20 models
> show #!14 models
> color zone #14 near #4 distance 10
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/halfcleaved_center_fullTS_top.tif"
> width 1984 height 1210 supersample 3 transparentBackground true
> turn x -90
> surface zone #14 nearAtoms #4 distance 8
> surface dust #14 size 7.25
> surface dust #14 size 10
> volume #14 level 0.1
> volume #14 level 0.08
> volume #14 level 0.075
> volume #14 level 0.085
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/halfcleaved_center_fullTS_bottom.tif"
> width 1984 height 1210 supersample 3 transparentBackground true
> show #!11 models
> show #!12 models
> hide #!12 models
> show #!15 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> fitmap #11 inMap #15
Fit map J804_006_volume_map_apo_HNH_center.mrc in map
J635_005_volume_map_2p4Å.mrc using 434058 points
correlation = -0.01986, correlation about mean = 0.001631, overlap = -2.4
steps = 1152, shift = 42.4, angle = 29.1 degrees
Position of J804_006_volume_map_apo_HNH_center.mrc (#11) relative to
J635_005_volume_map_2p4Å.mrc (#15) coordinates:
Matrix rotation and translation
-0.92823736 0.00639548 -0.37193347 288.63213432
0.00071198 -0.99981982 -0.01896901 293.61617111
-0.37198777 -0.01787255 0.92806555 -96.31290101
Axis 0.18941843 0.00938104 -0.98185165
Axis point 135.24107168 146.15648876 0.00000000
Rotation angle (degrees) 179.83417009
Shift along axis 151.99165106
> select #11
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.92824,0.0063955,-0.37193,318.54,0.00071198,-0.99982,-0.018969,345.48,-0.37199,-0.017873,0.92807,-24.205
> view matrix models
> #11,-0.92824,0.0063955,-0.37193,334.89,0.00071198,-0.99982,-0.018969,379.4,-0.37199,-0.017873,0.92807,23.615
> view matrix models
> #11,-0.92824,0.0063955,-0.37193,349.95,0.00071198,-0.99982,-0.018969,329.26,-0.37199,-0.017873,0.92807,70.301
> fitmap #11 inMap #15
Fit map J804_006_volume_map_apo_HNH_center.mrc in map
J635_005_volume_map_2p4Å.mrc using 434058 points
correlation = 0.3738, correlation about mean = 0.0702, overlap = 1985
steps = 204, shift = 12.5, angle = 10.6 degrees
Position of J804_006_volume_map_apo_HNH_center.mrc (#11) relative to
J635_005_volume_map_2p4Å.mrc (#15) coordinates:
Matrix rotation and translation
-0.97255950 -0.00509801 -0.23259841 332.84164042
-0.01727782 -0.99541653 0.09406066 301.74824732
-0.23201183 0.09549838 0.96801372 22.94857878
Axis 0.11709380 -0.04777356 -0.99197113
Axis point 168.24227131 149.80685974 0.00000000
Rotation angle (degrees) 179.64824782
Shift along axis 1.79377865
> view matrix models
> #11,-0.91603,-0.138,-0.37663,366.21,0.33654,-0.77532,-0.53444,315.53,-0.21825,-0.61631,0.75665,157.08
> view matrix models
> #11,-0.96076,-0.2035,-0.18846,352.27,0.27606,-0.76745,-0.57864,313.7,-0.026878,-0.60796,0.79351,113.58
> fitmap #11 inMap #15
Fit map J804_006_volume_map_apo_HNH_center.mrc in map
J635_005_volume_map_2p4Å.mrc using 434058 points
correlation = 0.391, correlation about mean = 0.03338, overlap = 2179
steps = 172, shift = 7.82, angle = 9.06 degrees
Position of J804_006_volume_map_apo_HNH_center.mrc (#11) relative to
J635_005_volume_map_2p4Å.mrc (#15) coordinates:
Matrix rotation and translation
-0.95915374 -0.25758407 -0.11693820 356.19351656
0.28195909 -0.83708372 -0.46881756 306.42353567
0.02287287 -0.48263991 0.87552016 72.25529471
Axis -0.02479190 -0.25076655 0.96773008
Axis point 156.79887525 188.71505966 0.00000000
Rotation angle (degrees) 163.81334800
Shift along axis -15.74786365
> hide #!11 models
> select subtract #11
Nothing selected
> show #!18 models
> select #18
2 models selected
> view matrix models #18,1,0,0,-3.3729,0,1,0,-5.3307,0,0,1,-4.3021
> fitmap #18 inMap #15
Fit map J343_006_volume_map.mrc in map J635_005_volume_map_2p4Å.mrc using
393673 points
correlation = 0.8565, correlation about mean = 0.6276, overlap = 6398
steps = 208, shift = 6.08, angle = 13.1 degrees
Position of J343_006_volume_map.mrc (#18) relative to
J635_005_volume_map_2p4Å.mrc (#15) coordinates:
Matrix rotation and translation
0.98794109 0.15047027 0.03648427 -25.60693635
-0.14232027 0.97533711 -0.16870823 49.38219037
-0.06097003 0.16148134 0.98499058 -19.10337179
Axis 0.73060662 0.21563599 -0.64785422
Axis point 0.00000000 125.96683261 268.77622582
Rotation angle (degrees) 13.05989240
Shift along axis 4.31618041
> select subtract #18
Nothing selected
> hide #!18 models
> hide #!15 models
> show #!16 models
> show #!12 models
> select #12
2 models selected
> view matrix models
> #12,-0.97119,-0.23758,0.018708,345.46,0.22901,-0.9521,-0.20265,315.91,0.065957,-0.19253,0.97907,-18.691
> view matrix models
> #12,-0.97119,-0.23758,0.018708,346.37,0.22901,-0.9521,-0.20265,317.15,0.065957,-0.19253,0.97907,11.988
> view matrix models
> #12,-0.97119,-0.23758,0.018708,334.04,0.22901,-0.9521,-0.20265,300.84,0.065957,-0.19253,0.97907,12.123
> fitmap #12 inMap #16
Fit map J811_006_volume_map_apo_HNH_in.mrc in map
J652_006_volume_map_HNH_in.mrc using 435273 points
correlation = 0.4278, correlation about mean = 0.04784, overlap = 1994
steps = 80, shift = 2.4, angle = 1.13 degrees
Position of J811_006_volume_map_apo_HNH_in.mrc (#12) relative to
J652_006_volume_map_HNH_in.mrc (#16) coordinates:
Matrix rotation and translation
-0.97156249 -0.23675453 0.00369053 334.49334436
0.23043620 -0.94898894 -0.21521883 301.17985455
0.05445631 -0.20824810 0.97655887 17.85233867
Axis 0.01483156 -0.10801401 0.99403873
Axis point 149.12417895 171.61834693 0.00000000
Rotation angle (degrees) 166.40859875
Shift along axis -9.82466976
> view matrix models
> #12,-0.97156,-0.23675,0.0036905,338.65,0.23044,-0.94899,-0.21522,294.13,0.054456,-0.20825,0.97656,20.164
> fitmap #12 inMap #16
Fit map J811_006_volume_map_apo_HNH_in.mrc in map
J652_006_volume_map_HNH_in.mrc using 435273 points
correlation = 0.8235, correlation about mean = 0.543, overlap = 5710
steps = 116, shift = 1.51, angle = 1.14 degrees
Position of J811_006_volume_map_apo_HNH_in.mrc (#12) relative to
J652_006_volume_map_HNH_in.mrc (#16) coordinates:
Matrix rotation and translation
-0.97120515 -0.23750280 0.01878772 335.80734733
0.22891777 -0.95212661 -0.20261186 291.45825332
0.06600917 -0.19247684 0.97907888 15.92487921
Axis 0.02161380 -0.10070377 0.99468165
Axis point 150.35057288 166.61137652 0.00000000
Rotation angle (degrees) 166.44037069
Shift along axis -6.25268666
> select subtract #12
Nothing selected
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> select #19
2 models selected
> view matrix models #19,1,0,0,-1.6439,0,1,0,-0.22094,0,0,1,-2.9798
> fitmap #19 inMap #16
Fit map J788_006_volume_map_HNH_in.mrc in map J652_006_volume_map_HNH_in.mrc
using 444158 points
correlation = 0.8206, correlation about mean = 0.4793, overlap = 4226
steps = 156, shift = 4.4, angle = 13.6 degrees
Position of J788_006_volume_map_HNH_in.mrc (#19) relative to
J652_006_volume_map_HNH_in.mrc (#16) coordinates:
Matrix rotation and translation
0.98625965 0.16331022 0.02493349 -25.31332630
-0.15674004 0.97270500 -0.17110680 52.42917765
-0.05219642 0.16484766 0.98493694 -20.67501764
Axis 0.71423662 0.16397760 -0.68042442
Axis point 0.00000000 132.16331142 280.93503406
Rotation angle (degrees) 13.60248602
Shift along axis 4.58529333
> select subtract #19
Nothing selected
> hide #!19 models
> show #!17 models
> hide #!16 models
> show #!20 models
> select #20
2 models selected
> view matrix models
> #20,0.99964,0.0086233,0.025456,-1.7728,-0.0088994,0.9999,0.010752,2.8474,-0.025361,-0.010974,0.99962,1.3842
> fitmap #20 inMap #17
Fit map J348_008_volume_map.mrc in map J651_005_volume_map_HNH_out.mrc using
430508 points
correlation = 0.8562, correlation about mean = 0.599, overlap = 5409
steps = 220, shift = 5.84, angle = 13.8 degrees
Position of J348_008_volume_map.mrc (#20) relative to
J651_005_volume_map_HNH_out.mrc (#17) coordinates:
Matrix rotation and translation
0.98370533 0.17298599 0.04898648 -29.98796419
-0.16268607 0.97243584 -0.16703823 52.45242015
-0.07653148 0.15634698 0.98473273 -16.59201528
Axis 0.66993749 0.26002795 -0.69539142
Axis point 277.15119285 219.16231782 0.00000000
Rotation angle (degrees) 13.96651326
Shift along axis 5.08697856
> select subtract #20
Nothing selected
> hide #!20 models
> show #!13 models
> select #13
2 models selected
> view matrix models
> #13,-0.97416,-0.22516,0.017849,335.39,0.21683,-0.95439,-0.20523,300.84,0.063245,-0.19605,0.97855,14.284
> view matrix models
> #13,-0.97416,-0.22516,0.017849,334.04,0.21683,-0.95439,-0.20523,296.82,0.063245,-0.19605,0.97855,15.486
> fitmap #13 inMap #17
Fit map J813_005_volume_map_HNH_outwards.mrc in map
J651_005_volume_map_HNH_out.mrc using 392698 points
correlation = 0.8001, correlation about mean = 0.4797, overlap = 5555
steps = 168, shift = 3.22, angle = 0.0119 degrees
Position of J813_005_volume_map_HNH_outwards.mrc (#13) relative to
J651_005_volume_map_HNH_out.mrc (#17) coordinates:
Matrix rotation and translation
-0.97419744 -0.22498324 0.01794149 334.36171799
0.21664235 -0.95444376 -0.20519066 294.31743602
0.06328860 -0.19600933 0.97855756 17.42979432
Axis 0.02067669 -0.10212334 0.99455683
Axis point 150.40004098 166.95660566 0.00000000
Rotation angle (degrees) 167.17221873
Shift along axis -5.80826592
> select subtract #13
Nothing selected
> hide #!17 models
> show #!17 models
> hide #!17 models
> volume #13 level 0.06
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> volume #13 level 0.07
> volume #13 level 0.06
> volume #11-20 level 0.06
> show #!11 models
> hide #!13 models
> show #!15 models
> hide #!11 models
> hide #!15 models
> show #!11 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/map_overview/apo_center_tilt.tif" width
> 1984 height 1210 supersample 3 transparentBackground true
> show #!12 models
> hide #!11 models
> show #!11 models
> hide #!12 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/map_overview/apo_center_tilt.tif" width
> 1984 height 1210 supersample 3 transparentBackground true
> show #!12 models
> hide #!11 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/map_overview/apo_in_tilt.tif" width
> 1984 height 1210 supersample 3 transparentBackground true
> hide #!12 models
> show #!13 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/map_overview/apo_out_tilt.tif" width
> 1984 height 1210 supersample 3 transparentBackground true
> show #!14 models
> hide #!13 models
> volume #14 level 0.08
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/map_overview/halfcleaved_center_fullTS_tilt.tif"
> width 1984 height 1210 supersample 3 transparentBackground true
> hide #!14 models
> show #!15 models
> volume #15 level 0.08
> volume #15 level 0.09
> volume #15 level 0.07
> volume #15 level 0.08
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/map_overview/halfcleaved_center_tilt.tif"
> width 1984 height 1210 supersample 3 transparentBackground true
> show #!16 models
> hide #!15 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/map_overview/halfcleaved_in_tilt.tif"
> width 1984 height 1210 supersample 3 transparentBackground true
> hide #!16 models
> show #!17 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/map_overview/halfcleaved_out_tilt.tif"
> width 1984 height 1210 supersample 3 transparentBackground true
> show #!18 models
> hide #!17 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/map_overview/post_center_tilt.tif"
> width 1984 height 1210 supersample 3 transparentBackground true
> show #!19 models
> hide #!18 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/map_overview/post_in_tilt.tif" width
> 1984 height 1210 supersample 3 transparentBackground true
> hide #!19 models
> show #!20 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/map_overview/post_out_tilt.tif" width
> 1984 height 1210 supersample 3 transparentBackground true
> hide #!20 models
> show #!20 models
> show #!10 models
> hide #!20 models
> show #!20 models
> select #10/De:253
9 atoms, 8 bonds, 1 residue, 1 model selected
> view matrix models
> #10,0.99964,0.0085026,0.025367,-5.7816,-0.0087819,0.9999,0.010921,-15.662,-0.025271,-0.011139,0.99962,-6.3091
> view matrix models
> #10,0.99964,0.0085026,0.025367,-5.1274,-0.0087819,0.9999,0.010921,1.1558,-0.025271,-0.011139,0.99962,-4.4986
> fitmap #10 inMap #20
Fit molecule postcleavage_HNH_outwards_refined.pdb (#10) to map
J348_008_volume_map.mrc (#20) using 23550 atoms
average map value = 0.1007, steps = 152
shifted from previous position = 5.92
rotated from previous position = 13.7 degrees
atoms outside contour = 6011, contour level = 0.06
Position of postcleavage_HNH_outwards_refined.pdb (#10) relative to
J348_008_volume_map.mrc (#20) coordinates:
Matrix rotation and translation
0.99999998 -0.00014449 -0.00012850 0.03699096
0.00014452 0.99999997 0.00019948 -0.04751356
0.00012847 -0.00019950 0.99999997 0.00484581
Axis -0.71805454 -0.46245661 0.52012648
Axis point 0.00000000 29.64688519 242.98010885
Rotation angle (degrees) 0.01591826
Shift along axis -0.00206813
> hide #!20 models
> show #!20 models
> transparency #20.1 0
> transparency #20.1 50
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> hide #!20 models
> select add #10
23550 atoms, 24255 bonds, 5 pseudobonds, 2757 residues, 2 models selected
> select subtract #10
Nothing selected
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!5 models
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_center_main_map_2p4Å.mrc"
Opened halfcleaved_HNH_center_main_map_2p4Å.mrc as #22, grid size
420,420,420, pixel 0.725, shown at level 0.0319, step 2, values float32
> close #22
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_center_main_model_refined2.pdb"
Chain information for halfcleaved_HNH_center_main_model_refined2.pdb #22
---
Chain | Description
Aa | No description available
Ba | No description available
Ca | No description available
DA | No description available
Da | No description available
Db | No description available
Dc | No description available
Dd | No description available
De | No description available
Df | No description available
EA | No description available
FA | No description available
> style stick
Changed 283320 atom styles
> hide #22 atoms
> show #22 cartoons
> select clear
> color #22/DA light gray
> color #22/EA dim gray
> color #22/FA dark red
> color #22/Ca rebecca purple
> color #22/Ba forest green
> color #22/Da,Db,Dc,Dd,De,Df khaki
> color #22/Aa steel blue
> color #22/Aa:232-350 dark turquoise
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> show #22/EA,DA,FA atoms
> hide #!5 models
> show #!5 models
> hide #!5 models
> lighting simple
> lighting soft
> lighting full
> lighting soft
> hide #!22 models
> show #!21 models
> color #21/DA light gray
> color #21/EA dim gray
> color #21/FA dark red
> color #21/Ca rebecca purple
> color #21/Ba forest green
> color #21/Da,Db,Dc,Dd,De,Df khaki
> color #21/Aa steel blue
> color #21/Aa:232-350 dark turquoise
> color #21/DA light gray
> color #21/EA dim gray
> color #21/FA dark red
> color #21/Ca rebecca purple
> color #21/Ba forest green
> color #21/Da,Db,Dc,Dd,De,Df khaki
> color #21/Aa steel blue
> select #21/Fa:42
19 atoms, 20 bonds, 1 residue, 1 model selected
> select up
917 atoms, 1020 bonds, 46 residues, 1 model selected
> color sel dark red
> select #21/Ea:6
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
885 atoms, 987 bonds, 42 residues, 1 model selected
> color sel dim gray
> select #21/Ed:0
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
200 atoms, 219 bonds, 10 residues, 1 model selected
> color sel light gray
> select #21/Ec:2
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
160 atoms, 175 bonds, 8 residues, 1 model selected
> select up
23201 atoms, 23901 bonds, 2693 residues, 1 model selected
> select down
160 atoms, 175 bonds, 8 residues, 1 model selected
> color sel dark red
> select clear
> select #21/Eb:1
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
100 atoms, 109 bonds, 5 residues, 1 model selected
> color sel dark red
> select clear
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> mmaker #21 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker halfcleaved_HNH_center_main_model_refined.pdb, chain Db (#5) with
J529_modelangelo.cif, chain Db (#21), sequence alignment score = 1651.7
RMSD between 322 pruned atom pairs is 0.268 angstroms; (across all 324 pairs:
0.434)
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #5 models
> hide #22 models
> show #5 models
> hide #21 models
> show #21 models
> hide #5 models
> show #5 models
> hide #21 models
> show #21 models
> hide #5 models
> show #5 models
> hide #21 models
> show #21 models
> hide #5 models
> show #5 models
> hide #21 models
> show #21 models
> hide #5 models
> show #5 models
> hide #21 models
> show #21 models
> hide #5 models
> show #5 models
> hide #21 models
> show #21 models
> hide #5 models
> show #5 models
> hide #21 models
> show #21 models
> hide #5 models
> show #5 models
> hide #21 models
> show #21 models
> hide #5 models
> show #5 models
> hide #21 models
> show #21 models
> hide #5 models
> show #5 models
> hide #21 models
> show #21 models
> hide #5 models
> show #5 models
> hide #21 models
> show #21 models
> hide #5 models
> show #5 models
> hide #21 models
> show #21 models
> hide #5 models
> show #5 models
> hide #21 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
===== Log before crash end =====
OpenGL version: 4.1 ATI-6.1.13
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,1
Processor Name: 8-Core Intel Core i9
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2069.80.3.0.0 (iBridge: 22.16.13060.0.0,0)
OS Loader Version: 582~3311
Software:
System Software Overview:
System Version: macOS 15.3.2 (24D81)
Kernel Version: Darwin 24.3.0
Time since boot: 5 days, 22 hours, 1 minute
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0002
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
AMD Radeon Pro 5500M:
Chipset Model: AMD Radeon Pro 5500M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0040
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32206U1-019
Option ROM Version: 113-D32206U1-019
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
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: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
biopython: 1.84
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
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: 2.2.4
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: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
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: 1.1.1
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: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
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-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
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: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
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-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
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: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
DiffFit: 0.2
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
fsspec: 2024.6.1
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
joblib: 1.4.2
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
mpmath: 1.3.0
mrcfile: 1.5.1
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
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: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scikit-learn: 1.5.1
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
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: 0.6.3
sympy: 1.13.0
tables: 3.8.0
tcia-utils: 1.5.1
threadpoolctl: 3.5.0
tifffile: 2024.1.30
tinyarray: 1.2.4
torch: 2.2.2
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
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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