![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 15 months ago
Closed 15 months ago
#15634 closed defect (duplicate)
Crash waking Mac 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-14.5-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.
After using ChimeraX, I left it running. After my computer came back from sleep mode, ChimeraX had crashed (in other words, it occurred when I was not actively using it)
Fatal Python error: Segmentation fault
Current thread 0x00007ff84774dfc0 (most recent call first):
File "/private/var/folders/7v/7mk1h4t57d3fdgl6w3z2f1440000gp/T/AppTranslocation/E4BA0D7C-66CE-430A-9DF4-D23CD4D77191/d/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 "/private/var/folders/7v/7mk1h4t57d3fdgl6w3z2f1440000gp/T/AppTranslocation/E4BA0D7C-66CE-430A-9DF4-D23CD4D77191/d/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 "/private/var/folders/7v/7mk1h4t57d3fdgl6w3z2f1440000gp/T/AppTranslocation/E4BA0D7C-66CE-430A-9DF4-D23CD4D77191/d/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, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, 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, lxml._elementpath, lxml.etree, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath (total: 59)
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{
"uptime" : 300000,
"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,1",
"coalitionID" : 2107,
"osVersion" : {
"train" : "macOS 14.5",
"build" : "23F79",
"releaseType" : "User"
},
"captureTime" : "2024-07-16 16:15:25.8974 -0400",
"codeSigningMonitor" : 0,
"incident" : "09A40133-1CC6-402A-867B-BC15945661FE",
"pid" : 19493,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-07-14 16:07:16.1944 -0400",
"procStartAbsTime" : 180994552496464,
"procExitAbsTime" : 302489009432235,
"procName" : "ChimeraX",
"procPath" : "\/private\/var\/folders\/*\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"D7D3B377-4527-5057-A8B7-1D0ECDF18636","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "D6D0BAE5-DDDC-7E4B-A5C4-407F474777DB",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 34165,
"bridgeVersion" : {"build":"21P5077","train":"8.5"},
"sleepWakeUUID" : "5BC695A2-F0BD-48A6-876E-4E7A6FE06145",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4336041984\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10272c000-102730000 [ 16K] r-x\/r-x SM=COW \/var\/folders\/*\/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":19493},
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4336041984\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10272c000-102730000 [ 16K] r-x\/r-x SM=COW \/var\/folders\/*\/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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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
> camera ortho
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/eb1MacPro/Dropbox/Hflu/Compare_Hflu_oldnew_2023.11.06.cxs format
> session
Opened hibs53mbrix.brix as #1, grid size 60,60,100, pixel 3.5, shown at level
3.3e+04, step 1, values float32
Opened postprocess_Hib_job113.mrc as #2, grid size 280,280,280, pixel 1.08,
shown at level 0.00681, step 1, values float32
Opened hibs53mbrix.brix as #3, grid size 60,60,100, pixel 3.5, shown at level
6.91e+04, step 1, values float32
Opened hibs53mbrix.brix z flip as #4, grid size 60,60,100, pixel 3.5, shown at
level 4.61e+04, step 1, values float32
Opened postprocess_Hib_job113.mrc as #5, grid size 280,280,280, pixel 1.08,
shown at level 0.00487, step 2, values float32
Opened postprocess_Hib_job113.mrc as #6, grid size 280,280,280, pixel 1.08,
shown at level 0.00501, step 2, values float32
opened ChimeraX session
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> open
> /Users/eb1MacPro/Dropbox/EB/Hflu_Cryo/Hib_Purdue_2022/PostProcess/PostProcjob183/HifA_3_subunits_try1.pdb
Chain information for HifA_3_subunits_try1.pdb #7
---
Chain | Description
A B C | No description available
> view
> select #7
8808 atoms, 8883 bonds, 588 residues, 1 model selected
> ui mousemode right "move picked models"
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models #7,1,0,0,11.791,0,1,0,-137.6,0,0,1,-146.84
> view matrix models #7,1,0,0,-124.93,0,1,0,-101.01,0,0,1,-138.43
> view matrix models #7,1,0,0,-150.37,0,1,0,-137.73,0,0,1,-135.05
> view matrix models #7,1,0,0,-137.23,0,1,0,-140.06,0,0,1,-139.34
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.95822,-0.037597,-0.28355,-83.072,0.04805,0.99839,0.029997,-151.49,0.28197,-0.042369,0.95849,-169.05
> ui tool show "Fit in Map"
> fitmap #7 inMap #5
Fit molecule HifA_3_subunits_try1.pdb (#7) to map postprocess_Hib_job113.mrc
(#5) using 8808 atoms
average map value = 0.004288, steps = 144
shifted from previous position = 13.5
rotated from previous position = 14.2 degrees
atoms outside contour = 4767, contour level = 0.0048659
Position of HifA_3_subunits_try1.pdb (#7) relative to
postprocess_Hib_job113.mrc (#5) coordinates:
Matrix rotation and translation
-0.01196724 -0.99804550 -0.06133493 311.73301767
0.99240991 -0.00434703 -0.12289701 20.45345436
0.12239018 -0.06234013 0.99052232 -11.50163111
Axis 0.03028095 -0.09187019 0.99531047
Axis point 146.07531995 164.34851109 0.00000000
Rotation angle (degrees) 90.73890521
Shift along axis -3.88718354
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.99794,-0.004421,-0.063998,-137.2,0.01323,0.99036,0.13789,-161.5,0.062771,-0.13845,0.98838,-131.96
> view matrix models
> #7,0.99794,-0.004421,-0.063998,-144.47,0.01323,0.99036,0.13789,-163.66,0.062771,-0.13845,0.98838,-135.82
> fitmap #7 inMap #5
Fit molecule HifA_3_subunits_try1.pdb (#7) to map postprocess_Hib_job113.mrc
(#5) using 8808 atoms
average map value = 0.005834, steps = 360
shifted from previous position = 26
rotated from previous position = 69.9 degrees
atoms outside contour = 3895, contour level = 0.0048659
Position of HifA_3_subunits_try1.pdb (#7) relative to
postprocess_Hib_job113.mrc (#5) coordinates:
Matrix rotation and translation
0.93491632 -0.35244470 -0.04140315 69.31164057
0.34981181 0.93492622 -0.05953720 -32.69981073
0.05969247 0.04117898 0.99736714 -6.51118911
Axis 0.14054554 -0.14107503 0.97997183
Axis point 122.06161474 170.93956117 0.00000000
Rotation angle (degrees) 20.99610141
Shift along axis 7.97378663
> hide #!2 models
> hide #!1 models
> hide #!6 models
> view matrix models
> #7,0.34935,0.93699,-0.00041691,-188.6,-0.93042,0.34696,0.11803,70.305,0.11073,-0.040845,0.99301,-137.88
> view matrix models
> #7,0.34935,0.93699,-0.00041691,-187.65,-0.93042,0.34696,0.11803,69.11,0.11073,-0.040845,0.99301,-137.75
> fitmap #7 inMap #5
Fit molecule HifA_3_subunits_try1.pdb (#7) to map postprocess_Hib_job113.mrc
(#5) using 8808 atoms
average map value = 0.005834, steps = 68
shifted from previous position = 1.55
rotated from previous position = 0.00717 degrees
atoms outside contour = 3895, contour level = 0.0048659
Position of HifA_3_subunits_try1.pdb (#7) relative to
postprocess_Hib_job113.mrc (#5) coordinates:
Matrix rotation and translation
0.93494566 -0.35235739 -0.04148369 69.30915042
0.34972297 0.93496136 -0.05950720 -32.69882289
0.05975346 0.04112819 0.99736559 -6.51171261
Axis 0.14046494 -0.14130487 0.97995027
Axis point 122.07519356 170.98390585 0.00000000
Rotation angle (degrees) 20.99106952
Shift along axis 7.97485413
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.4828,-0.8523,-0.20121,92.415,-0.84972,-0.40034,-0.34309,238.72,0.21187,0.33661,-0.9175,75.448
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.4828,-0.8523,-0.20121,92.183,-0.84972,-0.40034,-0.34309,242.36,0.21187,0.33661,-0.9175,83.318
> fitmap #7 inMap #5
Fit molecule HifA_3_subunits_try1.pdb (#7) to map postprocess_Hib_job113.mrc
(#5) using 8808 atoms
average map value = 0.008534, steps = 160
shifted from previous position = 0.744
rotated from previous position = 32.4 degrees
atoms outside contour = 2324, contour level = 0.0048659
Position of HifA_3_subunits_try1.pdb (#7) relative to
postprocess_Hib_job113.mrc (#5) coordinates:
Matrix rotation and translation
0.99996228 0.00866391 0.00061478 -1.36469757
0.00866306 -0.99996154 0.00137123 300.18455070
0.00062664 -0.00136585 -0.99999893 313.89919247
Axis -0.99999056 -0.00433343 -0.00031056
Axis point 0.00000000 150.20263009 156.84710274
Rotation angle (degrees) 179.92158780
Shift along axis -0.03363141
> combine #7 modelId #8 name HifA pdb v2
Expected a keyword
> combine modelId #7 modelId #8 name HifA pdb v2
Repeated keyword argument "modelId"
> combine modelId #7 modelId #8 name HifA_pdb_v2
Repeated keyword argument "modelId"
> combine modelId #7 name HifA_pdb_v2
Traceback (most recent call last):
File
"/private/var/folders/7v/7mk1h4t57d3fdgl6w3z2f1440000gp/T/AppTranslocation/E4BA0D7C-66CE-430A-9DF4-D23CD4D77191/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/private/var/folders/7v/7mk1h4t57d3fdgl6w3z2f1440000gp/T/AppTranslocation/E4BA0D7C-66CE-430A-9DF4-D23CD4D77191/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/private/var/folders/7v/7mk1h4t57d3fdgl6w3z2f1440000gp/T/AppTranslocation/E4BA0D7C-66CE-430A-9DF4-D23CD4D77191/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/cmd.py", line 169, in combine_cmd
session.models.add([combination])
File
"/private/var/folders/7v/7mk1h4t57d3fdgl6w3z2f1440000gp/T/AppTranslocation/E4BA0D7C-66CE-430A-9DF4-D23CD4D77191/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 756, in add
p = self._parent_for_added_model(model, parent, root_model = root_model)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/private/var/folders/7v/7mk1h4t57d3fdgl6w3z2f1440000gp/T/AppTranslocation/E4BA0D7C-66CE-430A-9DF4-D23CD4D77191/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 825, in _parent_for_added_model
raise ValueError('Tried to add model %s with the same id as another model %s'
ValueError: Tried to add model HifA_pdb_v2 #7 with the same id as another
model HifA_3_subunits_try1.pdb #7
ValueError: Tried to add model HifA_pdb_v2 #7 with the same id as another
model HifA_3_subunits_try1.pdb #7
File
"/private/var/folders/7v/7mk1h4t57d3fdgl6w3z2f1440000gp/T/AppTranslocation/E4BA0D7C-66CE-430A-9DF4-D23CD4D77191/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 825, in _parent_for_added_model
raise ValueError('Tried to add model %s with the same id as another model %s'
See log for complete Python traceback.
> combine #7 name HifA_pdb_v2
> combine #7 name HifA_pdb_v3
> hide #7 models
> hide #9 models
> show #!6 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!5 models
> hide #!6 models
> cofr #8
> turn y -163 models #8
> move y 27.5 models #8
> turn y -163 models #8
> fitmap #8 inMap #2
Fit molecule HifA_pdb_v2 (#8) to map postprocess_Hib_job113.mrc (#2) using
8808 atoms
average map value = 0.0085, steps = 200
shifted from previous position = 1.56
rotated from previous position = 44.1 degrees
atoms outside contour = 3224, contour level = 0.0068059
Position of HifA_pdb_v2 (#8) relative to postprocess_Hib_job113.mrc (#2)
coordinates:
Matrix rotation and translation
-0.95318800 0.30236388 0.00295348 248.66109660
0.30236175 0.95319255 -0.00115465 -38.29418254
-0.00316440 -0.00020758 -0.99999515 286.90580071
Axis 0.15298091 0.98822908 -0.00034421
Axis point 127.51924242 0.00000000 143.25152578
Rotation angle (degrees) 179.82264785
Shift along axis 0.09822127
> hide #!2 models
> hide #8 models
> show #9 models
> show #!6 models
> turn y -163 models #9
> move y -27.5 models #9
> select #9
8808 atoms, 8883 bonds, 588 residues, 1 model selected
> view matrix models
> #9,0.28727,0.95747,0.027111,-189.2,0.95329,-0.28303,-0.10549,-90.473,-0.093334,0.05615,-0.99405,210.91
> cofr #9
> turn y 163 models #9
> fitmap #8 inMap #2
Fit molecule HifA_pdb_v2 (#8) to map postprocess_Hib_job113.mrc (#2) using
8808 atoms
average map value = 0.0085, steps = 40
shifted from previous position = 0.0221
rotated from previous position = 0.0167 degrees
atoms outside contour = 3225, contour level = 0.0068059
Position of HifA_pdb_v2 (#8) relative to postprocess_Hib_job113.mrc (#2)
coordinates:
Matrix rotation and translation
-0.95311199 0.30260477 0.00280789 248.63710695
0.30260267 0.95311610 -0.00115333 -38.31853444
-0.00302528 -0.00024958 -0.99999557 286.91339264
Axis 0.15310569 0.98820976 -0.00035449
Axis point 127.50116796 0.00000000 143.26419024
Rotation angle (degrees) 179.83089826
Shift along axis 0.09929828
> fitmap #9 inMap #6
Fit molecule HifA_pdb_v3 (#9) to map postprocess_Hib_job113.mrc (#6) using
8808 atoms
average map value = 0.008534, steps = 176
shifted from previous position = 0.96
rotated from previous position = 45.1 degrees
atoms outside contour = 2382, contour level = 0.0050147
Position of HifA_pdb_v3 (#9) relative to postprocess_Hib_job113.mrc (#6)
coordinates:
Matrix rotation and translation
0.99996207 0.00867876 0.00074810 -1.39113756
0.00867779 -0.99996151 0.00130162 300.17943356
0.00075933 -0.00129503 -0.99999910 313.88525898
Axis -0.99999057 -0.00432749 -0.00037586
Axis point 0.00000000 150.19461045 156.84545615
Rotation angle (degrees) 179.92561049
Shift along axis -0.02587769
> hide #9 models
> hide #!6 models
> show #9 models
> show #8 models
> show #7 models
> show #!6 models
> select add #8
17616 atoms, 17766 bonds, 1176 residues, 2 models selected
> select subtract #8
8808 atoms, 8883 bonds, 588 residues, 1 model selected
> select add #8
17616 atoms, 17766 bonds, 1176 residues, 2 models selected
> select subtract #8
8808 atoms, 8883 bonds, 588 residues, 1 model selected
> select subtract #9
Nothing selected
> select add #8
8808 atoms, 8883 bonds, 588 residues, 1 model selected
> cofr #8
> move y -27.5 models #8
> turn y -163 models #8
> hide #!6 models
> hide #7 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #9 models
> hide #8 models
> show #9 models
> show #!6 models
> hide #!6 models
> hide #9 models
> show #7 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!2 models
> hide #!5 models
> hide #7 models
> show #8 models
> turn y -163 models #8
> fitmap #8 inMap #2
Fit molecule HifA_pdb_v2 (#8) to map postprocess_Hib_job113.mrc (#2) using
8808 atoms
average map value = 0.008367, steps = 228
shifted from previous position = 3.33
rotated from previous position = 59.4 degrees
atoms outside contour = 3364, contour level = 0.0068059
Position of HifA_pdb_v2 (#8) relative to postprocess_Hib_job113.mrc (#2)
coordinates:
Matrix rotation and translation
-0.94902635 -0.31518023 0.00323087 341.05552209
-0.31518598 0.94902883 -0.00144759 55.55309347
-0.00261003 -0.00239217 -0.99999413 341.93603023
Axis -0.15964364 0.98717423 -0.00097149
Axis point 175.27590480 0.00000000 170.73982106
Rotation angle (degrees) 179.83049618
Shift along axis 0.06104816
> hide #!2 models
> show #7 models
> show #9 models
> show #!6 models
> show #!5 models
> show #!2 models
> save
> /Users/eb1MacPro/Dropbox/Hflu/2024HIB/3newHib_into_oldHib_w_pdbs_2024.07.15.cxs
> show #!1 models
> graphics silhouettes true
> graphics silhouettes false
> transparency #1.1#2.1#5.1#6.1 0
> transparency #1.1#2.1#5.1#6.1 50
> select subtract #8
Nothing selected
> select add #2
2 models selected
> transparency sel 0
> transparency sel 50
> hide #!1 models
> hide #!2 models
> hide #!5 models
> hide #!6 models
> select subtract #2
Nothing selected
> show #!1 models
> hide #!1 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> ortho
Unknown command: ortho
> camera ortho
> color #8 #75edebff
> show #!2 models
> color #8 #dbee40ff
> color #8 #eee923ff
> color #8 #eec544ff
> color #8 #eeba37ff
> hide #!2 models
> show #!5 models
> hide #8 models
> hide #9 models
> show #9 models
> show #7 models
> hide #9 models
> show #9 models
> show #!6 models
> hide #!5 models
> hide #7 models
> color #9 #5dedeaff
> color #9 #53dfedff
> color #9 #42daedff
> color #9 #3ec1edff
> show #8 models
> show #7 models
> hide #!6 models
> hide #8 models
> hide #9 models
> show #!5 models
> select #7
8808 atoms, 8883 bonds, 588 residues, 1 model selected
> move y 27.5 models #7
> turn y -163 models #7
> fitmap #7 inMap #5
Fit molecule HifA_3_subunits_try1.pdb (#7) to map postprocess_Hib_job113.mrc
(#5) using 8808 atoms
average map value = 0.008367, steps = 120
shifted from previous position = 1.04
rotated from previous position = 15.6 degrees
atoms outside contour = 2409, contour level = 0.0048659
Position of HifA_3_subunits_try1.pdb (#7) relative to
postprocess_Hib_job113.mrc (#5) coordinates:
Matrix rotation and translation
-0.94904213 -0.31513324 0.00317530 341.05130751
-0.31513944 0.94904390 -0.00167804 55.59108791
-0.00248469 -0.00259317 -0.99999350 341.96468820
Axis -0.15961106 0.98717939 -0.00108181
Axis point 175.26801244 0.00000000 170.76519349
Rotation angle (degrees) 179.83574708
Shift along axis 0.07287375
> hide #!5 models
> show #8 models
> show #9 models
> select subtract #7
Nothing selected
> show #!5 models
> show #!6 models
> show #!2 models
> save
> /Users/eb1MacPro/Dropbox/Hflu/2024HIB/3newHib_into_oldHib_w_pdbs_2024.07.15.cxs
> select #7-9
26424 atoms, 26649 bonds, 1764 residues, 3 models selected
> move y -27.5
> move y 27.5
> move y -27.5 sel
Expected an integer >= 1 or a keyword
> move y -27.5 models #7-9
> turn y -163 models #7-9
> close session
> open
> /Users/eb1MacPro/Dropbox/Hflu/2024HIB/3newHib_into_oldHib_w_pdbs_2024.07.15.cxs
> format session
Opened hibs53mbrix.brix as #1, grid size 60,60,100, pixel 3.5, shown at level
3.3e+04, step 1, values float32
Opened postprocess_Hib_job113.mrc as #2, grid size 280,280,280, pixel 1.08,
shown at level 0.00681, step 1, values float32
Opened hibs53mbrix.brix as #3, grid size 60,60,100, pixel 3.5, shown at level
6.91e+04, step 1, values float32
Opened hibs53mbrix.brix z flip as #4, grid size 60,60,100, pixel 3.5, shown at
level 4.61e+04, step 1, values float32
Opened postprocess_Hib_job113.mrc as #5, grid size 280,280,280, pixel 1.08,
shown at level 0.00487, step 2, values float32
Opened postprocess_Hib_job113.mrc as #6, grid size 280,280,280, pixel 1.08,
shown at level 0.00501, step 2, values float32
opened ChimeraX session
> set bgColor white
> hide #!5 models
> hide #!6 models
> hide #!2 models
> hide #7/a-b #8/a-b #9/a-b
> hide #7/A-B #8/A-B #9/A-B
> hide #8 models
> hide #9 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> hide #7/B
> hide ribbons #7/A-B #8/A-B #9/A-B
Expected ',' or a keyword
> hide #7/A-B #8/A-B #9/A-B ribbons
> show #8 models
> show #9 models
> hide #8 models
> show #8 models
> hide #9 models
> show #!2 models
> hide #7 models
> hide #8 models
> show #!1 models
> hide #!1 models
> show #!5 models
> cofr #2
> turn y 120 models #2
> select add #2
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.046908,0.99771,-0.048765,-150.74,-0.99724,0.049588,0.055283,133.07,0.057574,0.046037,0.99728,-150.25
> view matrix models
> #2,0.084098,0.99576,-0.037145,-157.82,-0.99496,0.085955,0.051611,127.81,0.054585,0.032618,0.99798,-147.89
> view matrix models
> #2,-0.16048,0.9867,-0.025882,-121.17,-0.98618,-0.15919,0.045883,164.22,0.041152,0.032888,0.99861,-145.99
> view matrix models
> #2,-0.15228,0.98686,0.053939,-134.43,-0.98684,-0.15483,0.046672,163.54,0.054411,-0.046122,0.99745,-135.94
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.15228,0.98686,0.053939,-130.8,-0.98684,-0.15483,0.046672,163.58,0.054411,-0.046122,0.99745,-135.99
> view matrix models
> #2,-0.15228,0.98686,0.053939,-131.44,-0.98684,-0.15483,0.046672,165.28,0.054411,-0.046122,0.99745,-135.91
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.00057809,0.99966,0.02597,-152.09,-0.99983,-0.0010498,0.018154,148.39,0.018175,-0.025955,0.9995,-133.78
> view matrix models
> #2,-0.0051394,0.99923,0.038881,-153.27,-0.99986,-0.0045252,-0.015867,154.03,-0.015679,-0.038958,0.99912,-126.65
> view matrix models
> #2,0.0033244,0.9999,0.01364,-150.86,-0.99874,0.0026356,0.050211,142.86,0.05017,-0.01379,0.99865,-140.32
> view matrix models
> #2,-0.042504,0.99837,0.038117,-147.38,-0.99704,-0.044833,0.0625,147.9,0.064107,-0.035347,0.99732,-138.98
> view matrix models
> #2,-0.042928,0.99829,0.039602,-147.53,-0.99725,-0.045211,0.058663,148.56,0.060354,-0.036975,0.99749,-138.19
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.042928,0.99829,0.039602,-146.57,-0.99725,-0.045211,0.058663,146.36,0.060354,-0.036975,0.99749,-137.32
> show #!6 models
> turn y -120 models #2
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.87596,-0.45732,0.15346,-88.876,0.45571,0.88885,0.047646,-207.94,-0.15819,0.028196,0.98701,-112.41
> ui tool show "Side View"
> show #8 models
> show #7-9 ribbons
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 3 maps.
> ui tool show "Fit in Map"
> fitmap #8 inMap #2
Fit molecule HifA_pdb_v2 (#8) to map postprocess_Hib_job113.mrc (#2) using
8808 atoms
average map value = 0.008367, steps = 108
shifted from previous position = 5.47
rotated from previous position = 10.3 degrees
atoms outside contour = 3358, contour level = 0.0068059
Position of HifA_pdb_v2 (#8) relative to postprocess_Hib_job113.mrc (#2)
coordinates:
Matrix rotation and translation
-0.94903779 -0.31514582 0.00322349 341.04744198
-0.31515186 0.94903995 -0.00156823 55.56803627
-0.00256507 -0.00250424 -0.99999386 341.96153508
Axis -0.15962651 0.98717694 -0.00103040
Axis point 175.27030012 0.00000000 170.75653587
Rotation angle (degrees) 179.83201567
Shift along axis 0.06291469
> show #9 models
> show #7 models
> hide #!2 models
> hide #!5 models
> hide #!6 models
> ui tool show "Side View"
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
> camera ortho
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-5.5.17
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: 32 GB
System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.5077.0.0,0)
OS Loader Version: 580~2215
Software:
System Software Overview:
System Version: macOS 14.5 (23F79)
Kernel Version: Darwin 23.5.0
Time since boot: 10 days, 2 hours, 22 minutes
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 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): 8 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: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
B247W:
Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
UI Looks like: 1920 x 1200 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: TD3AA0018532
Mirror: Off
Online: Yes
Rotation: Supported
Adapter Type: DVI or HDMI
Adapter Firmware Version: ff.c8
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
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
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
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
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
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
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
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
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 , 15 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash waking Mac from sleep |
comment:2 by , 15 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
This ChimeraX crash is in the Qt window toolkit and we have most often seen it when an external display is unplugged or plugged in. The crash report says it crashed in Qt routine displayConfigFinalizedProc(). Did you plugin or unplug an external display while ChimeraX was running? Of course that should work but the Qt window toolkit version 6.6 often crashes on Mac when you do that. It happens especially often on older Macs with AMD or Intel graphics. We are hoping it is fixed in Qt 6.7 and you could try the ChimeraX daily build which is currently using Qt 6.7. We don't have any way to fix the Qt 6.6 problem in ChimeraX 1.8 and I can only suggest saving a ChimeraX session if you have to plugin or unplug an external display.
Sorry for the delayed reply. I was on vacation last week.
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Reported by Esther Bullitt