Opened 12 months ago

Closed 12 months ago

#16251 closed defect (can't reproduce)

Crash on Mac waking from sleep, Qt 6.7

Reported by: chimerax-bug-report@… 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-12.7.6-x86_64-i386-64bit
ChimeraX Version: 1.9rc202411012347 (2024-11-01 23:47:45 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x000070001c2ad000 (most recent call first):
  File "/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000070001b2aa000 (most recent call first):
  File "/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000070001a2a7000 (most recent call first):
  File "/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
  File "/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007000192a4000 (most recent call first):
  File "/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007000182a1000 (most recent call first):
  File "/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000070001729e000 (most recent call first):
  File "/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000070001629b000 (most recent call first):
  File "/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x00000001116da600 (most recent call first):
  File "/Applications/ChimeraX-1.9-rc2024.11.01.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-rc2024.11.01.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-rc2024.11.01.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.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PIL._imagingmath, chimerax.mlp._mlp, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 56)


{"app_name":"ChimeraX","timestamp":"2024-11-05 07:51:53.00 +0100","app_version":"1.9.0","slice_uuid":"079d39d3-a489-3e56-92d8-c781f5a4bb98","build_version":"1.9.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 12.7.6 (21H1320)","incident_id":"630F2DE8-ED6C-4252-9E63-DD1CB6462EDA","name":"ChimeraX"}
{
  "uptime" : 54000,
  "procLaunch" : "2024-11-04 10:45:15.9898 +0100",
  "procRole" : "Background",
  "version" : 2,
  "userID" : 502,
  "deployVersion" : 210,
  "modelCode" : "MacBookAir7,2",
  "procStartAbsTime" : 43178458576989,
  "coalitionID" : 10452,
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  "captureTime" : "2024-11-05 07:51:03.7472 +0100",
  "incident" : "630F2DE8-ED6C-4252-9E63-DD1CB6462EDA",
  "bug_type" : "309",
  "pid" : 10642,
  "procExitAbsTime" : 54772966825965,
  "cpuType" : "X86-64",
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.9-rc2024.11.01.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"5FED03AC-385B-5F77-AA6A-C83F44CA00BB","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "74FC4B35-B27C-733E-A1A8-23C0C10459C6",
  "wakeTime" : 7,
  "sleepWakeUUID" : "95ADC0F8-4CBE-424E-B1CB-D6BB47148A74",
  "sip" : "enabled",
  "vmRegionInfo" : "0 is not in any region.  Bytes before following region: 4494434304\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      10be3a000-10be3e000    [   16K] r-x\/r-x SM=COW  ...acOS\/ChimeraX",
  "isCorpse" : 1,
  "exception" : {"codes":"0x000000000000000d, 0x0000000000000000","rawCodes":[13,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"UNKNOWN_0xD at 0x0000000000000000"},
  "vmregioninfo" : "0 is not in any region.  Bytes before following region: 4494434304\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      10be3a000-10be3e000    [   16K] r-x\/r-x SM=COW  ...acOS\/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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    "arch" : "x86_64",
    "base" : 4680278016,
    "size" : 66404352,
    "uuid" : "7048d1fd-b9a9-3f6a-b752-ae8be69f6c3f",
    "path" : "\/Applications\/ChimeraX-1.9-rc2024.11.01.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
    "name" : "libopenblas64_.0.dylib"
  }
],
  "sharedCache" : {
  "base" : 140703158018048,
  "size" : 19331678208,
  "uuid" : "246818c3-4b9f-3462-bcaf-fdf71975e5fe"
},
  "vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=1.2G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.2G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework              1152K        9 \nActivity Tracing                   256K        1 \nCG backing stores                  720K        4 \nCG image                           512K       71 \nColorSync                          232K       28 \nCoreAnimation                     1744K      170 \nCoreGraphics                        16K        3 \nCoreImage                            8K        2 \nCoreUI image data                 3168K       46 \nFoundation                          40K        2 \nIOKit                             15.5M        2 \nKernel Alloc Once                  404K        4 \nMALLOC                           378.5M      536 \nMALLOC guard page                   32K        8 \nMALLOC_LARGE (reserved)            256K        1         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           384.0M        1         reserved VM address space (unallocated)\nMach message                        16K        2 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        140K       35 \nStack                            314.3M       36 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      165.3M      213 \n__CTF                               756        1 \n__DATA                            39.7M      727 \n__DATA_CONST                      42.0M      446 \n__DATA_DIRTY                      1805K      238 \n__FONT_DATA                          4K        1 \n__GLSLBUILTINS                    5176K        1 \n__LINKEDIT                       676.7M      161 \n__OBJC_RO                         82.9M        1 \n__OBJC_RW                         3200K        2 \n__TEXT                           857.0M      730 \n__UNICODE                          592K        1 \ndyld private memory               1064K        3 \nmapped file                      202.5M       47 \nshared memory                     2972K       26 \n===========                     =======  ======= \nTOTAL                              3.2G     3564 \nTOTAL, minus reserved VM space     2.8G     3564 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "5fb4245a1bbfe8005e33a1e1",
      "factorPackIds" : {

      },
      "deploymentId" : 240000021
    },
    {
      "rolloutId" : "5fc94383418129005b4e9ae0",
      "factorPackIds" : {

      },
      "deploymentId" : 240000614
    }
  ],
  "experiments" : [

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}
}
===== Log before crash start =====
Startup Messages  
---  
warning | QCoreApplication::postEvent: Unexpected null receiver  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.9rc202411012347 (2024-11-01)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/fredrikleo/Library/CloudStorage/OneDrive-GenovisAB(2)/PhD/Paper
> 3 - MdpS2/Figures for manuscript/Structural comparison/MdpS -
> AF-A0A1X1FWK3-F1-model_v4.pdb"
> "/Users/fredrikleo/Library/CloudStorage/OneDrive-GenovisAB(2)/PhD/Paper 3 -
> MdpS2/Figures for manuscript/Structural comparison/MdpS2 -
> AF-A0A1X1FVD9-F1-model_v4.pdb"

Summary of feedback from opening
/Users/fredrikleo/Library/CloudStorage/OneDrive-GenovisAB(2)/PhD/Paper 3 -
MdpS2/Figures for manuscript/Structural comparison/MdpS -
AF-A0A1X1FWK3-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 38  
DBREF XXXX A 1 336 UNP A0A1X1FWK3 A0A1X1FWK3_STROR 1 336  
  
Summary of feedback from opening
/Users/fredrikleo/Library/CloudStorage/OneDrive-GenovisAB(2)/PhD/Paper 3 -
MdpS2/Figures for manuscript/Structural comparison/MdpS2 -
AF-A0A1X1FVD9-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 40  
DBREF XXXX A 1 227 UNP A0A1X1FVD9 A0A1X1FVD9_STROR 1 227  
  
MdpS - AF-A0A1X1FWK3-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for TRNA N6-adenosine
threonylcarbamoyltransferase (A0A1X1FWK3) [more info...]  
  
Chain information for MdpS - AF-A0A1X1FWK3-F1-model_v4.pdb #1  
---  
Chain | Description  
A | TRNA N6-adenosine threonylcarbamoyltransferase  
  
MdpS2 - AF-A0A1X1FVD9-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for TRNA
(adenosine(37)-N6)-threonylcarbamoyltransferase complex dimerization subunit
type 1 tsab (A0A1X1FVD9) [more info...]  
  
Chain information for MdpS2 - AF-A0A1X1FVD9-F1-model_v4.pdb #2  
---  
Chain | Description  
A | TRNA (adenosine(37)-N6)-threonylcarbamoyltransferase complex dimerization subunit type 1 tsab  
  
Computing secondary structure  

> matchmaker #1 to #2

Computing secondary structure  
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 MdpS2 - AF-A0A1X1FVD9-F1-model_v4.pdb, chain A (#2) with MdpS -
AF-A0A1X1FWK3-F1-model_v4.pdb, chain A (#1), sequence alignment score = 203.3  
RMSD between 79 pruned atom pairs is 0.924 angstroms; (across all 197 pairs:
22.814)  
  

> color #2 #b1c1dfff

> color #2 #ffec83ff

> color #2 #ffe000ff

> color #2 #fff7d0ff

> color #1 #1e4589ff

> color #1 #9197c2ff

> color #1 #1e4589ff

> color #1 #ef7748ff

> color #1 #a9115fff

> color #1 #e96aa4ff

> color #2 #b1c1dfff

> color #2 #e1f1efff

> color #2 #deecd5ff

> color #2 #b6d6a7ff

> color #2 #deecd5ff

> color #2 #c8c3dcff

> color #1 #453777ff

> color #1 #968eb8ff

> color #1 #453777ff

> color #1 #ffe000ff

> color #1 #ffec83ff

> color #1 #ef7748ff

> color #1 black

> color #1 silver

> color #2 #929000ff

> color #2 #4f8f00ff

> color #1 #ff9300ff

> color #1 #fffb00ff

> color #1 #0096ffff

> color #1 #ff2f92ff

> color #1 #ff7e79ff

> color #1 #ffd479ff

> color #1 #fffc79ff

> color #1 #d4fb79ff

> color #1 #76d6ffff

> color #1 #7a81ffff

> color #1 #d783ffff

> color #1 #ff85ffff

> color #1 #d783ffff

> color #2 #941100ff

> color #2 #008f00ff

> color #2 #009193ff

> color #2 #005493ff

> color #2 #531b93ff

> color #2 #ff2600ff

> color #2 #941751ff

> color #2 #0096ffff

> color #2 #ffd479ff

> set bgColor white

> set bgColor #ffffff00

> set bgColor black

> set bgColor transparent

> set bgColor white

> set bgColor #ffffff00

> color #2 #4f8f00ff

> color #1 silver

> color #1 #929292ff

> color #1 darkgrey

> color #1 #424242ff

> color #1 black

> set bgColor black

> set bgColor transparent

> set bgColor white

> set bgColor #ffffff00

> color #1 white

> set bgColor black

> set bgColor transparent

> color #1 #e1f1efff

> color #1 #ecececff

> color #1 white

> color #1 #ff40ffff

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/fredrikleo/Desktop/movie1.mp4

Movie saved to /Users/fredrikleo/Desktop/movie1.mp4  
  

> style stick

Changed 4310 atom styles  

> style sphere

Changed 4310 atom styles  

> style ball

Changed 4310 atom styles  

> color byhetero

> color bychain

> color byhetero

> undo

> ui tool show "Side View"

> lighting simple

> view

> ui mousemode right "color key"

> ui mousemode right translate

> hide #3 models

> select add #1

2527 atoms, 2572 bonds, 336 residues, 1 model selected  

> select subtract #1

Nothing selected  

> select add #2

1783 atoms, 1819 bonds, 227 residues, 1 model selected  

> select subtract #2

Nothing selected  

> ui mousemode right "clip rotate"

> undo

> select subtract #1

Nothing selected  

> hide #1 models

> show #1 models

> rainbow

> color bfactor

4310 atoms, 563 residues, atom bfactor range 38.5 to 98.9  

> mlp

Map values for surface "MdpS - AF-A0A1X1FWK3-F1-model_v4.pdb_A SES surface":
minimum -32.48, mean -5.429, maximum 21.22  
Map values for surface "MdpS2 - AF-A0A1X1FVD9-F1-model_v4.pdb_A SES surface":
minimum -25.18, mean -4.859, maximum 22.47  
To also show corresponding color key, enter the above mlp command and add key
true  

> color bynucleotide

> color bfactor

4310 atoms, 563 residues, 2 surfaces, atom bfactor range 38.5 to 98.9  

> color byhetero

> color bychain

> style stick

Changed 4310 atom styles  

> style sphere

Changed 4310 atom styles  

> undo

> show #!2 cartoons

> show #!2 surfaces

> hide #!2 models

> show #!2 models

> show #!1 models

> color bynucleotide

> style stick

Changed 4310 atom styles  

> style sphere

Changed 4310 atom styles  

> style ball

Changed 4310 atom styles  

> show cartoons

> show atoms

> color bynucleotide

> style ball

Changed 4310 atom styles  

> show target m

> hide target m

> show #!1 models

> show #!2 models

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> style ball

Changed 4310 atom styles  

> style sphere

Changed 4310 atom styles  

> style stick

Changed 4310 atom styles  

> nucleotides fill

> style nucleic stick

Changed 0 atom styles  

> style stick

Changed 4310 atom styles  

> style sphere

Changed 4310 atom styles  

> style ball

Changed 4310 atom styles  

> color bychain

> style sphere

Changed 4310 atom styles  

> style stick

Changed 4310 atom styles  

> style ball

Changed 4310 atom styles  

> show cartoons

> hide atoms

> color #1 #00f900ff

> color #2 #ff40ffff

> undo

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> undo

> show cartoons

> hide atoms

> label #1/A text MdpS color green

> undo

> hide atoms

> color #1 #00f900ff

> color #2 #ff40ffff

> label #1/A

> undo

> unlabel #1/A

Unknown command: unlabel #1/A  

> label #1.2#!1-2 text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"

> undo

> show cartoons

> hide atoms

> ~label #1/A

> ~label #1/A text MdpS color green

> label delete #1/A text MdpS color green

Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword  

> hide atoms

> ~label #1.2#!1-2 text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"

> label delete #1.2#!1-2 text "/{0.chain_id} {0.name}
> {0.number}{0.insertion_code}"

Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword  

> ~label #2.2#!1-2 residues

> label #1/A models text MdpS color white

> label #2/A models text MdpS2 color white

> label #1/B models text MdpS color white

> color #1 #00f900ff

> color #2 #ff40ffff

> ~label #1/B models text "MdpS" color white

> label delete #1/B models text "MdpS" color white

Expected a keyword  

> ~label #1/A models text "MdpS" color white

> label delete #1/A models text "MdpS" color white

Expected a keyword  

> show atoms

> show cartoons

> hide atoms

> ~label #1/A models text "MdpS" color white

> label delete #1/A models text "MdpS" color white

Expected a keyword  

> ~label #2/A models text "MdpS2" color white

> label delete #2/A models text "MdpS2" color white

Expected a keyword  

> ~label #2/A

> ~label #1/A

> ~label #1/B

> color bynucleotide

> set bgColor gray

> set bgColor #80808000

> set bgColor black

> set bgColor transparent

> set bgColor white

> set bgColor #ffffff00

> set bgColor gray

> set bgColor #80808000

> set bgColor black

> set bgColor transparent

> set bgColor gray

> set bgColor #80808000

Color zone shortcut requires 1 displayed atomic model and 1 map, got 2 atomic
models, 0 maps.  

> show #3 models

> hide #3 models

> select add #3

1 model selected  

> show #3 models

> hide #3 models

> select subtract #3

Nothing selected  

> ui mousemode right distance

> ui mousemode right "color key"

> ui mousemode right distance

> color byhetero #1/A

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color byhetero #1

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color byhetero models #1

Expected ',' or a keyword  

> color byhetero models #1

Expected ',' or a keyword  

> color byhet, models #1

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color byhet, models #1 green

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color byhetero green, models #1

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color byhetero green, 'models' #1

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color byhetero models #1 green

Expected ',' or a keyword  

> color byhet, 'models' #1 green

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color byhetero models #1, green

Expected ',' or a keyword  

> color byattribute seq_conservation #1

No known/registered numeric attribute seq_conservation  

> color byhetero seq_conservation #1

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> select #1: 1-100

736 atoms, 744 bonds, 100 residues, 1 model selected  

> select #1: 1-100

736 atoms, 744 bonds, 100 residues, 1 model selected  

> color green sel

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color green sel

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  


===== Log before crash end =====

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9rc202411012347 (2024-11-01)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 INTEL-18.8.16
OpenGL renderer: Intel(R) HD Graphics 6000
OpenGL vendor: Intel Inc.

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 Air
      Model Identifier: MacBookAir7,2
      Processor Name: Dual-Core Intel Core i5
      Processor Speed: 1,8 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 3 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 489.0.0.0.0
      OS Loader Version: 540.120.3~37
      SMC Version (system): 2.27f2

Software:

    System Software Overview:

      System Version: macOS 12.7.6 (21H1320)
      Kernel Version: Darwin 21.6.0
      Time since boot: 5 days 20:30

Graphics/Displays:

    Intel HD Graphics 6000:

      Chipset Model: Intel HD Graphics 6000
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x1626
      Revision ID: 0x0009
      Metal Family: Supported, Metal GPUFamily macOS 1
      Displays:
        Color LCD:
          Display Type: LCD
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Mirror: On
          Mirror Status: Hardware Mirror
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        HP E273:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: CNK9130CWH  
          Main Display: Yes
          Mirror: On
          Mirror Status: Master Mirror
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.7.1
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    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: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.7
    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: 2.4.7
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13
    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: 1.9rc202411012347
    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: 1.2.5
    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
    ChimeraX-Label: 1.1.11
    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: 2.7.1
    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: 1.5.17
    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-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: 1.6.1
    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: 3.2.4
    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: 1.3.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.7
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.54.1
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.12.1
    html2text: 2024.2.26
    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: 2.10.1
    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: 2.4.1
    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
    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: 6.4.1
    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 (5)

comment:1 by Eric Pettersen, 12 months ago

Component: Unassigned → Window Toolkit
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash running modal dialog

comment:2 by Eric Pettersen, 12 months ago

Resolution: → can't reproduce
Status: accepted → closed

comment:3 by Eric Pettersen, 12 months ago

Resolution: can't reproduce
Status: closed → reopened
Summary: Crash running modal dialog → Crash on Mac waking from sleep

comment:4 by Eric Pettersen, 12 months ago

Owner: changed from Eric Pettersen to Tom Goddard
Status: reopened → assigned

Unfortunately, again 1.9

comment:5 by Tom Goddard, 12 months ago

Resolution: → can't reproduce
Status: assigned → closed
Summary: Crash on Mac waking from sleep → Crash on Mac waking from sleep, Qt 6.7

Crud. Maybe my previous assessment that Qt 6.7 mostly fixed this crash is wrong. Hard to say since it was based on guesses about how much the ChimeraX daily build gets used.

This crash on Intel Mac is in _NSViewHierarchyDidChangeBackingProperties. That is the location of the ChimeraX 1.8 Mac ARM crashes, but Mac Intel crashed in a different routine displayConfigFinalize (?). So maybe Qt 6.7 has a new crash mode for Intel Mac.

As usual this report shows multiple displays connected.

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