Opened 3 years ago

Closed 3 years ago

Last modified 3 years ago

#8782 closed defect (can't reproduce)

Crash closing tool window

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: VR Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-13.2.1-arm64-arm-64bit
ChimeraX Version: 1.6rc202303310103 (2023-03-31 01:03:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x0000000293e5b000 (most recent call first):
  File "/private/var/folders/wl/2vvbpk2s77s4pqp0j3pf3k1h0000gn/T/AppTranslocation/88240679-389A-4387-BD09-39CA7DCC7AE5/d/ChimeraX-1.6-rc2023.03.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
  File "/private/var/folders/wl/2vvbpk2s77s4pqp0j3pf3k1h0000gn/T/AppTranslocation/88240679-389A-4387-BD09-39CA7DCC7AE5/d/ChimeraX-1.6-rc2023.03.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
  File "/private/var/folders/wl/2vvbpk2s77s4pqp0j3pf3k1h0000gn/T/AppTranslocation/88240679-389A-4387-BD09-39CA7DCC7AE5/d/ChimeraX-1.6-rc2023.03.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1297 in run
  File "/private/var/folders/wl/2vvbpk2s77s4pqp0j3pf3k1h0000gn/T/AppTranslocation/88240679-389A-4387-BD09-39CA7DCC7AE5/d/ChimeraX-1.6-rc2023.03.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/private/var/folders/wl/2vvbpk2s77s4pqp0j3pf3k1h0000gn/T/AppTranslocation/88240679-389A-4387-BD09-39CA7DCC7AE5/d/ChimeraX-1.6-rc2023.03.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Current thread 0x00000001f4cc4140 (most recent call first):
  File "/private/var/folders/wl/2vvbpk2s77s4pqp0j3pf3k1h0000gn/T/AppTranslocation/88240679-389A-4387-BD09-39CA7DCC7AE5/d/ChimeraX-1.6-rc2023.03.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2297 in destroy
  File "/private/var/folders/wl/2vvbpk2s77s4pqp0j3pf3k1h0000gn/T/AppTranslocation/88240679-389A-4387-BD09-39CA7DCC7AE5/d/ChimeraX-1.6-rc2023.03.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2161 in _destroy
  File "/private/var/folders/wl/2vvbpk2s77s4pqp0j3pf3k1h0000gn/T/AppTranslocation/88240679-389A-4387-BD09-39CA7DCC7AE5/d/ChimeraX-1.6-rc2023.03.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 776 in remove_tool
  File "/private/var/folders/wl/2vvbpk2s77s4pqp0j3pf3k1h0000gn/T/AppTranslocation/88240679-389A-4387-BD09-39CA7DCC7AE5/d/ChimeraX-1.6-rc2023.03.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 347 in remove_tool
  File "/private/var/folders/wl/2vvbpk2s77s4pqp0j3pf3k1h0000gn/T/AppTranslocation/88240679-389A-4387-BD09-39CA7DCC7AE5/d/ChimeraX-1.6-rc2023.03.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/tools.py", line 154 in delete
  File "/private/var/folders/wl/2vvbpk2s77s4pqp0j3pf3k1h0000gn/T/AppTranslocation/88240679-389A-4387-BD09-39CA7DCC7AE5/d/ChimeraX-1.6-rc2023.03.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/swap_res/tool.py", line 297 in delete
  File "/private/var/folders/wl/2vvbpk2s77s4pqp0j3pf3k1h0000gn/T/AppTranslocation/88240679-389A-4387-BD09-39CA7DCC7AE5/d/ChimeraX-1.6-rc2023.03.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/swap_res/tool.py", line 347 in _apply_rotamer
  File "/private/var/folders/wl/2vvbpk2s77s4pqp0j3pf3k1h0000gn/T/AppTranslocation/88240679-389A-4387-BD09-39CA7DCC7AE5/d/ChimeraX-1.6-rc2023.03.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/private/var/folders/wl/2vvbpk2s77s4pqp0j3pf3k1h0000gn/T/AppTranslocation/88240679-389A-4387-BD09-39CA7DCC7AE5/d/ChimeraX-1.6-rc2023.03.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
  File "/private/var/folders/wl/2vvbpk2s77s4pqp0j3pf3k1h0000gn/T/AppTranslocation/88240679-389A-4387-BD09-39CA7DCC7AE5/d/ChimeraX-1.6-rc2023.03.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in 
  File "/private/var/folders/wl/2vvbpk2s77s4pqp0j3pf3k1h0000gn/T/AppTranslocation/88240679-389A-4387-BD09-39CA7DCC7AE5/d/ChimeraX-1.6-rc2023.03.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/private/var/folders/wl/2vvbpk2s77s4pqp0j3pf3k1h0000gn/T/AppTranslocation/88240679-389A-4387-BD09-39CA7DCC7AE5/d/ChimeraX-1.6-rc2023.03.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main


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  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookAir10,1",
  "coalitionID" : 50965,
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    "releaseType" : "User"
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  "captureTime" : "2023-04-04 10:36:49.5883 -0400",
  "incident" : "34A0E1CC-DD66-4DA0-9309-2AE762E81905",
  "pid" : 53966,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2023-04-04 09:18:43.3216 -0400",
  "procStartAbsTime" : 14274728811126,
  "procExitAbsTime" : 14387199303218,
  "procName" : "ChimeraX",
  "procPath" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.6-rc2023.03.31.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.6.0","CFBundleVersion":"1.6.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"4ECA8338-2F60-5F74-B16B-7AEAB4EDD302","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
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  "crashReporterKey" : "B7861D6D-8C4E-A60F-D07B-58AE9818B833",
  "throttleTimeout" : 2147483647,
  "wakeTime" : 5893,
  "sleepWakeUUID" : "16E34FAD-1A37-4BEC-9651-A6BABC9B027F",
  "sip" : "enabled",
  "vmRegionInfo" : "0x4ece55ef4fa8 is not in any region.  Bytes after previous region: 86167075639209  Bytes before following region: 18905004290136\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)        1000000000-7000000000   [384.0G] ---\/--- SM=NUL  ...(unallocated)\n--->  GAP OF 0x5f9000000000 BYTES\n      MALLOC_NANO              600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV  ",
  "exception" : {"codes":"0x0000000000000001, 0x0000cece55ef4fa8","rawCodes":[1,227385600331688],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000cece55ef4fa8 -> 0x00004ece55ef4fa8 (possible pointer authentication failure)"},
  "ktriageinfo" : "VM - pmap_enter retried due to resource shortage\nVM - pmap_enter retried due to resource shortage\nVM - pmap_enter retried due to resource shortage\nVM - pmap_enter retried due to resource shortage\nVM - pmap_enter retried due to resource shortage\n",
  "vmregioninfo" : "0x4ece55ef4fa8 is not in any region.  Bytes after previous region: 86167075639209  Bytes before following region: 18905004290136\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)        1000000000-7000000000   [384.0G] ---\/--- SM=NUL  ...(unallocated)\n--->  GAP OF 0x5f9000000000 BYTES\n      MALLOC_NANO              600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV  ",
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    "name" : "QtWidgets"
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    "arch" : "arm64",
    "base" : 4774182912,
    "size" : 3080192,
    "uuid" : "7665a44d-b6d3-323b-bb24-6ce940fbfbeb",
    "path" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.6-rc2023.03.31.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/QtWidgets.abi3.so",
    "name" : "QtWidgets.abi3.so"
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    "path" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.6-rc2023.03.31.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/Python",
    "name" : "Python",
    "CFBundleVersion" : "3.9.11"
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    "name" : "QtCore.abi3.so"
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    "name" : "QtCore"
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    "uuid" : "e580e17d-2c19-39bf-bdd1-9f96d62b6172",
    "path" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.6-rc2023.03.31.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtGui.framework\/Versions\/A\/QtGui",
    "name" : "QtGui"
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    "arch" : "arm64e",
    "base" : 7028367360,
    "CFBundleShortVersionString" : "2.1.1",
    "CFBundleIdentifier" : "com.apple.HIToolbox",
    "size" : 3358720,
    "uuid" : "c68fe2e2-e0f3-3caf-ada3-bcc72fba79d0",
    "path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
    "name" : "HIToolbox"
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    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.AppKit",
    "size" : 15777792,
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    "path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
    "name" : "AppKit",
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    "uuid" : "191e84f1-4b95-39c8-b253-1c1ef56c0fa8",
    "path" : "\/usr\/lib\/dyld",
    "name" : "dyld"
  },
  {
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    "base" : 5821693952,
    "size" : 154959872,
    "uuid" : "1b766dc4-2490-3425-8726-45387675bc14",
    "path" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.6-rc2023.03.31.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
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    "name" : "libopenblas64_.0.dylib"
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  {
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    "source" : "A",
    "base" : 0,
    "uuid" : "00000000-0000-0000-0000-000000000000"
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],
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "610d52e1fc54bc3389840408",
      "factorPackIds" : {
        "SIRI_UNDERSTANDING_ASR_ASSISTANT" : "641f89df25e4504c378ef777",
        "SIRI_UNDERSTANDING_MORPHUN" : "62ec7220c682040ba94e6a20"
      },
      "deploymentId" : 240000674
    },
    {
      "rolloutId" : "5f72dc58705eff005a46b3a9",
      "factorPackIds" : {

      },
      "deploymentId" : 240000015
    }
  ],
  "experiments" : [
    {
      "treatmentId" : "c28e4ee6-1b08-4f90-8e05-2809e78310a3",
      "experimentId" : "6317d2003d24842ff850182a",
      "deploymentId" : 400000012
    }
  ]
},
  "reportNotes" : [
  "dyld_process_snapshot_create_for_process failed with 5"
]
}
===== Log before crash start =====
UCSF ChimeraX version: 1.6rc202303310103 (2023-03-31)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> help help:quickstart

> ui tool show "Command Line Interface"

> open 148L

Summary of feedback from opening 148L fetched from pdb  
---  
notes | Fetching compressed mmCIF 148l from
http://files.rcsb.org/download/148l.cif  
Fetching CCD FGA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/FGA/FGA.cif  
Fetching CCD API from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/I/API/API.cif  
Fetching CCD DAL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/DAL/DAL.cif  
Fetching CCD MUB from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/B/MUB/MUB.cif  
Fetching CCD NAG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/NAG/NAG.cif  
Fetching CCD BME from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/BME/BME.cif  
  
148l title:  
A covalent enzyme-substrate intermediate with saccharide distortion In A
mutant T4 lysozyme [more info...]  
  
Chain information for 148l #1  
---  
Chain | Description | UniProt  
E | T4 LYSOZYME | LYCV_BPT4 1-164  
S | SUBSTRATE CLEAVED FROM CELL WALL OF ESCHERICHIA COLI |  
  
Non-standard residues in 148l #1  
---  
BME — β-mercaptoethanol  
MUB — N-acetyl-alpha-muramic acid  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
  

> preset "initial styles" sticks

Using preset: Initial Styles / Sticks  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "initial styles" "original look"

Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> show atoms

> hide atoms

> rainbow

> mlp

Map values for surface "148l_E SES surface": minimum -27.97, mean -5.264,
maximum 22.47  
Map values for surface "148l_S SES surface": minimum -11.91, mean 86.19,
maximum 154.4  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide surfaces

> preset "initial styles" "original look"

Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> color #1 #8b6fd7ff

> color #1 #af8bd7ff

> color #1 #a34cd7ff

> color #1 #a34dd7ff

> ui tool show "Show Sequence Viewer"

> sequence chain /E

Alignment identifier is 1/E  

> select
> /E:3-11,39-50,60-80,82-90,93-106,108-113,115-123,126-134,137-141,143-155

859 atoms, 861 bonds, 107 residues, 1 model selected  

> select /E:14-19,25-28,31-34

123 atoms, 123 bonds, 14 residues, 1 model selected  

> select
> /E:3-11,39-50,60-80,82-90,93-106,108-113,115-123,126-134,137-141,143-155

859 atoms, 861 bonds, 107 residues, 1 model selected  

> select /E:14-19,25-28,31-34

123 atoms, 123 bonds, 14 residues, 1 model selected  

> select /E:1-56

441 atoms, 446 bonds, 56 residues, 1 model selected  

> select /E:1-57

448 atoms, 453 bonds, 57 residues, 1 model selected  

> rainbow sel

> select
> /E:3-11,39-50,60-80,82-90,93-106,108-113,115-123,126-134,137-141,143-155

859 atoms, 861 bonds, 107 residues, 1 model selected  

> select /E:1-57

448 atoms, 453 bonds, 57 residues, 1 model selected  

> select /E:57

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /E:1-57

448 atoms, 453 bonds, 57 residues, 1 model selected  

> rainbow sel

> hide sel surfaces

> hide sel cartoons

> show sel surfaces

> hide sel surfaces

> show sel cartoons

> preset "initial styles" "original look"

Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> select ligand

36 atoms, 36 bonds, 3 residues, 1 model selected  

> style sel ball

Changed 36 atom styles  

> color sel orange

> color sel byhetero

> ui tool show "Color Actions"

> set bgColor white

> select /E:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /E:1-163

1295 atoms, 1315 bonds, 163 residues, 1 model selected  

> color (#!1 & sel) purple

> ui tool show "Color Actions"

> set bgColor white

> set bgColor magenta

> set bgColor white

> select /E:1-163

1295 atoms, 1315 bonds, 163 residues, 1 model selected  

> ui windowfill toggle

> color (#!1 & sel) byhetero

> save "/Users/tiffanismith/Desktop/Lysozyme T4 _TSmith.jpg" width 820 height
> 722 supersample 3

> save

Missing or invalid "fileName" argument: Expected a file name  

> ui windowfill toggle

> save Lysozyme T4 session 1

Cannot determine format for 'Lysozyme'  

> save Lys T4 session 1

Cannot determine format for 'Lys'  

> save LysT4session1

Cannot determine format for 'LysT4session1'  

> save:LysT4session1

Unknown command: save:LysT4session1  

> save LysozymeT4_TSmith

Cannot determine format for 'LysozymeT4_TSmith'  

> save[LysozymeT4session1.py]

Unknown command: save[LysozymeT4session1.py]  

> save LysozymeT4session1.py

No known data format for file suffix '.py'  

> save LysozymeT4session1.py

No known data format for file suffix '.py'  

> save "/Users/tiffanismith/Desktop/Lysozyme T4 session 1.cxs"

> select:8

Unknown command: select:8  

> ui tool show "Command Line Interface"

> select:8

Unknown command: select:8  

> ui tool show "Show Sequence Viewer"

> sequence chain /E

Alignment identifier is 1/E  

> select: 8

Unknown command: select: 8  
Destroying pre-existing alignment with identifier 1/E  
Alignment identifier is 1/E  

> select ligand

36 atoms, 36 bonds, 3 residues, 1 model selected  

> select
> /E:3-11,39-50,60-80,82-90,93-106,108-113,115-123,126-134,137-141,143-155

859 atoms, 861 bonds, 107 residues, 1 model selected  

> select /E:8

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select /E:8

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show (#!1 & sel) target ab

> turn y 1 360

> movie record

> turn y 1 360

> wait

> movie encode

Movie saved to /Users/tiffanismith/Desktop/movie.mp4  
  

> ui tool show Rotamers

> swapaa interactive sel ARG rotLib Dunbrack

/E ARG 8 (alt loc A): phi -63.5, psi -39.7 trans  
Changed 600 bond radii  

> swapaa #!1/E:8 ARG criteria 31 rotLib Dunbrack retain false

Using Dunbrack library  
148l #!1/E ARG 8 (alt loc A): phi -63.5, psi -39.7 trans  
148l #!1/E ARG 8 (alt loc B): phi -64.9, psi -39.0 trans  
Applying ARG rotamer (chi angles: 66.8 -176.4 -177.5 -179.2) to 148l #!1/E ARG
8 using alt loc A  
Applying ARG rotamer (chi angles: 66.8 -176.4 -177.5 -179.2) to 148l #!1/E ARG
8 using alt loc B  


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

Log:
UCSF ChimeraX version: 1.6rc202303310103 (2023-03-31)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir10,1
      Model Number: MGND3LL/A
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 8419.80.7
      OS Loader Version: 8419.80.7

Software:

    System Software Overview:

      System Version: macOS 13.2.1 (22D68)
      Kernel Version: Darwin 22.3.0
      Time since boot: 27 days, 6 hours, 40 minutes

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 7
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9
    ChimeraX-AddH: 2.2.4
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6rc202303310103
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    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: 1.2.1
    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-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.2
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.6
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.2.22
    imagesize: 1.4.1
    importlib-metadata: 6.1.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.2.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

Change History (3)

comment:1 by Eric Pettersen, 3 years ago

Cc: Tom Goddard added
Component: Unassigned → VR
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash closing tool window

comment:2 by Eric Pettersen, 3 years ago

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

comment:3 by Tom Goddard, 3 years ago

I recall being able to reproduce this 3-6 months ago, drag and drop a floating tool onto the main ChimeraX, it sometimes half drops, then click on a button in that tool. Boom.

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