Crash in garbage collection from timer after structure closed

[ppratap@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x000070000f205000 (most recent call first):
  File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
  File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
  File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1297 in run
  File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Current thread 0x00007ff856f088c0 (most recent call first):
  File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 341 in _cleanup
  File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 381 in cb
  File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 283 in event_loop
  File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 884 in init
  File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1035 in 
  File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/Applications/ChimeraX-1.5.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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{
  "uptime" : 37000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro15,1",
  "coalitionID" : 1312,
  "osVersion" : {
    "train" : "macOS 13.1",
    "build" : "22C65",
    "releaseType" : "User"
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  "captureTime" : "2023-03-02 09:32:51.0835 -0800",
  "incident" : "D6A583DC-A123-4158-ACD5-CB09590D3995",
  "pid" : 8386,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2023-03-02 09:12:55.2680 -0800",
  "procStartAbsTime" : 36797339772305,
  "procExitAbsTime" : 37993170521350,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.5.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.5.0","CFBundleVersion":"1.5.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"21DB3AA5-29D1-53D9-99FD-D4395733B3E6","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "3BFB893F-B9E4-7F14-D28B-9ACF7D947603",
  "throttleTimeout" : 2147483647,
  "wakeTime" : 7066,
  "bridgeVersion" : {"build":"20P2059","train":"7.1"},
  "sleepWakeUUID" : "49E3CD85-C9CC-471C-A87E-AB72C3374652",
  "sip" : "enabled",
  "vmRegionInfo" : "0xa9 is not in any region.  Bytes before following region: 140737486573399\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      shared memory            7fffffe4d000-7fffffe4e000 [    4K] r-x\/r-x SM=SHM  ",
  "exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
  "vmregioninfo" : "0xa9 is not in any region.  Bytes before following region: 140737486573399\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      shared memory            7fffffe4d000-7fffffe4e000 [    4K] r-x\/r-x SM=SHM  ",
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  "faultingThread" : 0,
  "threads" : 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    "base" : 4564701184,
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    "size" : 4964352,
    "uuid" : "f36760e5-d1e7-3a93-ae8c-1c3e55e3fc35",
    "path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWidgets.framework\/Versions\/A\/QtWidgets",
    "name" : "QtWidgets"
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    "path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/plugins\/platforms\/libqcocoa.dylib",
    "name" : "libqcocoa.dylib"
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    "CFBundleIdentifier" : "com.apple.CoreFoundation",
    "size" : 4825088,
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    "path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
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    "path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
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    "path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
    "name" : "AppKit",
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    "uuid" : "5df621ee-554e-36a8-b448-93b2334e5480",
    "path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/MacOS\/ChimeraX",
    "name" : "ChimeraX",
    "CFBundleVersion" : "1.5.0.0"
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    "size" : 609392,
    "uuid" : "bb7a0970-8c62-3dce-a7a2-5cec9c501f11",
    "path" : "\/usr\/lib\/dyld",
    "name" : "dyld"
  },
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    "arch" : "x86_64",
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    "size" : 64028672,
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    "path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
    "name" : "libopenblas64_.0.dylib"
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    "arch" : "x86_64",
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    "path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
    "name" : "QtWebEngineCore"
  }
],
  "vmSummary" : "ReadOnly portion of Libraries: Total=1.1G resident=0K(0%) swapped_out_or_unallocated=1.1G(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               256K        2 \nActivity Tracing                   256K        1 \nCG backing stores                 5408K        8 \nCG image                           196K       21 \nColorSync                          248K       29 \nCoreAnimation                       80K       12 \nCoreGraphics                        24K        4 \nCoreUI image data                 3736K       28 \nFoundation                          36K        2 \nKernel Alloc Once                    8K        1 \nMALLOC                           829.0M      691 \nMALLOC guard page                   32K        7 \nMALLOC_LARGE (reserved)            384K        1         reserved VM address space (unallocated)\nMach message                        16K        4 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        116K       29 \nStack                            173.2M       30 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      126.8M      157 \nVM_ALLOCATE (reserved)            96.0M        1         reserved VM address space (unallocated)\n__CTF                               756        1 \n__DATA                            47.1M      742 \n__DATA_CONST                      53.4M      392 \n__DATA_DIRTY                      1823K      226 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__LINKEDIT                       211.8M      133 \n__OBJC_RO                         65.4M        1 \n__OBJC_RW                         1988K        2 \n__TEXT                           911.7M      747 \ndyld private memory                416K        3 \nmapped file                      220.6M       59 \nshared memory                     3512K       28 \n===========                     =======  ======= \nTOTAL                              2.7G     3369 \nTOTAL, minus reserved VM space     2.7G     3369 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "610d52e1fc54bc3389840408",
      "factorPackIds" : {
        "SIRI_UNDERSTANDING_ASR_ASSISTANT" : "63619607c8a2104545a570c7",
        "SIRI_UNDERSTANDING_MORPHUN" : "62ec7220c682040ba94e6a20"
      },
      "deploymentId" : 240000625
    },
    {
      "rolloutId" : "63582c5f8a53461413999550",
      "factorPackIds" : {

      },
      "deploymentId" : 240000002
    }
  ],
  "experiments" : [

  ]
},
  "reportNotes" : [
  "dyld_process_snapshot_create_for_process failed with 5"
]
}
===== Log before crash start =====
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/payalpratap/Desktop/Desktop
> Folder/CryoEMPEM/32613_wk42/32613-IF3-coot-local-directory/IF3_Boost2_Fv-
> coot-20.pdb"

Summary of feedback from opening /Users/payalpratap/Desktop/Desktop
Folder/CryoEMPEM/32613_wk42/32613-IF3-coot-local-directory/IF3_Boost2_Fv-
coot-20.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 13
GLY B 16 1 4  
Start residue of secondary structure not found: HELIX 2 2 MET B 19 LEU B 34 1
16  
Start residue of secondary structure not found: HELIX 3 3 GLN B 52 LYS B 56 1
5  
Start residue of secondary structure not found: HELIX 4 4 THR B 58 TRP B 85 1
28  
Start residue of secondary structure not found: HELIX 5 5 LEU B 108 TRP B 112
1 5  
1 messages similar to the above omitted  
End residue of secondary structure not found: HELIX 7 7 VAL C 38 HIS C 42 1 5  
Start residue of secondary structure not found: HELIX 8 8 ASN C 69 LEU C 86 1
18  
Start residue of secondary structure not found: HELIX 9 9 THR C 93 LEU C 95 1
3  
Start residue of secondary structure not found: HELIX 10 10 ARG C 140 ASP C
142 1 3  
Start residue of secondary structure not found: HELIX 11 11 ILE C 164 CYS C
166 1 3  
Start residue of secondary structure not found: HELIX 12 12 LYS C 304 PHE C
322 1 19  
8 messages similar to the above omitted  
End residue of secondary structure not found: HELIX 21 21 VAL D 38 HIS D 42 1
5  
Start residue of secondary structure not found: HELIX 22 22 ASN D 69 LEU D 86
1 18  
Start residue of secondary structure not found: HELIX 23 23 THR D 93 LEU D 95
1 3  
Start residue of secondary structure not found: HELIX 24 24 ARG D 140 ASP D
142 1 3  
Start residue of secondary structure not found: HELIX 25 25 ILE D 164 CYS D
166 1 3  
Start residue of secondary structure not found: HELIX 26 26 LYS D 304 PHE D
322 1 19  
14 messages similar to the above omitted  
End residue of secondary structure not found: SHEET 7 7 7 LEU C 116 THR C 124
0  
Start residue of secondary structure not found: SHEET 8 8 8 LYS C 131 TYR C
139 0  
Start residue of secondary structure not found: SHEET 9 9 9 VAL C 143 GLN C
145 0  
Start residue of secondary structure not found: SHEET 10 1010 TYR C 161 LEU C
163 0  
Start residue of secondary structure not found: SHEET 11 1111 ALA C 170 GLN C
173 0  
Start residue of secondary structure not found: SHEET 12 1212 HIS C 186 CYS C
188 0  
26 messages similar to the above omitted  
End residue of secondary structure not found: SHEET 39 3939 LEU D 116 THR D
124 0  
Start residue of secondary structure not found: SHEET 40 4040 LYS D 131 TYR D
139 0  
Start residue of secondary structure not found: SHEET 41 4141 VAL D 143 GLN D
145 0  
Start residue of secondary structure not found: SHEET 42 4242 TYR D 161 LEU D
163 0  
Start residue of secondary structure not found: SHEET 43 4343 ALA D 170 GLN D
173 0  
Start residue of secondary structure not found: SHEET 44 4444 HIS D 186 CYS D
188 0  
20 messages similar to the above omitted  
End residue of secondary structure not found: SHEET 74 7474 ALA H 101 CYS H
104 0  
Start residue of secondary structure not found: SHEET 75 7575 ALA H 124 ALA H
127 0  
Start residue of secondary structure not found: SHEET 83 8383 ALA L 122 ALA L
125 0  
  
Chain information for IF3_Boost2_Fv-coot-20.pdb #1  
---  
Chain | Description  
A C | No description available  
B E F | No description available  
D | No description available  
H | No description available  
L | No description available  
  

> show cartoons

> style stick

Changed 15937 atom styles  

> hide atoms

> ui tool show "Show Sequence Viewer"

> sequence chain /A /C

Alignment identifier is 1  

> select /A,C:66

20 atoms, 20 bonds, 2 residues, 1 model selected  

> select /A,C:66

20 atoms, 20 bonds, 2 residues, 1 model selected  

> show sel atoms

> select /H:18

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select /H:90

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select up

30 atoms, 29 bonds, 6 residues, 1 model selected  

> select up

644 atoms, 651 bonds, 117 residues, 1 model selected  

> select add /L:41

649 atoms, 655 bonds, 118 residues, 1 model selected  

> select up

674 atoms, 680 bonds, 123 residues, 1 model selected  

> select up

1262 atoms, 1272 bonds, 236 residues, 1 model selected  

> select up

15937 atoms, 16235 bonds, 2097 residues, 1 model selected  

> select down

1262 atoms, 1272 bonds, 236 residues, 1 model selected  

> name frozen IF3 sel

> select zone IF3 5 #1/A

Selected 47 atoms  

> show sel atoms

> select up

111 atoms, 108 bonds, 12 residues, 1 model selected  

> show sel atoms

> open "/Users/payalpratap/Desktop/Desktop
> Folder/CryoEMPEM/32613_wk42/32613-N355-coot-local-
> directory/Trimer_Fv_N355-coot-3.pdb"

Summary of feedback from opening /Users/payalpratap/Desktop/Desktop
Folder/CryoEMPEM/32613_wk42/32613-N355-coot-local-
directory/Trimer_Fv_N355-coot-3.pdb  
---  
warnings | Start residue of secondary structure not found: SHEET 90 9090 TRP H
41 ALA H 44 0  
End residue of secondary structure not found: SHEET 96 9696 ALA H 101 CYS H
104 0  
Start residue of secondary structure not found: SHEET 97 9797 ALA H 124 ALA H
127 0  
Start residue of secondary structure not found: SHEET 105 10510 ALA L 122 ALA
L 125 0  
  
Chain information for Trimer_Fv_N355-coot-3.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
H | No description available  
L | No description available  
  

> style sel stick

Changed 111 atom styles  

> show sel cartoons

> hide sel atoms

> close #1


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

Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/payalpratap/Desktop/Desktop
> Folder/CryoEMPEM/32613_wk42/32613-N355-coot-local-
> directory/Trimer_Fv_N355-coot-3.pdb"

Summary of feedback from opening /Users/payalpratap/Desktop/Desktop
Folder/CryoEMPEM/32613_wk42/32613-N355-coot-local-
directory/Trimer_Fv_N355-coot-3.pdb  
---  
warnings | Start residue of secondary structure not found: SHEET 90 9090 TRP H
41 ALA H 44 0  
End residue of secondary structure not found: SHEET 96 9696 ALA H 101 CYS H
104 0  
Start residue of secondary structure not found: SHEET 97 9797 ALA H 124 ALA H
127 0  
Start residue of secondary structure not found: SHEET 105 10510 ALA L 122 ALA
L 125 0  
  
Chain information for Trimer_Fv_N355-coot-3.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
H | No description available  
L | No description available  
  

Failed to send bug report. Bug report server www.rbvi.ucsf.edu is unavailable  




OpenGL version: 4.1 ATI-4.9.51
OpenGL renderer: AMD Radeon Pro 555X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,1
      Processor Name: 6-Core Intel Core i7
      Processor Speed: 2.2 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 9 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 1916.60.2.0.0 (iBridge: 20.16.2059.0.0,0)
      OS Loader Version: 564.40.4~55

Software:

    System Software Overview:

      System Version: macOS 13.1 (22C65)
      Kernel Version: Darwin 22.2.0
      Time since boot: 19 hours, 41 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: 0x0000
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3

    Radeon Pro 555X:

      Chipset Model: Radeon Pro 555X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67ef
      Revision ID: 0x00e3
      ROM Revision: 113-C980AL-075
      VBIOS Version: 113-C97501P-005
      EFI Driver Version: 01.A1.075
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        LG Ultra HD:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: Thunderbolt/DisplayPort


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    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: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 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: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    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-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    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
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    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: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.6
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.4.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.11.0

[Eric Pettersen]

Hi Payal,

Thanks for reporting this problem. I'm guessing this crash was a one-time thing and not something you can reproduce?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[Eric Pettersen]

Fixed in 1.8 release candidate