Opened 4 years ago

Closed 4 years ago

Last modified 4 years ago

#6338 closed defect (can't reproduce)

Crash getting Structure._graphics_changeds attribute after selection changed

Reported by: chimerax-bug-report@… Owned by: pett
Priority: normal Milestone:
Component: Core 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-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error

Current thread 0x000000010643b600 (most recent call first):
  File "/private/var/folders/9y/_7x0vft91v5_1vv1x4l_77rm0000gn/T/AppTranslocation/7CF99393-F96B-4441-AF07-C54810BF3B03/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/molc.py", line 197 in get_prop
  File "/private/var/folders/9y/_7x0vft91v5_1vv1x4l_77rm0000gn/T/AppTranslocation/7CF99393-F96B-4441-AF07-C54810BF3B03/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/structure.py", line 1646 in _update_graphics_if_needed
  File "/private/var/folders/9y/_7x0vft91v5_1vv1x4l_77rm0000gn/T/AppTranslocation/7CF99393-F96B-4441-AF07-C54810BF3B03/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 134 in invoke
  File "/private/var/folders/9y/_7x0vft91v5_1vv1x4l_77rm0000gn/T/AppTranslocation/7CF99393-F96B-4441-AF07-C54810BF3B03/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 217 in _activate
  File "/private/var/folders/9y/_7x0vft91v5_1vv1x4l_77rm0000gn/T/AppTranslocation/7CF99393-F96B-4441-AF07-C54810BF3B03/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 186 in activate
  File "/private/var/folders/9y/_7x0vft91v5_1vv1x4l_77rm0000gn/T/AppTranslocation/7CF99393-F96B-4441-AF07-C54810BF3B03/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/tri

{"app_name":"ChimeraX","timestamp":"2022-03-09 11:08:26.00 +0200","app_version":"","slice_uuid":"9596eff5-d2be-396c-9c4e-6177235c3dae","build_version":"","platform":1,"share_with_app_devs":0,"is_first_party":1,"bug_type":"309","os_version":"macOS 12.2.1 (21D62)","incident_id":"A3A304A3-BB5F-4096-9FF6-FC235F876BDA","name":"ChimeraX"}
{
  "uptime" : 1000,
  "procLaunch" : "2022-03-09 11:06:02.3591 +0200",
  "procRole" : "Background",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro14,1",
  "procStartAbsTime" : 898196880294,
  "coalitionID" : 928,
  "osVersion" : {
    "train" : "macOS 12.2.1",
    "build" : "21D62",
    "releaseType" : "User"
  },
  "captureTime" : "2022-03-09 11:08:26.1021 +0200",
  "incident" : "A3A304A3-BB5F-4096-9FF6-FC235F876BDA",
  "bug_type" : "309",
  "pid" : 1333,
  "procExitAbsTime" : 1041803810726,
  "cpuType" : "X86-64",
  "procName" : "ChimeraX",
  "procPath" : "\/private\/var\/folders\/*\/ChimeraX-1.3.app\/Contents\/MacOS\/ChimeraX",
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "4E2E5C64-9A76-B5A0-904A-5BE5E3F4186F",
  "sip" : "enabled",
  "vmRegionInfo" : "0x102c34899 is in 0x102abe000-0x102d23000;  bytes after start: 1534105  bytes before end: 976742\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      ColorSync                   102abd000-102abe000    [    4K] r--\/r-- SM=PRV  \n--->  mapped file                 102abe000-102d23000    [ 2452K] r-x\/rwx SM=COW  ...t_id=5ca397b9\n      mapped file                 102d23000-102d5d000    [  232K] rw-\/rwx SM=COW  ...t_id=5b82aab9",
  "isCorpse" : 1,
  "exception" : {"codes":"0x000000000000000a, 0x0000000102c34899","rawCodes":[10,4341319833],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_MEMORY_ERROR at 0x0000000102c34899"},
  "termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"exc handler","byPid":1333},
  "vmregioninfo" : "0x102c34899 is in 0x102abe000-0x102d23000;  bytes after start: 1534105  bytes before end: 976742\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      ColorSync                   102abd000-102abe000    [    4K] r--\/r-- SM=PRV  \n--->  mapped file                 102abe000-102d23000    [ 2452K] r-x\/rwx SM=COW  ...t_id=5ca397b9\n      mapped file                 102d23000-102d5d000    [  232K] rw-\/rwx SM=COW  ...t_id=5b82aab9",
  "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" : [{"triggered":true,"id":17374,"name":"CrBrowserMain","threadState":{"r13":{"value":1},"rax":{"value":1},"rflags":{"value":66054},"cpu":{"value":1},"r14":{"value":140595195849007},"rsi":{"value":140595195849007},"r8":{"value":140595195850568},"cr2":{"value":4341319833},"rdx":{"value":0},"r10":{"value":4400068268,"symbolLocation":172,"symbol":"_main_thread"},"r9":{"value":13355911402766314907},"r15":{"value":7},"rbx":{"value":105},"trap":{"value":14,"description":"(no mapping for user instruction read)"},"err":{"value":20},"r11":{"value":518},"rip":{"value":4341319833,"matchesCrashFrame":1},"rbp":{"value":140595195848944},"rsp":{"value":140595195848896},"r12":{"value":1},"rcx":{"value":140703234590838},"flavor":"x86_THREAD_STATE","rdi":{"value":7}},"frames":[{"imageOffset":4341319833,"imageIndex":0},{"imageOffset":4341278243,"imageIndex":0},{"imageOffset":4341278556,"imageIndex":0},{"imageOffset":4341279347,"imageIndex":0},{"imageOffset":4341686856,"imageIndex":0},{"imageOffset":140703234915885,"imageIndex":0},{"imageOffset":0,"imageIndex":0},{"imageOffset":140702013785632,"imageIndex":0}]},{"id":17426,"frames":[{"imageOffset":140703234589958,"imageIndex":0},{"imageOffset":4468955807,"imageIndex":0},{"imageOffset":140703234827508,"imageIndex":0},{"imageOffset":140703234809871,"imageIndex":0}]},{"id":17484,"name":"ThreadPoolServiceThread","frames":[{"imageOffset":140703234615750,"imageIndex":0},{"imageOffset":4816108743,"imageIndex":0},{"imageOffset":4815619627,"imageIndex":0},{"imageOffset":4815374283,"imageIndex":0},{"imageOffset":4815665812,"imageIndex":0},{"imageOffset":4815747709,"imageIndex":0},{"imageOffset":4816047623,"imageIndex":0},{"imageOffset":140703234827508,"imageIndex":0},{"imageOffset":140703234809871,"imageIndex":0}]},{"id":17486,"name":"ThreadPoolBackgroundWorker","frames":[{"imageOffset":140703234579130,"imageIndex":0},{"imageOffset":140703234580011,"imageIndex":0},{"imageOffset":4816065682,"imageIndex":0},{"imageOffset":4815705976,"imageIndex":0},{"imageOffset":4815708496,"imageIndex":0},{"imageOffset":4815707204,"imageIndex":0},{"imageOffset":4816047623,"imageIndex":0},{"imageOffset":140703234827508,"imageIndex":0},{"imageOffset":140703234809871,"imageIndex":0}]},{"id":17487,"name":"Chrome_IOThread","frames":[{"imageOffset":140703234615750,"imageIndex":0},{"imageOffset":4816108743,"imageIndex":0},{"imageOffset":4815619627,"imageIndex":0},{"imageOffset":4815374283,"imageIndex":0},{"imageOffset":4881960710,"imageIndex":0},{"imageOffset":4815747709,"imageIndex":0},{"imageOffset":4816047623,"imageIndex":0},{"imageOffset":140703234827508,"imageIndex":0},{"imageOffset":140703234809871,"imageIndex":0}]},{"id":17488,"name":"NetworkConfigWatcher","frames":[{"imageOffset":140703234579130,"imageIndex":0},{"imageOffset":140703234580011,"imageIndex":0},{"imageOffset":4816065682,"imageIndex":0},{"imageOffset":4816065231,"imageIndex":0},{"imageOffset":4815180251,"imageIndex":0},{"imageOffset":4815619627,"imageIndex":0},{"imageOffset":4815374283,"imageIndex":0},{"imageOffset":4815747709,"imageIndex":0},{"imageOffset":4816047623,"imageIndex":0},{"imageOffset":140703234827508,"imageIndex":0},{"imageOffset":140703234809871,"imageIndex":0}]},{"id":17492,"name":"Chrome_InProcGpuThread","frames":[{"imageOffset":140703234579130,"imageIndex":0},{"imageOffset":140703234580011,"imageIndex":0},{"imageOffset":4816065682,"imageIndex":0},{"imageOffset":4815180303,"imageIndex":0},{"imageOffset":4815619627,"imageIndex":0},{"imageOffset":4815374283,"imageIndex":0},{"imageOffset":4815747709,"imageIndex":0},{"imageOffset":4816047623,"imageIndex":0},{"imageOffset":140703234827508,"imageIndex":0},{"imageOffset":140703234809871,"imageIndex":0}]},{"id":17493,"name":"Chrome_ChildIOThread","frames":[{"imageOffset":140703234615750,"imageIndex":0},{"imageOffset":4816108743,"imageIndex":0},{"imageOffset":4815619627,"imageIndex":0},{"imageOffset":4815374283,"imageIndex":0},{"imageOffset":4815747709,"imageIndex":0},{"imageOffset":4816047623,"imageIndex":0},{"imageOffset":140703234827508,"imageIndex":0},{"imageOffset":140703234809871,"imageIndex":0}]},{"id":17494,"name":"CompositorTileWorker1","frames":[{"imageOffset":140703234589958,"imageIndex":0},{"imageOffset":4816031256,"imageIndex":0},{"imageOffset":4835657208,"imageIndex":0},{"imageOffset":4816047623,"imageIndex":0},{"imageOffset":140703234827508,"imageIndex":0},{"imageOffset":140703234809871,"imageIndex":0}]},{"id":17495,"name":"NetworkConfigWatcher","frames":[{"imageOffset":140703234579130,"imageIndex":0},{"imageOffset":140703234580011,"imageIndex":0},{"imageOffset":4816065682,"imageIndex":0},{"imageOffset":4816065231,"imageIndex":0},{"imageOffset":4815180251,"imageIndex":0},{"imageOffset":4815619627,"imageIndex":0},{"imageOffset":4815374283,"imageIndex":0},{"imageOffset":4815747709,"imageIndex":0},{"imageOffset":4816047623,"imageIndex":0},{"imageOffset":140703234827508,"imageIndex":0},{"imageOffset":140703234809871,"imageIndex":0}]},{"id":17496,"name":"VizCompositorThread","frames":[{"imageOffset":140703234579130,"imageIndex":0},{"imageOffset":140703234580011,"imageIndex":0},{"imageOffset":4816065682,"imageIndex":0},{"imageOffset":4816065231,"imageIndex":0},{"imageOffset":4815180251,"imageIndex":0},{"imageOffset":4815619627,"imageIndex":0},{"imageOffset":4815374283,"imageIndex":0},{"imageOffset":4815747709,"imageIndex":0},{"imageOffset":4816047623,"imageIndex":0},{"imageOffset":140703234827508,"imageIndex":0},{"imageOffset":140703234809871,"imageIndex":0}]},{"id":17507,"name":"ThreadPoolSingleThreadForegroundBlocking0","frames":[{"imageOffset":140703234579130,"imageIndex":0},{"imageOffset":140703234580011,"imageIndex":0},{"imageOffset":4816065682,"imageIndex":0},{"imageOffset":4816065231,"imageIndex":0},{"imageOffset":4815705962,"imageIndex":0},{"imageOffset":4815708496,"imageIndex":0},{"imageOffset":4815707444,"imageIndex":0},{"imageOffset":4816047623,"imageIndex":0},{"imageOffset":140703234827508,"imageIndex":0},{"imageOffset":140703234809871,"imageIndex":0}]},{"id":17509,"name":"NetworkConfigWatcher","frames":[{"imageOffset":140703234579130,"imageIndex":0},{"imageOffset":140703234580011,"imageIndex":0},{"imageOffset":4816065682,"imageIndex":0},{"imageOffset":4816065231,"imageIndex":0},{"imageOffset":4815180251,"imageIndex":0},{"imageOffset":4815619627,"imageIndex":0},{"imageOffset":4815374283,"imageIndex":0},{"imageOffset":4815747709,"imageIndex":0},{"imageOffset":4816047623,"imageIndex":0},{"imageOffset":140703234827508,"imageIndex":0},{"imageOffset":140703234809871,"imageIndex":0}]},{"id":17530,"name":"MemoryInfra","frames":[{"imageOffset":140703234579130,"imageIndex":0},{"imageOffset":140703234580011,"imageIndex":0},{"imageOffset":4816065682,"imageIndex":0},{"imageOffset":4816065231,"imageIndex":0},{"imageOffset":4815180251,"imageIndex":0},{"imageOffset":4815619627,"imageIndex":0},{"imageOffset":4815374283,"imageIndex":0},{"imageOffset":4815747709,"imageIndex":0},{"imageOffset":4816047623,"imageIndex":0},{"imageOffset":140703234827508,"imageIndex":0},{"imageOffset":140703234809871,"imageIndex":0}]},{"id":17568,"name":"NetworkConfigWatcher","frames":[{"imageOffset":140703234579130,"imageIndex":0},{"imageOffset":140703234580011,"imageIndex":0},{"imageOffset":4816065682,"imageIndex":0},{"imageOffset":4816065231,"imageIndex":0},{"imageOffset":4815180251,"imageIndex":0},{"imageOffset":4815619627,"imageIndex":0},{"imageOffset":4815374283,"imageIndex":0},{"imageOffset":4815747709,"imageIndex":0},{"imageOffset":4816047623,"imageIndex":0},{"imageOffset":140703234827508,"imageIndex":0},{"imageOffset":140703234809871,"imageIndex":0}]},{"id":17605,"name":"com.apple.NSEventThread","frames":[{"imageOffset":140703234579130,"imageIndex":0},{"imageOffset":140703234580011,"imageIndex":0},{"imageOffset":140703235644146,"imageIndex":0},{"imageOffset":140703235637707,"imageIndex":0},{"imageOffset":140703235634653,"imageIndex":0},{"imageOffset":140703281369048,"imageIndex":0},{"imageOffset":140703234827508,"imageIndex":0},{"imageOffset":140703234809871,"imageIndex":0}]},{"id":17625,"name":"ThreadPoolForegroundWorker","frames":[{"imageOffset":140703234579130,"imageIndex":0},{"imageOffset":140703234580011,"imageIndex":0},{"imageOffset":4816065682,"imageIndex":0},{"imageOffset":4815705976,"imageIndex":0},{"imageOffset":4815708496,"imageIndex":0},{"imageOffset":4815707348,"imageIndex":0},{"imageOffset":4816047623,"imageIndex":0},{"imageOffset":140703234827508,"imageIndex":0},{"imageOffset":140703234809871,"imageIndex":0}]},{"id":17635,"name":"ThreadPoolSingleThreadSharedBackgroundBlocking1","frames":[{"imageOffset":140703234579130,"imageIndex":0},{"imageOffset":140703234580011,"imageIndex":0},{"imageOffset":4816065682,"imageIndex":0},{"imageOffset":4816065231,"imageIndex":0},{"imageOffset":4815705962,"imageIndex":0},{"imageOffset":4815707709,"imageIndex":0},{"imageOffset":4815707252,"imageIndex":0},{"imageOffset":4816047623,"imageIndex":0},{"imageOffset":140703234827508,"imageIndex":0},{"imageOffset":140703234809871,"imageIndex":0}]},{"id":18519,"frames":[{"imageOffset":140703234809836,"imageIndex":0}]},{"id":18721,"frames":[{"imageOffset":140703234809836,"imageIndex":0}]}],
  "usedImages" : [
  {
    "size" : 0,
    "source" : "A",
    "base" : 0,
    "uuid" : "00000000-0000-0000-0000-000000000000"
  }
],
  "sharedCache" : {
  "base" : 140703231569920,
  "size" : 15216836608,
  "uuid" : "0939015d-8308-3e69-b095-bd928f835202"
},
  "vmSummary" : "ReadOnly portion of Libraries: Total=628K resident=0K(0%) swapped_out_or_unallocated=628K(100%)\nWritable regions: Total=884.6M written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=884.6M(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               256K        2 \nActivity Tracing                   256K        1 \nCG backing stores                 2160K        4 \nCG image                           112K       10 \nColorSync                          236K       26 \nCoreAnimation                      148K       11 \nCoreGraphics                        12K        2 \nCoreUI image data                 3180K       23 \nFoundation                          16K        1 \nKernel Alloc Once                    8K        1 \nMALLOC                           290.5M      458 \nMALLOC guard page                   32K        7 \nMALLOC_LARGE (reserved)            384K        1         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           384.0M        1         reserved VM address space (unallocated)\nMach message                        24K        4 \nOpenGL GLSL                        384K        5 \nSTACK GUARD                         76K       19 \nStack                            130.1M       20 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                       70.2M      130 \nVM_ALLOCATE (reserved)              12K        2         reserved VM address space (unallocated)\n__DATA                              16K        1 \n__DATA_CONST                        80K        1 \n__LINKEDIT                         208K        2 \n__TEXT                             432K        1 \ndyld private memory               1024K        1 \nmapped file                      762.6M      435 \nshared memory                     8528K       40 \n===========                     =======  ======= \nTOTAL                              1.7G     1210 \nTOTAL, minus reserved VM space     1.3G     1210 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain"
  }
},
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "607844aa04477260f58a8077",
      "factorPackIds" : {
        "SIRI_MORPHUN_ASSETS" : "6103050cbfe6dc472e1c982a"
      },
      "deploymentId" : 240000066
    },
    {
      "rolloutId" : "60da5e84ab0ca017dace9abf",
      "factorPackIds" : {

      },
      "deploymentId" : 240000008
    },
    {
      "rolloutId" : "602ad4dac86151000cf27e46",
      "factorPackIds" : {
        "SIRI_DICTATION_ASSETS" : "6193d03f2171a2330e561dfc"
      },
      "deploymentId" : 240000305
    },
    {
      "rolloutId" : "601d9415f79519000ccd4b69",
      "factorPackIds" : {
        "SIRI_TEXT_TO_SPEECH" : "621d4d11f441df278b2334c9"
      },
      "deploymentId" : 240000409
    },
    {
      "rolloutId" : "5fc94383418129005b4e9ae0",
      "factorPackIds" : {

      },
      "deploymentId" : 240000263
    },
    {
      "rolloutId" : "5ffde50ce2aacd000d47a95f",
      "factorPackIds" : {

      },
      "deploymentId" : 240000119
    },
    {
      "rolloutId" : "60356660bbe37970735c5624",
      "factorPackIds" : {

      },
      "deploymentId" : 240000027
    }
  ],
  "experiments" : [

  ]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/nitsan/Downloads/1stp.pdb format pdb

1stp.pdb title:  
Structural origins of high-affinity biotin binding to streptavidin [more
info...]  
  
Chain information for 1stp.pdb #1  
---  
Chain | Description | UniProt  
A | streptavidin complex with biotin | SAV_STRAV  
  
Non-standard residues in 1stp.pdb #1  
---  
BTN — biotin  
  

> open 1stp

Summary of feedback from opening 1stp fetched from pdb  
---  
notes | Fetching compressed mmCIF 1stp from
http://files.rcsb.org/download/1stp.cif  
Fetching CCD BTN from http://ligand-expo.rcsb.org/reports/B/BTN/BTN.cif  
  
1stp title:  
Structural origins of high-affinity biotin binding to streptavidin [more
info...]  
  
Chain information for 1stp #2  
---  
Chain | Description | UniProt  
A | streptavidin complex with biotin | SAV_STRAV  
  
Non-standard residues in 1stp #2  
---  
BTN — biotin  
  
1stp mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> select #1

1001 atoms, 940 bonds, 206 residues, 1 model selected  

> select #2

1001 atoms, 940 bonds, 206 residues, 1 model selected  

> ~select #2

Nothing selected  

> select #2

1001 atoms, 940 bonds, 206 residues, 1 model selected  

> select #1

1001 atoms, 940 bonds, 206 residues, 1 model selected  

> ~select #1

Nothing selected  


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

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 INTEL-18.4.6
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro14,1
      Processor Name: Dual-Core Intel Core i5
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 4 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 447.80.3.0.0
      OS Loader Version: 540.80.2~11
      SMC Version (system): 2.43f11

Software:

    System Software Overview:

      System Version: macOS 12.2.1 (21D62)
      Kernel Version: Darwin 21.3.0
      Time since boot: 19 minutes

Graphics/Displays:

    Intel Iris Plus Graphics 640:

      Chipset Model: Intel Iris Plus Graphics 640
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x5926
      Revision ID: 0x0006
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    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
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    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
    suds-jurko: 0.6
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

Change History (3)

comment:1 by pett, 4 years ago

Cc: Tom Goddard added
Component: Unassigned → Core
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash getting Structure._graphics_changeds attribute after selection changed

comment:2 by pett, 4 years ago

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

comment:3 by Tom Goddard, 4 years ago

The user just opened the 1stp in PDB format and mmCIF format and selected and unselected the models. That is a pretty minimal set of commands. I wonder if there is a reference counting problem in the mmCIF or PDB reader that results in one of these two models being deleted. Or maybe the Structure.del() method which removes the graphics update handler did not prevent that handler from being called later (e.g. if it was in the middle of dispatching graphics update triggers?)

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