Opened 3 years ago

Closed 3 years ago

#8344 closed defect (duplicate)

Bad set of Atoms.aniso_u6 from remove_invalid_anisou?

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

Description 

The following bug report has been submitted:
Platform:        macOS-12.2.1-arm64-arm-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 0x000000028a073000 (most recent call first):
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 576 in _handle_results
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000000289067000 (most recent call first):
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 528 in _handle_tasks
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x000000028805b000 (most recent call first):
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py", line 416 in select
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py", line 936 in wait
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 499 in _wait_for_updates
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 519 in _handle_workers
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x000000028704f000 (most recent call first):
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000000286043000 (most recent call first):
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000000285037000 (most recent call first):
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x000000028402b000 (most recent call first):
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x000000028301f000 (most recent call first):
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000000282013000 (most recent call first):
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000000281007000 (most recent call first):
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x000000017f0a7000 (most recent call first):
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Current thread 0x000000010038c580 (most recent call first):
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/molarray.py", line 846 in _set_aniso_u6
  File "/Users/deeptomozumdar/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/sanity_check.py", line 12 in remove_invalid_anisou
  File "/Users/deeptomozumdar/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/symmetry.py", line 667 in _anisou_sanity_check
  File "/Users/deeptomozumdar/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/symmetry.py", line 636 in add_model
  File "/Users/deeptomozumdar/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/symmetry.py", line 594 in __init__
  File "/Users/deeptomozumdar/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/symmetry.py", line 170 in _get_symmetry_handler
  File "/Users/deeptomozumdar/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/symmetry.py", line 159 in get_symmetry_handler
  File "/Users/deeptomozumdar/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/symmetry.py", line 183 in get_map_mgr
  File "/Users/deeptomozumdar/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/cmd.py", line 122 in associate_volumes
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 319 in execute
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/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 "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/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 "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/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 "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/AA47AA7D-99B3-42D8-9366-1E508A9968C8/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main


{"app_name":"ChimeraX","timestamp":"2023-01-20 18:31:39.00 -0800","app_version":"1.5.0","slice_uuid":"a5992708-d5b4-36ec-ac0a-e525f6105b56","build_version":"1.5.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":1,"is_first_party":0,"bug_type":"309","os_version":"macOS 12.2.1 (21D62)","incident_id":"840DB52F-958F-4AAB-8FD5-E102DA652A32","name":"ChimeraX"}
{
  "uptime" : 6700000,
  "procLaunch" : "2023-01-20 18:29:13.4789 -0800",
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "iMac21,1",
  "procStartAbsTime" : 161083067931869,
  "coalitionID" : 301450,
  "osVersion" : {
    "train" : "macOS 12.2.1",
    "build" : "21D62",
    "releaseType" : "User"
  },
  "captureTime" : "2023-01-20 18:31:39.4945 -0800",
  "incident" : "840DB52F-958F-4AAB-8FD5-E102DA652A32",
  "bug_type" : "309",
  "pid" : 63697,
  "procExitAbsTime" : 161086572283270,
  "translated" : false,
  "cpuType" : "ARM-64",
  "procName" : "ChimeraX",
  "procPath" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.5.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.5.0","CFBundleVersion":"1.5.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"33BF781F-5099-5B18-8D5D-3A5C03B9541B","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "53AE252A-5438-BCC8-8FFE-E3508434C6E6",
  "wakeTime" : 8632,
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    "name" : "QtWebEngineCore"
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    "source" : "P",
    "arch" : "arm64e",
    "base" : 7322271744,
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    "CFBundleIdentifier" : "com.apple.CoreFoundation",
    "size" : 5521408,
    "uuid" : "35473de6-c433-332c-aee0-013fd5f6d4fd",
    "path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
    "name" : "CoreFoundation",
    "CFBundleVersion" : "1856.107"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 4830789632,
    "size" : 16384,
    "uuid" : "cfed1505-cef2-372b-abff-2a9183ec018e",
    "path" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/lib-dynload\/_queue.cpython-39-darwin.so",
    "name" : "_queue.cpython-39-darwin.so"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 4314562560,
    "size" : 32768,
    "uuid" : "ff7d40db-95e6-320a-b57f-faed8f2333d9",
    "path" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/lib-dynload\/select.cpython-39-darwin.so",
    "name" : "select.cpython-39-darwin.so"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 11009671168,
    "size" : 19300352,
    "uuid" : "5431bff3-be1a-3fe5-a552-bcdbb3e0536e",
    "path" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/scipy\/.dylibs\/libopenblas.0.dylib",
    "name" : "libopenblas.0.dylib"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 4416569344,
    "size" : 20709376,
    "uuid" : "6b8373ed-7142-34ea-9b4b-9f502e8a6f33",
    "path" : "\/Volumes\/VOLUME\/*\/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"
  },
  {
    "size" : 0,
    "source" : "A",
    "base" : 0,
    "uuid" : "00000000-0000-0000-0000-000000000000"
  }
],
  "sharedCache" : {
  "base" : 7318781952,
  "size" : 3091218432,
  "uuid" : "296eb28e-6aeb-3129-8fa6-feb92261a4eb"
},
  "vmSummary" : "ReadOnly portion of Libraries: Total=1.3G resident=0K(0%) swapped_out_or_unallocated=1.3G(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                 3392K        4 \nCG image                           224K       11 \nColorSync                          640K       27 \nCoreAnimation                      224K       11 \nCoreGraphics                        32K        2 \nCoreUI image data                 3424K       24 \nDispatch continuations            64.0M        1 \nFoundation                          32K        2 \nKernel Alloc Once                   48K        2 \nMALLOC                           256.3M      100 \nMALLOC guard page                  192K       10 \nMALLOC_MEDIUM (reserved)          24.0M        1         reserved VM address space (unallocated)\nMach message                        64K        4 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        848K       53 \nStack                            341.4M       54 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      249.3M      343 \nVM_ALLOCATE (reserved)           320.0M        4         reserved VM address space (unallocated)\n__AUTH                            2577K      309 \n__AUTH_CONST                      19.8M      501 \n__DATA                            25.4M      709 \n__DATA_CONST                      28.0M      709 \n__DATA_DIRTY                      1787K      215 \n__FONT_DATA                          4K        1 \n__GLSLBUILTINS                    5176K        1 \n__LINKEDIT                       616.9M      208 \n__OBJC_CONST                      3580K      274 \n__OBJC_RO                         82.1M        1 \n__OBJC_RW                         3104K        1 \n__TEXT                           741.4M      728 \n__UNICODE                          588K        1 \ndyld private memory               1216K        3 \nmapped file                      184.2M       46 \nshared memory                     3168K       26 \n===========                     =======  ======= \nTOTAL                              3.0G     4394 \nTOTAL, minus reserved VM space     2.6G     4394 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "601d9415f79519000ccd4b69",
      "factorPackIds" : {
        "SIRI_TEXT_TO_SPEECH" : "622657ce37186c771d5404ad"
      },
      "deploymentId" : 240000416
    },
    {
      "rolloutId" : "607844aa04477260f58a8077",
      "factorPackIds" : {
        "SIRI_MORPHUN_ASSETS" : "6103050cbfe6dc472e1c982a"
      },
      "deploymentId" : 240000066
    },
    {
      "rolloutId" : "60356660bbe37970735c5624",
      "factorPackIds" : {

      },
      "deploymentId" : 240000027
    },
    {
      "rolloutId" : "602ad4dac86151000cf27e46",
      "factorPackIds" : {
        "SIRI_DICTATION_ASSETS" : "61fb0e87c773c43cde3bb80e"
      },
      "deploymentId" : 240000305
    },
    {
      "rolloutId" : "60da5e84ab0ca017dace9abf",
      "factorPackIds" : {

      },
      "deploymentId" : 240000008
    },
    {
      "rolloutId" : "60186475825c62000ccf5450",
      "factorPackIds" : {

      },
      "deploymentId" : 240000026
    },
    {
      "rolloutId" : "60f8ddccefea4203d95cbeef",
      "factorPackIds" : {

      },
      "deploymentId" : 240000021
    },
    {
      "rolloutId" : "63582c5f8a53461413999550",
      "factorPackIds" : {

      },
      "deploymentId" : 240000002
    },
    {
      "rolloutId" : "5fb4245a1bbfe8005e33a1e1",
      "factorPackIds" : {

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

      },
      "deploymentId" : 240000576
    },
    {
      "rolloutId" : "5ffde50ce2aacd000d47a95f",
      "factorPackIds" : {

      },
      "deploymentId" : 240000242
    }
  ],
  "experiments" : [

  ]
}
}
===== 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  

> isolde demo cryo_em_intro modelOnly true startIsolde false

6out.pdb title:  
Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP
asymmetric unit In T=3 symmetry [more info...]  
  
Chain information for 6out.pdb #1  
---  
Chain | Description | UniProt  
A B C | capsid protein VP1 | CAPSD_NVN68  
  
Loaded cryo-EM demo: PDB ID 6out, EMDB ID 20205  

> open 20205 fromDatabase emdb

Opened emdb 20205 as #2, grid size 98,112,104, pixel 1.07,1.07,1.07, shown at
level 0.287, step 1, values float32  

> clipper associate #2 toModel #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  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1
OpenGL vendor: Apple

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: iMac
      Model Identifier: iMac21,1
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 7429.81.3
      OS Loader Version: 7429.81.3

Software:

    System Software Overview:

      System Version: macOS 12.2.1 (21D62)
      Kernel Version: Darwin 21.3.0
      Time since boot: 134 days 3:55

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 4.5K (4480 x 2520)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


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-Clipper: 0.19.0
    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-ISOLDE: 1.5
    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

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Cc: Tristan Croll added
Component: Unassigned → Structure Editing
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Bad set of Atoms.aniso_u6 from remove_invalid_anisou?

comment:2 by Eric Pettersen, 3 years ago

Resolution: → duplicate
Status: accepted → closed

Duplicate of #8342

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