id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
18021	Graphics hardware encountered an error and was reset	nomin.bp@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-12.7.6-x86_64-i386-64bit
ChimeraX Version: 1.10rc202506130232 (2025-06-13 02:32:35 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. This is an Apple Intel or AMD graphics driver crash that may be related to showing a scene that is complex and uses too much graphics memory. Apple is unlikely to ever fix this since they no longer make computers with Intel or AMD graphics. The crash does not happen with Apple M1,M2,M3... graphics.
Fatal Python error: Aborted

Thread 0x000070001f8de000 (most recent call first):
  File ""/Applications/ChimeraX-1.10-rc2025.06.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results
  File ""/Applications/ChimeraX-1.10-rc2025.06.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.10-rc2025.06.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.10-rc2025.06.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000070001e8db000 (most recent call first):
  File ""/Applications/ChimeraX-1.10-rc2025.06.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks
  File ""/Applications/ChimeraX-1.10-rc2025.06.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.10-rc2025.06.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.10-rc2025.06.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000070001d8d8000 (most recent call first):
  File ""/Applications/ChimeraX-1.10-rc2025.06.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select
  File ""/Applications/ChimeraX-1.10-rc2025.06.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait
  File ""/Applications/ChimeraX-1.10-rc2025.06.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates
  File ""/Applications/ChimeraX-1.10-rc2025.06.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers
  File ""/Applications/ChimeraX-1.10-rc2025.06.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.10-rc2025.06.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.10-rc2025.06.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000070001c8d5000 (most recent call first):
  File ""/Applications/ChimeraX-1.10-rc2025.06.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.10-rc2025.06.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.10-rc2025.06.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.10-rc2025.06.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000070001b8d2000 (most recent call first):
  File ""/Applications/ChimeraX-1.10-rc2025.06.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.10-rc2025.06.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.10-rc2025.06.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.10-rc2025.06.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000070001a8cf000 (most recent call first):
  File ""/Applications/ChimeraX-1.10-rc2025.06.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.10-rc2025.06.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.10-rc2025.06.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.10-rc2025.06.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x00007000198cc000 (most recent call first):
  File ""/Applications/ChimeraX-1.10-rc2025.06.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.10-rc2025.06.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.10-rc2025.06.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.10-rc2025.06.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Current thread 0x00000001143dc600 (most recent call first):
  File ""/Applications/ChimeraX-1.10-rc2025.06.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/GL/VERSION/GL_1_5.py"", line 125 in glBufferSubData
  File ""/Applications/ChimeraX-1.10-rc2025.06.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 1769 in set_multishadow_view
  File ""/Applications/ChimeraX-1.10-rc2025.06.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 251 in _draw_scene
  File ""/Applications/ChimeraX-1.10-rc2025.06.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 188 in draw
  File ""/Applications/ChimeraX-1.10-rc2025.06.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 84 in draw_new_frame
  File ""/Applications/ChimeraX-1.10-rc2025.06.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 150 in _redraw_timer_callback
  File ""/Applications/ChimeraX-1.10-rc2025.06.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 368 in event_loop
  File ""/Applications/ChimeraX-1.10-rc2025.06.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1057 in init
  File ""/Applications/ChimeraX-1.10-rc2025.06.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1220 in 
  File """", line 88 in _run_code
  File """", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, psutil._psutil_osx, psutil._psutil_posix, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imaging, PIL._imagingmath (total: 48)


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{
  ""uptime"" : 360000,
  ""procLaunch"" : ""2025-06-18 17:08:44.4721 +0900"",
  ""procRole"" : ""Foreground"",
  ""version"" : 2,
  ""userID"" : 501,
  ""deployVersion"" : 210,
  ""modelCode"" : ""MacBookAir7,2"",
  ""procStartAbsTime"" : 367377672883004,
  ""coalitionID"" : 41607,
  ""osVersion"" : {
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    ""build"" : ""21H1320"",
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  ""captureTime"" : ""2025-06-18 17:33:30.1026 +0900"",
  ""incident"" : ""903CD5DE-BE56-47B9-9056-68DBAF77C099"",
  ""bug_type"" : ""309"",
  ""pid"" : 86052,
  ""procExitAbsTime"" : 368862019069208,
  ""cpuType"" : ""X86-64"",
  ""procName"" : ""ChimeraX"",
  ""procPath"" : ""\/Applications\/ChimeraX-1.10-rc2025.06.17.app\/Contents\/MacOS\/ChimeraX"",
  ""bundleInfo"" : {""CFBundleShortVersionString"":""1.10.0"",""CFBundleVersion"":""1.10.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""},
  ""storeInfo"" : {""deviceIdentifierForVendor"":""8C5CAC86-61CA-57A4-B15B-819EB5DA1E99"",""thirdParty"":true},
  ""parentProc"" : ""launchd"",
  ""parentPid"" : 1,
  ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"",
  ""crashReporterKey"" : ""E7567382-8C20-38A9-E41D-B10E8BA6D8DF"",
  ""wakeTime"" : 3455,
  ""sleepWakeUUID"" : ""80811952-BE03-4BA5-9C73-0EF1992A192B"",
  ""sip"" : ""enabled"",
  ""isCorpse"" : 1,
  ""exception"" : {""codes"":""0x0000000000000000, 0x0000000000000000"",""rawCodes"":[0,0],""type"":""EXC_CRASH"",""signal"":""SIGABRT""},
  ""ktriageinfo"" : ""VM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\n"",
  ""asi"" : {""libsystem_c.dylib"":[""abort() called""]},
  ""asiSignatures"" : [""Graphics hardware encountered an error and was reset: 0x00000002\n""],
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  ""faultingThread"" : 0,
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    ""base"" : 140712432832512,
    ""CFBundleShortVersionString"" : ""18.8.16"",
    ""CFBundleIdentifier"" : ""com.apple.driver.AppleIntelBDWGraphicsGLDriver"",
    ""size"" : 5259264,
    ""uuid"" : ""56bc8aa2-2042-39cb-91a7-1b4968cc47b7"",
    ""path"" : ""\/System\/Library\/Extensions\/AppleIntelBDWGraphicsGLDriver.bundle\/Contents\/MacOS\/AppleIntelBDWGraphicsGLDriver"",
    ""name"" : ""AppleIntelBDWGraphicsGLDriver"",
    ""CFBundleVersion"" : ""18.0.8""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""x86_64"",
    ""base"" : 140712558837760,
    ""size"" : 1613824,
    ""uuid"" : ""7cb910d9-50b4-3813-b927-08ebb1034ec1"",
    ""path"" : ""\/System\/Library\/Frameworks\/OpenGL.framework\/Versions\/A\/Resources\/GLEngine.bundle\/GLEngine"",
    ""name"" : ""GLEngine""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""x86_64"",
    ""base"" : 140703789469696,
    ""size"" : 24576,
    ""uuid"" : ""80cc2bbe-c07b-3415-837e-dffd527e93a8"",
    ""path"" : ""\/usr\/lib\/libffi.dylib"",
    ""name"" : ""libffi.dylib""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""x86_64"",
    ""base"" : 5165207552,
    ""size"" : 200445952,
    ""uuid"" : ""a86c7ae2-0ab4-329f-96a5-799c662db2d5"",
    ""path"" : ""\/Applications\/ChimeraX-1.10-rc2025.06.17.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore"",
    ""name"" : ""QtWebEngineCore""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""x86_64h"",
    ""base"" : 140703549685760,
    ""CFBundleShortVersionString"" : ""6.9"",
    ""CFBundleIdentifier"" : ""com.apple.CoreFoundation"",
    ""size"" : 5255168,
    ""uuid"" : ""fdd28505-5456-3c40-a5ba-7890b064db39"",
    ""path"" : ""\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation"",
    ""name"" : ""CoreFoundation"",
    ""CFBundleVersion"" : ""1866""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""x86_64"",
    ""base"" : 140703564877824,
    ""CFBundleShortVersionString"" : ""6.9"",
    ""CFBundleIdentifier"" : ""com.apple.Foundation"",
    ""size"" : 3919872,
    ""uuid"" : ""61133096-d5f9-34bd-94b1-1e526ea018b1"",
    ""path"" : ""\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation"",
    ""name"" : ""Foundation"",
    ""CFBundleVersion"" : ""1866""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""x86_64"",
    ""base"" : 4891774976,
    ""size"" : 16384,
    ""uuid"" : ""ab3e7bb1-b4dd-35a0-a44b-f87a59b1adbb"",
    ""path"" : ""\/Applications\/ChimeraX-1.10-rc2025.06.17.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_queue.cpython-311-darwin.so"",
    ""name"" : ""_queue.cpython-311-darwin.so""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""x86_64"",
    ""base"" : 4487462912,
    ""size"" : 32768,
    ""uuid"" : ""ce09d1ac-f6df-3770-9dda-8f52871a152d"",
    ""path"" : ""\/Applications\/ChimeraX-1.10-rc2025.06.17.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/select.cpython-311-darwin.so"",
    ""name"" : ""select.cpython-311-darwin.so""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""x86_64"",
    ""base"" : 140703594242048,
    ""CFBundleShortVersionString"" : ""6.9"",
    ""CFBundleIdentifier"" : ""com.apple.AppKit"",
    ""size"" : 15269888,
    ""uuid"" : ""5dd484cf-ed6a-3633-b42e-6518aeecd5b9"",
    ""path"" : ""\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit"",
    ""name"" : ""AppKit"",
    ""CFBundleVersion"" : ""2113.65.150""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""x86_64"",
    ""base"" : 4634787840,
    ""size"" : 66404352,
    ""uuid"" : ""7048d1fd-b9a9-3f6a-b752-ae8be69f6c3f"",
    ""path"" : ""\/Applications\/ChimeraX-1.10-rc2025.06.17.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib"",
    ""name"" : ""libopenblas64_.0.dylib""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""x86_64"",
    ""base"" : 140703547400192,
    ""size"" : 180224,
    ""uuid"" : ""0ff21147-73cd-36dc-99e9-606217a75b77"",
    ""path"" : ""\/usr\/lib\/system\/libsystem_malloc.dylib"",
    ""name"" : ""libsystem_malloc.dylib""
  },
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    ""source"" : ""P"",
    ""arch"" : ""x86_64"",
    ""base"" : 140703547580416,
    ""size"" : 290816,
    ""uuid"" : ""37860d89-d337-3140-8973-ac199acbc361"",
    ""path"" : ""\/usr\/lib\/system\/libdispatch.dylib"",
    ""name"" : ""libdispatch.dylib""
  }
],
  ""sharedCache"" : {
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  ""size"" : 19331678208,
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},
  ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=4.0G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=4.0G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               384K        3 \nActivity Tracing                   256K        1 \nCG backing stores                  544K        4 \nCG image                           120K       20 \nColorSync                          228K       27 \nCoreAnimation                       80K       15 \nCoreGraphics                        12K        2 \nCoreUI image data                 1564K       22 \nFoundation                          36K        2 \nIOKit                             7940K        1 \nKernel Alloc Once                    8K        1 \nMALLOC                             3.4G      239 \nMALLOC guard page                   32K        8 \nMALLOC_LARGE (reserved)            384K        1         reserved VM address space (unallocated)\nMach message                        16K        2 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        148K       37 \nStack                            307.8M       38 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      328.6M      201 \n__CTF                               756        1 \n__DATA                            42.3M      719 \n__DATA_CONST                      41.7M      449 \n__DATA_DIRTY                      1805K      238 \n__FONT_DATA                          4K        1 \n__GLSLBUILTINS                    5176K        1 \n__LINKEDIT                       675.0M      147 \n__OBJC_RO                         82.9M        1 \n__OBJC_RW                         3200K        2 \n__TEXT                           863.5M      716 \n__UNICODE                          592K        1 \ndyld private memory               1088K        3 \nmapped file                      189.6M       48 \nshared memory                     2976K       23 \n===========                     =======  ======= \nTOTAL                              6.0G     2979 \nTOTAL, minus reserved VM space     6.0G     2979 \n"",
  ""legacyInfo"" : {
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},
  ""trialInfo"" : {
  ""rollouts"" : [
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}
}
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.10rc202506130232 (2025-06-13)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/user/Downloads/8z70-pdb-bundle/8z70-pdb-bundle1.pdb

Summary of feedback from opening /Users/user/Downloads/8z70-pdb-
bundle/8z70-pdb-bundle1.pdb  
---  
warning | Ignored bad PDB record found on line 1  
HEADER RIBOSOME 2024-04-19 XXXX  
  
Chain information for 8z70-pdb-bundle1.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  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
  

> open /Users/user/Downloads/8z70-pdb-bundle/8z70-pdb-bundle2.pdb

Summary of feedback from opening /Users/user/Downloads/8z70-pdb-
bundle/8z70-pdb-bundle2.pdb  
---  
warning | Ignored bad PDB record found on line 1  
HEADER RIBOSOME 2024-04-19 XXXX  
  
Chain information for 8z70-pdb-bundle2.pdb #2  
---  
Chain | Description  
A | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
U | No description available  
V | No description available  
  
1555 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> open /Users/user/Downloads/8z70-pdb-bundle/8z70-pdb-bundle3.pdb

Summary of feedback from opening /Users/user/Downloads/8z70-pdb-
bundle/8z70-pdb-bundle3.pdb  
---  
warning | Ignored bad PDB record found on line 1  
HEADER RIBOSOME 2024-04-19 XXXX  
  
Chain information for 8z70-pdb-bundle3.pdb #3  
---  
Chain | Description  
W | No description available  
X | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
x | No description available  
  

> hide atoms

> show cartoons

Computing secondary structure  

> show cartoons

> select #1/i:45

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #1/A:1180

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select up

39355 atoms, 44016 bonds, 1847 residues, 1 model selected  

> select ~sel

166694 atoms, 177305 bonds, 9 pseudobonds, 15113 residues, 5 models selected  

> hide sel cartoons

> select #1/A:1179

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #1/A:1180

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select add #1/A:1178

66 atoms, 71 bonds, 3 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 66 atom styles  

> select #1/i:36

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #1/i:35

44 atoms, 48 bonds, 2 residues, 1 model selected  

> select add #1/i:34

64 atoms, 69 bonds, 3 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 64 atom styles  

> select #1/A:1441

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #1/A:1440

40 atoms, 42 bonds, 2 residues, 1 model selected  

> select add #1/A:1439

60 atoms, 63 bonds, 3 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 60 atom styles  

> select #1/A:1640

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #1/A:1639

40 atoms, 42 bonds, 2 residues, 1 model selected  

> select add #1/A:1638

63 atoms, 67 bonds, 3 residues, 1 model selected  

> select add #1/A:1637

83 atoms, 88 bonds, 4 residues, 1 model selected  

> select add #1/A:1636

103 atoms, 109 bonds, 5 residues, 1 model selected  

> select add #1/A:1635

125 atoms, 133 bonds, 6 residues, 1 model selected  

> select add #1/A:1634

145 atoms, 154 bonds, 7 residues, 1 model selected  

> select add #1/A:1633

167 atoms, 178 bonds, 8 residues, 1 model selected  

> select add #1/A:1632

187 atoms, 199 bonds, 9 residues, 1 model selected  

> select add #1/A:1631

209 atoms, 223 bonds, 10 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 209 atom styles  

> select clear

> hide atoms

> select #1/A:1770-1790

449 atoms, 501 bonds, 21 residues, 1 model selected  

> color sel red

> select #1/A:1640-1760

2593 atoms, 2903 bonds, 121 residues, 1 model selected  

> color sel cyan

> select clear

> select #1/A:1777

23 atoms, 25 bonds, 1 residue, 1 model selected  

> show sel atoms

> style sel stick

Changed 23 atom styles  

> select #1/A:1773

20 atoms, 21 bonds, 1 residue, 1 model selected  

> show sel atoms

> style sel stick

Changed 20 atom styles  

> select #1/A:1787

20 atoms, 21 bonds, 1 residue, 1 model selected  

> show sel atoms

> style sel stick

Changed 20 atom styles  

> select #1/A:1786

23 atoms, 25 bonds, 1 residue, 1 model selected  

> show sel atoms

> style sel stick

Changed 23 atom styles  

> select #1/A:1788

23 atoms, 25 bonds, 1 residue, 1 model selected  

> show sel atoms

> style sel stick

Changed 23 atom styles  

> select clear

> select #1/A:1773@C4

1 atom, 1 residue, 1 model selected  

> select up

20 atoms, 21 bonds, 1 residue, 1 model selected  

> color sel purple

> color sel lime


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

Log:
UCSF ChimeraX version: 1.10rc202506130232 (2025-06-13)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




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

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir7,2
      Processor Name: Dual-Core Intel Core i5
      Processor Speed: 1.8 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 3 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 489.0.0.0.0
      OS Loader Version: 540.120.3~37
      SMC Version (system): 2.27f2

Software:

    System Software Overview:

      System Version: macOS 12.7.6 (21H1320)
      Kernel Version: Darwin 21.6.0
      Time since boot: 21 days 3:36

Graphics/Displays:

    Intel HD Graphics 6000:

      Chipset Model: Intel HD Graphics 6000
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x1626
      Revision ID: 0x0009
      Metal Family: Supported, Metal GPUFamily macOS 1
      Displays:
        Color LCD:
          Display Type: LCD
          Resolution: 1440 x 900 (Widescreen eXtended Graphics Array Plus)
          UI Looks like: 1440 x 900
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.4.0
    build: 1.2.2.post1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.18
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10rc202506130232
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5.1
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.6.2
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.3
    ChimeraX-ProfileGrids: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.45.1
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.2
    coverage: 7.9.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.14
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.58.4
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.4.4
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.32
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.0
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 27.0.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.0
    tzdata: 2025.2
    urllib3: 2.4.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14
}}}
"	defect	closed	normal		Graphics		nonchimerax						all	ChimeraX