id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15646 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.5-x86_64-i386-64bit ChimeraX Version: 1.7rc202311100232 (2023-11-10 02:32:35 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x000070001056e000 (most recent call first): File ""/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00007ff85c7bffc0 (most recent call first): Garbage-collecting File ""/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py"", line 243 in set_c_pointer File ""/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 108 in __init__ File ""/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 2403 in File ""/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/struct_edit.py"", line 164 in add_bond File ""/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/struct_edit.py"", line 108 in add_atom File ""/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/cmd.py"", line 949 in new_hydrogen File ""/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/cmd.py"", line 910 in add_altloc_hyds File ""/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/hbond.py"", line 909 in _attach_hydrogens File ""/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/hbond.py"", line 225 in add_hydrogens File ""/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/cmd.py"", line 184 in hbond_add_hydrogens File ""/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/cmd.py"", line 77 in cmd_addh File ""/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/coulombic.py"", line 95 in assign_charges File ""/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/cmd.py"", line 99 in cmd_coulombic File ""/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2908 in run File ""/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py"", line 49 in run File ""/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 525 in run File ""/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 582 in run_expanded_command File ""/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 72 in func_plus_tip File ""/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 339 in run File ""/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 420 in run_shortcut File ""/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 402 in try_shortcut File ""/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 1376 in run_provider File ""/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/__init__.py"", line 66 in run_provider File ""/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py"", line 1302 in run_provider File ""/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/info.py"", line 397 in run_provider File ""/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/toolbar/tool.py"", line 205 in callback File ""/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 918 in init File ""/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1069 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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, lxml._elementpath, lxml.etree, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, chimerax.mlp._mlp (total: 58) {""app_name"":""ChimeraX"",""timestamp"":""2024-07-21 21:13:42.00 -0500"",""app_version"":""1.7.0"",""slice_uuid"":""194a3167-3db5-3029-8d22-1d742b826bb9"",""build_version"":""1.7.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 14.5 (23F79)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""E0E12260-D305-4CD5-B43D-01A8135F00AC""} { ""uptime"" : 570000, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 1019509796, ""deployVersion"" : 210, ""modelCode"" : ""iMac20,1"", ""coalitionID"" : 18325, ""osVersion"" : { ""train"" : ""macOS 14.5"", ""build"" : ""23F79"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2024-07-21 21:13:42.0811 -0500"", ""codeSigningMonitor"" : 0, ""incident"" : ""E0E12260-D305-4CD5-B43D-01A8135F00AC"", ""pid"" : 56755, ""cpuType"" : ""X86-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2024-07-21 20:43:42.8727 -0500"", ""procStartAbsTime"" : 574995451773618, ""procExitAbsTime"" : 576794564495332, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Volumes\/VOLUME\/*\/ChimeraX-1.7-rc2023.11.10.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.7.0"",""CFBundleVersion"":""1.7.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""BB8F601C-4C57-552E-9FE6-13CCD1FAA87B"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""534E2971-3E00-0E0B-D1E3-DDAE6765C493"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""bridgeVersion"" : {""build"":""21P5077"",""train"":""8.5""}, ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0xa9 is not in any region. Bytes before following region: 4357050199\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 103b35000-103b39000 [ 16K] r-x\/r-x SM=COW \/var\/folders\/*\/ChimeraX-1.7-rc2023.11.10.app\/Contents\/MacOS\/ChimeraX"", ""exception"" : {""codes"":""0x0000000000000001, 0x00000000000000a9"",""rawCodes"":[1,169],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x00000000000000a9""}, ""termination"" : {""flags"":0,""code"":11,""namespace"":""SIGNAL"",""indicator"":""Segmentation fault: 11"",""byProc"":""ChimeraX"",""byPid"":56755}, ""vmregioninfo"" : ""0xa9 is not in any region. 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""65a8115446dfa0720068876d"", ""SIRI_UNDERSTANDING_NL"" : ""65a811c046dfa0720068876e"", ""SIRI_EXPERIENCE_CAM"" : ""65a81173096f6a1f1ba46525"", ""SIRI_UNDERSTANDING_MORPHUN"" : ""65a811a96c2f903aa921c246"" }, ""deploymentId"" : 240000116 } ], ""experiments"" : [ { ""treatmentId"" : ""c47ab4cc-c9c3-4b5d-a87c-e2433ce02597"", ""experimentId"" : ""6639bc6ba73d460582162323"", ""deploymentId"" : 400000006 } ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.7rc202311100232 (2023-11-10) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/suj/Downloads/fold_2024_07_21_20_47_rice_dimer/fold_2024_07_21_20_47_rice_dimer_model_0.cif Chain information for fold_2024_07_21_20_47_rice_dimer_model_0.cif #1 --- Chain | Description A B | . > coulombic Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for fold_2024_07_21_20_47_rice_dimer_model_0.cif_A SES surface #1.1: minimum, -14.14, mean -1.99, maximum 10.03 Coulombic values for fold_2024_07_21_20_47_rice_dimer_model_0.cif_B SES surface #1.2: minimum, -14.42, mean -1.99, maximum 10.07 To also show corresponding color key, enter the above coulombic command and add key true > close > open > /Users/suj/Downloads/fold_2024_07_21_20_53_soybean_dimer/fold_2024_07_21_20_53_soybean_dimer_model_0.cif Chain information for fold_2024_07_21_20_53_soybean_dimer_model_0.cif #1 --- Chain | Description A B | . > coulombic Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for fold_2024_07_21_20_53_soybean_dimer_model_0.cif_A SES surface #1.1: minimum, -11.98, mean 0.22, maximum 11.23 Coulombic values for fold_2024_07_21_20_53_soybean_dimer_model_0.cif_B SES surface #1.2: minimum, -12.17, mean 0.21, maximum 12.50 To also show corresponding color key, enter the above coulombic command and add key true > close > open > /Users/suj/Downloads/fold_2024_07_21_21_06_liverworts/fold_2024_07_21_21_06_liverworts_model_0.cif Chain information for fold_2024_07_21_21_06_liverworts_model_0.cif #1 --- Chain | Description A B | . > coulombic Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for fold_2024_07_21_21_06_liverworts_model_0.cif_A SES surface #1.1: minimum, -12.03, mean 0.17, maximum 14.54 Coulombic values for fold_2024_07_21_21_06_liverworts_model_0.cif_B SES surface #1.2: minimum, -11.86, mean 0.16, maximum 14.97 To also show corresponding color key, enter the above coulombic command and add key true > hide surfaces > show atoms > mlp Map values for surface ""fold_2024_07_21_21_06_liverworts_model_0.cif_A SES surface"": minimum -25.74, mean -3.189, maximum 21.66 Map values for surface ""fold_2024_07_21_21_06_liverworts_model_0.cif_B SES surface"": minimum -25.9, mean -3.159, maximum 21.5 To also show corresponding color key, enter the above mlp command and add key true > coulombic Coulombic values for fold_2024_07_21_21_06_liverworts_model_0.cif_A SES surface #1.1: minimum, -12.03, mean 0.17, maximum 14.54 Coulombic values for fold_2024_07_21_21_06_liverworts_model_0.cif_B SES surface #1.2: minimum, -11.86, mean 0.16, maximum 14.97 To also show corresponding color key, enter the above coulombic command and add key true > close > open > /Users/suj/Downloads/fold_2024_07_21_21_09_amoeba/fold_2024_07_21_21_09_amoeba_model_0.cif Chain information for fold_2024_07_21_21_09_amoeba_model_0.cif #1 --- Chain | Description A B | . > coulombic ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.7rc202311100232 (2023-11-10) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 ATI-5.5.17 OpenGL renderer: AMD Radeon Pro 5300 OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.11.2 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: iMac20,1 Processor Name: 6-Core Intel Core i5 Processor Speed: 3.3 GHz Number of Processors: 1 Total Number of Cores: 6 L2 Cache (per Core): 256 KB L3 Cache: 12 MB Hyper-Threading Technology: Enabled Memory: 32 GB System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.5077.0.0,0) OS Loader Version: 580~2215 Software: System Software Overview: System Version: macOS 14.5 (23F79) Kernel Version: Darwin 23.5.0 Time since boot: 6 days, 16 hours, 13 minutes Graphics/Displays: AMD Radeon Pro 5300: Chipset Model: AMD Radeon Pro 5300 Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0047 ROM Revision: 113-D3220I-231 VBIOS Version: 113-D322A1XL-011 Option ROM Version: 113-D322A1XL-011 EFI Driver Version: 01.01.231 Metal Support: Metal 3 Displays: iMac: Display Type: Built-In Retina LCD Resolution: Retina 5K (5120 x 2880) Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.1 Babel: 2.13.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.12 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.1 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7rc202311100232 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.2 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-ListInfo: 1.2.1 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.12 ChimeraX-ModelPanel: 1.4 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-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0.1 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: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 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: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.2 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.33.2 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.0 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.44.0 funcparserlib: 1.0.1 glfw: 2.6.2 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.5.0 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.8 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.7 numpy: 1.25.1 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: 10.0.1 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.11.0 prompt-toolkit: 3.0.39 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 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: 2023.3.post1 pyzmq: 25.1.1 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.7 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.5 sphinxcontrib-htmlhelp: 2.0.4 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.6 sphinxcontrib-serializinghtml: 1.1.9 stack-data: 0.6.3 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.3 traitlets: 5.9.0 typing-extensions: 4.8.0 tzdata: 2023.3 urllib3: 2.0.7 wcwidth: 0.2.9 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Core duplicate Tom Goddard all ChimeraX