id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17309 Some kind of memory/pager failure chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-12.1-x86_64-i386-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x000000020280a600 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 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, 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, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, openmm._openmm, openmm.app.internal.compiled, lxml._elementpath, lxml.etree, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, chimerax.dssp._dssp, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.alignment_algs._nw (total: 64) {""app_name"":""ChimeraX"",""timestamp"":""2025-04-07 16:30:52.00 +1000"",""app_version"":""1.8.0"",""slice_uuid"":""194a3167-3db5-3029-8d22-1d742b826bb9"",""build_version"":""1.8.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 12.1 (21C52)"",""incident_id"":""19E83816-3C7C-4079-812A-AE0F76B0A5B9"",""name"":""ChimeraX""} { ""uptime"" : 43000, ""procLaunch"" : ""2025-04-07 15:00:46.5640 +1000"", ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""MacBookAir10,1"", ""procStartAbsTime"" : 904771047725, ""coalitionID"" : 1493, ""osVersion"" : { ""train"" : ""macOS 12.1"", ""build"" : ""21C52"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2025-04-07 16:30:38.6011 +1000"", ""incident"" : ""19E83816-3C7C-4079-812A-AE0F76B0A5B9"", ""bug_type"" : ""309"", ""pid"" : 11975, ""procExitAbsTime"" : 1033511567242, ""translated"" : true, ""cpuType"" : ""X86-64"", ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.8.0"",""CFBundleVersion"":""1.8.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""6B8556C9-71EB-5517-B328-F73577F2DC82"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""76685193-F55C-E9C2-726A-6C7B93E7C7B4"", ""sleepWakeUUID"" : ""33B004D4-C842-43CE-91B0-CDF810DC3D97"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0xff00000169 is not in any region. 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(2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > open /Users/michaelakaoullas/Documents/PhD/Structures/XY6/M4R-ACh- > XY6_real_space_refined_consensus_coot-1_real_space_refined_015-coot-0_real_space_refined_MGK.cxs opened ChimeraX session > open > /Users/michaelakaoullas/Documents/PhD/Results/CryoEM/M4mGsi_ACh_CVL231/RealSpaceRefine_64/M4RmGsi_AChCVL_refine_34_refine_11_JM_MGK_refine_59_v2_refine_061_v2_refine_62_JM_real_space_refined_064.pdb Chain information for M4RmGsi_AChCVL_refine_34_refine_11_JM_MGK_refine_59_v2_refine_061_v2_refine_62_JM_real_space_refined_064.pdb #2 --- Chain | Description A | No description available B | No description available G | No description available N | No description available R | No description available > hide atoms > show cartoons > select add #2 8001 atoms, 8172 bonds, 2 pseudobonds, 1029 residues, 2 models selected > ui tool show ""Color Actions"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > color sel light steel blue > select subtract #2 Nothing selected > hide #2.1 models > dssp > open > /Users/michaelakaoullas/Documents/PhD/Results/CryoEM/M4mGsi_xanomeline_MK6884/RealSpaceRefine_46/M4R_mGsi_xano_MK6884_real_space_refined_44_real_space_refined_045-coot-0_real_space_refined_046.pdb Chain information for M4R_mGsi_xano_MK6884_real_space_refined_44_real_space_refined_045-coot-0_real_space_refined_046.pdb #3 --- Chain | Description A | No description available B | No description available G | No description available N | No description available R | No description available > hide #3.1 models > hide atoms > show cartoons > dssp > select add #3 7982 atoms, 8156 bonds, 2 pseudobonds, 1026 residues, 2 models selected > color sel thistle > select subtract #3 Nothing selected > open 7trp 7trp title: Human M4 muscarinic acetylcholine receptor complex with Gi1 and the agonist iperoxo and positive allosteric modulator LY2033298 [more info...] Chain information for 7trp #4 --- Chain | Description | UniProt A | Guanine nucleotide-binding protein G(i) subunit alpha-1 | GNAI1_HUMAN 1-354 B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340 G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 2-71 H | Antibody fragment scFv16 | R | Muscarinic acetylcholine receptor M4 | ACM4_HUMAN 1-387 388-479 Non-standard residues in 7trp #4 --- IUE — 3-amino-5-chloro-N- cyclopropyl-6-methoxy-4-methylthieno[2,3-b]pyridine-2-carboxamide IXO — 4-(4,5-dihydro-1,2-oxazol-3-yloxy)-N,N,N-trimethylbut-2-yn-1-aminium (Iperoxo) > hide atoms > show cartoons > hide #4.1 models > dssp > select add #4 8681 atoms, 8869 bonds, 3 pseudobonds, 1124 residues, 2 models selected > color sel gray > color sel light gray > color sel gainsboro > color sel tan > color sel burly wood > color sel tan > select clear > open 7trs 7trs title: Human M4 muscarinic acetylcholine receptor complex with Gi1 and the endogenous agonist acetylcholine [more info...] Chain information for 7trs #5 --- Chain | Description | UniProt A | Guanine nucleotide-binding protein G(i) subunit alpha-1 | GNAI1_HUMAN 1-354 B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340 G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 2-71 H | Antibody fragment scFv16 | R | Muscarinic acetylcholine receptor M4 | ACM4_HUMAN 1-387 388-479 Non-standard residues in 7trs #5 --- ACH — acetylcholine > hide atoms > show cartoons > select add #5 8571 atoms, 8757 bonds, 3 pseudobonds, 1122 residues, 2 models selected > hide #5.1 models > dssp > color sel misty rose > color sel wheat > color sel silver > color sel dim gray > color sel gray > color sel gainsboro > select clear > ui tool show Matchmaker The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > matchmaker #!2-5 to #1/R pairing bs Parameters --- Chain pairing | bs Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker M4R-ACh- XY6_real_space_consensus_coot-1_real_space_refined_015-coot-0_real_space_refined_001.pdb, chain R (#1) with M4RmGsi_AChCVL_refine_34_refine_11_JM_MGK_refine_59_v2_refine_061_v2_refine_62_JM_real_space_refined_064.pdb, chain R (#2), sequence alignment score = 1395.3 RMSD between 266 pruned atom pairs is 0.635 angstroms; (across all 270 pairs: 0.706) Matchmaker M4R-ACh- XY6_real_space_consensus_coot-1_real_space_refined_015-coot-0_real_space_refined_001.pdb, chain R (#1) with M4R_mGsi_xano_MK6884_real_space_refined_44_real_space_refined_045-coot-0_real_space_refined_046.pdb, chain R (#3), sequence alignment score = 1395.9 RMSD between 263 pruned atom pairs is 0.607 angstroms; (across all 268 pairs: 0.698) Matchmaker M4R-ACh- XY6_real_space_consensus_coot-1_real_space_refined_015-coot-0_real_space_refined_001.pdb, chain R (#1) with 7trp, chain R (#4), sequence alignment score = 1381.2 RMSD between 267 pruned atom pairs is 0.475 angstroms; (across all 267 pairs: 0.475) Matchmaker M4R-ACh- XY6_real_space_consensus_coot-1_real_space_refined_015-coot-0_real_space_refined_001.pdb, chain R (#1) with 7trs, chain R (#5), sequence alignment score = 1400.4 RMSD between 270 pruned atom pairs is 0.497 angstroms; (across all 270 pairs: 0.497) > select /a-h, n 31199 atoms, 31804 bonds, 8 pseudobonds, 4063 residues, 10 models selected > hide sel cartoons > select clear > select /r:413 70 atoms, 75 bonds, 5 residues, 5 models selected > show sel atoms > style sel stick Changed 70 atom styles > color sel byhetero > select clear > cartoon style width 1.3 thickness 0.3 > select /R:413:412:415 140 atoms, 145 bonds, 15 residues, 5 models selected > show sel atoms > style sel stick Changed 140 atom styles > color sel byhetero > select /R:129:130:131 155 atoms, 155 bonds, 15 residues, 5 models selected > show sel atoms > style sel stick Changed 155 atom styles > color sel byhetero > select /R:449:450:453:451:452 190 atoms, 195 bonds, 25 residues, 5 models selected > show sel atoms > style sel stick Changed 190 atom styles > color sel byhetero > select /R:207:120:409 125 atoms, 120 bonds, 15 residues, 5 models selected > show sel atoms > style sel stick Changed 125 atom styles > color sel byhetero > open 5dsg 5dsg title: Structure of the M4 muscarinic acetylcholine receptor (M4-mT4L) bound to tiotropium [more info...] Chain information for 5dsg #6 --- Chain | Description | UniProt A B | Muscarinic acetylcholine receptor M4,Endolysin,Endolysin,Muscarinic acetylcholine receptor M4 | ACM4_HUMAN 22-226 390-478, ENLYS_BPT4 1002-1011 1018-1118 Non-standard residues in 5dsg #6 --- 0HK — (1R,2R,4S,5S,7S)-7-{[hydroxy(dithiophen-2-yl)acetyl]oxy}-9,9-dimethyl-3-oxa-9-azoniatricyclo[3.3.1.0~2,4~]nonane (Tiotropium) EDT — {[-(bis-carboxymethyl-amino)-ethyl]-carboxymethyl-amino}-acetic acid OLA — oleic acid OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol) P6G — hexaethylene glycol (polyethylene glycol PEG400) PG6 — 1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane 5dsg mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly 3| software_defined_assembly > select add #5 8671 atoms, 8853 bonds, 3 pseudobonds, 1134 residues, 6 models selected > select subtract #5 100 atoms, 96 bonds, 12 residues, 4 models selected > select add #4 8756 atoms, 8941 bonds, 3 pseudobonds, 1133 residues, 5 models selected > select subtract #4 75 atoms, 72 bonds, 9 residues, 3 models selected > select add #3 8032 atoms, 8204 bonds, 2 pseudobonds, 1032 residues, 4 models selected > select subtract #3 50 atoms, 48 bonds, 6 residues, 2 models selected > select add #2 8026 atoms, 8196 bonds, 2 pseudobonds, 1032 residues, 3 models selected > select subtract #2 25 atoms, 24 bonds, 3 residues, 1 model selected > select add #1 8731 atoms, 8921 bonds, 3 pseudobonds, 1131 residues, 2 models selected > select subtract #1 Nothing selected > select add #6 6516 atoms, 6636 bonds, 3 pseudobonds, 834 residues, 2 models selected > hide sel atoms > show sel cartoons > select clear > select #6/A 3254 atoms, 3309 bonds, 2 pseudobonds, 418 residues, 2 models selected > delete atoms (#!6 & sel) > delete bonds (#!6 & sel) > select #6 /B 3262 atoms, 3327 bonds, 1 pseudobond, 416 residues, 2 models selected > select clear > hide #6.1 models > select add #6 3262 atoms, 3327 bonds, 1 pseudobond, 416 residues, 2 models selected > color sel olive > color sel olive drab > color sel forest green > color sel dark red > color sel dark goldenrod > color sel dim gray > color sel gray > ui tool show Matchmaker The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > matchmaker #!2-6 to #1/R pairing bs Parameters --- Chain pairing | bs Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker M4R-ACh- XY6_real_space_consensus_coot-1_real_space_refined_015-coot-0_real_space_refined_001.pdb, chain R (#1) with M4RmGsi_AChCVL_refine_34_refine_11_JM_MGK_refine_59_v2_refine_061_v2_refine_62_JM_real_space_refined_064.pdb, chain R (#2), sequence alignment score = 1395.3 RMSD between 266 pruned atom pairs is 0.635 angstroms; (across all 270 pairs: 0.706) Matchmaker M4R-ACh- XY6_real_space_consensus_coot-1_real_space_refined_015-coot-0_real_space_refined_001.pdb, chain R (#1) with M4R_mGsi_xano_MK6884_real_space_refined_44_real_space_refined_045-coot-0_real_space_refined_046.pdb, chain R (#3), sequence alignment score = 1395.9 RMSD between 263 pruned atom pairs is 0.607 angstroms; (across all 268 pairs: 0.698) Matchmaker M4R-ACh- XY6_real_space_consensus_coot-1_real_space_refined_015-coot-0_real_space_refined_001.pdb, chain R (#1) with 7trp, chain R (#4), sequence alignment score = 1381.2 RMSD between 267 pruned atom pairs is 0.475 angstroms; (across all 267 pairs: 0.475) Matchmaker M4R-ACh- XY6_real_space_consensus_coot-1_real_space_refined_015-coot-0_real_space_refined_001.pdb, chain R (#1) with 7trs, chain R (#5), sequence alignment score = 1400.4 RMSD between 270 pruned atom pairs is 0.497 angstroms; (across all 270 pairs: 0.497) Matchmaker M4R-ACh- XY6_real_space_consensus_coot-1_real_space_refined_015-coot-0_real_space_refined_001.pdb, chain R (#1) with 5dsg, chain B (#6), sequence alignment score = 1285.3 RMSD between 212 pruned atom pairs is 0.853 angstroms; (across all 274 pairs: 2.423) > select subtract #6 Nothing selected > select add #5 8571 atoms, 8757 bonds, 3 pseudobonds, 1122 residues, 2 models selected > color sel lavender blush > color sel light coral > color sel medium purple > color sel rosy brown > select subtract #5 Nothing selected > select add #6 3262 atoms, 3327 bonds, 1 pseudobond, 416 residues, 2 models selected > color sel gray > color sel silver > color sel light gray > color sel gainsboro > color sel light gray > select clear > select /R:413:412:415:129:130:131:449:450:453:451:452:207:120:409 610 atoms, 615 bonds, 70 residues, 5 models selected > show sel atoms > style sel stick Changed 610 atom styles > color sel byhetero > select #6 /b:413:412:415:129:130:131:449:450:453:451:452:207:120:409 122 atoms, 123 bonds, 14 residues, 1 model selected > show sel atoms > style sel stick Changed 122 atom styles > color sel byhetero > select clear > cartoon style width 1.3 thickness 0.3 transparenc 60 cartoons Expected a keyword > cartoon style width 1.3 thickness 0.3 > lighting soft multiShadow 128 > transparency 60 cartoons > select /R:395 45 atoms, 40 bonds, 5 residues, 5 models selected > show sel atoms > style sel stick Changed 45 atom styles > color sel byhetero > select #6 /B:395 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select clear > select add #6 3262 atoms, 3327 bonds, 1 pseudobond, 416 residues, 2 models selected > color sel gray > color (#!6 & sel) byhetero > select clear > select #6 /B:394-1017 719 atoms, 738 bonds, 1 pseudobond, 91 residues, 2 models selected > select clear > select #6 /B:1017-1118 788 atoms, 802 bonds, 102 residues, 1 model selected > hide sel cartoons > select #6/B:1010 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 73 atoms, 73 bonds, 9 residues, 1 model selected > select up 1663 atoms, 1705 bonds, 213 residues, 1 model selected > select down 73 atoms, 73 bonds, 9 residues, 1 model selected > hide sel cartoons > select #6/B:1011 5 atoms, 4 bonds, 1 residue, 1 model selected > hide sel cartoons > select clear > select #6 /B:415 7 atoms, 7 bonds, 1 residue, 1 model selected > select #6 /B:451 5 atoms, 4 bonds, 1 residue, 1 model selected > hide sel atoms > select /r:451 25 atoms, 20 bonds, 5 residues, 5 models selected > hide sel atoms > select clear > select ::name=""ACH"" 30 atoms, 27 bonds, 3 residues, 3 models selected > show sel atoms > color sel byhetero > select ::name=""XNO"" 19 atoms, 20 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select ::name=""IXO"" 14 atoms, 14 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select clear > ui tool show ""Side View"" > transparency 80 cartoons > view > select /3:452 Nothing selected > select /r:452 30 atoms, 25 bonds, 5 residues, 5 models selected > hide sel atoms > select #6 /B:452 6 atoms, 5 bonds, 1 residue, 1 model selected > hide sel atoms > select clear > save ""/Users/michaelakaoullas/Documents/PhD/Milestones/36 > Month/CVL_XanMK_XY6_7trp_7trs_5dsg.png"" width 2000 height 1189 supersample 4 > save ""/Users/michaelakaoullas/Documents/PhD/Milestones/36 > Month/CVL_XanMK_XY6_7trp_7trs_5dsg.cxs"" includeMaps true > select #6 /b:413:412:415:129:130:131:449:450:453:451:452:207:120:409 122 atoms, 123 bonds, 14 residues, 1 model selected > hide sel atoms > select /r:413:412:415:129:130:131:449:450:453:451:452:207:120:409 610 atoms, 615 bonds, 70 residues, 5 models selected > hide sel atoms > select /r:413:412:415:129:130:131:449:450:453:451:452:207:120:409:395 655 atoms, 655 bonds, 75 residues, 5 models selected > hide sel atoms > select #6 /b:413:412:415:129:130:131:449:450:453:451:452:207:120:409:395 131 atoms, 131 bonds, 15 residues, 1 model selected > hide sel atoms > select clear > select add #1 8731 atoms, 8921 bonds, 3 pseudobonds, 1131 residues, 2 models selected > select add #2 16732 atoms, 17093 bonds, 5 pseudobonds, 2160 residues, 4 models selected > select add #3 24714 atoms, 25249 bonds, 7 pseudobonds, 3186 residues, 6 models selected > select add #4 33395 atoms, 34118 bonds, 10 pseudobonds, 4310 residues, 8 models selected > select add #5 41966 atoms, 42875 bonds, 13 pseudobonds, 5432 residues, 10 models selected > show sel cartoons > select clear > transparency 0 cartoons > select g Expected an objects specifier or a keyword > select /h 5337 atoms, 5475 bonds, 3 pseudobonds, 704 residues, 6 models selected > hide sel cartoons > select /n 1948 atoms, 1992 bonds, 256 residues, 2 models selected > hide sel cartoons > select clear > select /b 16173 atoms, 16473 bonds, 1 pseudobond, 2110 residues, 7 models selected > hide sel cartoons > select /g 2091 atoms, 2121 bonds, 282 residues, 5 models selected > hide sel cartoons ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 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: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: MacBookAir10,1 Processor Name: Unknown Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache: 8 MB Memory: 8 GB Software: System Software Overview: System Version: macOS 12.1 (21C52) Kernel Version: Darwin 21.2.0 Time since boot: 2 days 5:10 Graphics/Displays: Apple G13G: Chipset Model: Apple G13G Type: GPU Bus: Built-In Total Number of Cores: 7 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal PHL 241S9: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 75.00Hz Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.23.1 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 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-ISOLDE: 1.8 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 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: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 ChimeraX-ModelPanel: 1.5 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: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 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: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 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-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 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 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: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 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: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Core can't reproduce Tom Goddard all ChimeraX