id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16776 Crash in event loop chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-15.1-x86_64-i386-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 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 0x00007ff84e997b40 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 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, chimerax.surface._surface, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, 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, lxml._elementpath, lxml.etree, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.alignment_algs._nw, chimerax.morph._morph (total: 61) {""app_name"":""ChimeraX"",""timestamp"":""2025-02-03 14:19:30.00 -0800"",""app_version"":""1.9.0"",""slice_uuid"":""079d39d3-a489-3e56-92d8-c781f5a4bb98"",""build_version"":""1.9.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 15.1 (24B83)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""EF2B7324-A4A5-4935-98B2-B7BDC9A542A2""} { ""uptime"" : 200000, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 504, ""deployVersion"" : 210, ""modelCode"" : ""Macmini8,1"", ""coalitionID"" : 13600, ""osVersion"" : { ""train"" : ""macOS 15.1"", ""build"" : ""24B83"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2025-02-03 14:19:25.8274 -0800"", ""codeSigningMonitor"" : 0, ""incident"" : ""EF2B7324-A4A5-4935-98B2-B7BDC9A542A2"", ""pid"" : 14880, ""cpuType"" : ""X86-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2025-02-03 13:08:03.7161 -0800"", ""procStartAbsTime"" : 203976596389428, ""procExitAbsTime"" : 208258711298586, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.9.0"",""CFBundleVersion"":""1.9.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""72F5BE26-D4F3-56D4-A641-50D41F3BD97D"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""85C55B7C-3B71-960C-DE44-2BC20A8921CD"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""bootSessionUUID"" : ""86CFB0F9-25E5-4157-9DE9-C59CFCE81D03"", ""wakeTime"" : 4547, ""bridgeVersion"" : {""build"":""22P1072"",""train"":""9.1""}, ""sleepWakeUUID"" : ""A4E779D5-2EC4-445C-981F-EA49A1426E5C"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x5d50c80ffd40 is not in any region. 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swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=71.4G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=71.4G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG image 188K 36 \nColorSync 244K 31 \nCoreAnimation 2088K 58 \nCoreGraphics 36K 5 \nCoreServices 620K 2 \nCoreUI image data 2172K 32 \nFoundation 32K 2 \nIOKit 7940K 1 \nKernel Alloc Once 8K 1 \nMALLOC 70.7G 3805 \nMALLOC guard page 48K 12 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMach message 16K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 148K 37 \nStack 191.8M 38 \nStack Guard 56.0M 1 \nVM_ALLOCATE 306.1M 347 \nVM_ALLOCATE (reserved) 64.0M 1 reserved VM address space (unallocated)\n__CTF 824 1 \n__DATA 44.7M 1158 \n__DATA_CONST 109.5M 1072 \n__DATA_DIRTY 2609K 354 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 215.1M 180 \n__OBJC_RO 76.3M 1 \n__OBJC_RW 2355K 2 \n__TEXT 1.4G 1175 \n__TPRO_CONST 272K 2 \ndyld private memory 40K 2 \nmapped file 544.9M 80 \nowned unmapped memory 86.1M 1 \nshared memory 3004K 31 \n=========== ======= ======= \nTOTAL 73.8G 8481 \nTOTAL, minus reserved VM space 73.8G 8481 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""7398f1095c6d7222c290babf111e397e800a45a1"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""6410af69ed1e1e7ab93ed169"", ""factorPackIds"" : { }, ""deploymentId"" : 240000011 }, { ""rolloutId"" : ""65a8173205d942272410674b"", ""factorPackIds"" : { ""SIRI_HOME_AUTOMATION_SERVER_FLOW_DEPRECATION"" : ""65d39fa4cb0e2417d11ce5f6"" }, ""deploymentId"" : 240000001 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/zachpilon/Desktop/ZackPilon W25/Hemoglobin red blue all parts > move no hem.cxs"" opened ChimeraX session > set bgColor color white Invalid ""bgColor"" argument: Invalid color name or specifier > set bgColor white > select add #1.1 26 pseudobonds, 1 model selected > show #!1 models > hide #!3 models > hide #1.1 models > select subtract #1.1 Nothing selected > show #!2 models > hide #!2 models > hide #!1 models > show #!3 models > show sel > hide #3.1 models > select subtract #3.1 Nothing selected > ui tool show Log > morph #2,1,2 frames 150 hideModels false hideResidues false Expected a keyword > morph #2,1,2 frames 150 hideModels false Computed 151 frame morph #4 > coordset #4 1,151 Called accessibilityLabel on invalid object: 2148138997 > hide #!3 models > close #4 > show #!3 models > morph #1,2 frames 80 hideModels false :morph #2,1 frames 80 hideModels false Expected a keyword > morph #1,2 frames 80 hideModels false:morph #2,1 frames 80 hideModels false Invalid ""hideModels"" argument: Expected true or false (or 1 or 0) > morph #1,2 frames 80 hideModels false : morph #2,1 frames 80 hideModels > false Expected a keyword > morph #1,2 frames 80 hideModels false Computed 81 frame morph #4 > coordset #4 1,81 > morph #2,1 frames 80 hideModels false Computed 81 frame morph #5 > coordset #5 1,81 > hide #!3 models > close #4 > close #5 > show #!3 models > hide #!3 models > show #!2 models > show #!1 models > hide #!2 models > select add #1 5222 atoms, 4677 bonds, 26 pseudobonds, 1245 residues, 2 models selected > select subtract #1/B:147@FE 5221 atoms, 4677 bonds, 19 pseudobonds, 1245 residues, 2 models selected > select subtract #1/B:147@ND 5220 atoms, 4675 bonds, 19 pseudobonds, 1245 residues, 2 models selected > select subtract #1/B:147@C4D 5219 atoms, 4673 bonds, 19 pseudobonds, 1245 residues, 2 models selected > select subtract #1/B:147@O1D 5218 atoms, 4670 bonds, 19 pseudobonds, 1245 residues, 2 models selected > select #1/B:91 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/B:147@FE 1 atom, 1 residue, 1 model selected > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 43 atoms, 46 bonds, 1 residue, 1 model selected > select up 1356 atoms, 1195 bonds, 338 residues, 1 model selected > select up 5222 atoms, 4677 bonds, 1245 residues, 1 model selected > select up 14168 atoms, 13805 bonds, 2453 residues, 3 models selected > select up 14168 atoms, 13805 bonds, 2453 residues, 3 models selected > select up 14168 atoms, 13805 bonds, 2453 residues, 3 models selected > select up 14168 atoms, 13805 bonds, 2453 residues, 3 models selected > select up 14168 atoms, 13805 bonds, 2453 residues, 3 models selected > hide sel > show sel > hide sel & #!1 atoms > show sel & #!1 atoms > select #1/B:52 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 45 atoms, 45 bonds, 7 residues, 1 model selected > select up 1121 atoms, 1148 bonds, 146 residues, 1 model selected > select up 1356 atoms, 1195 bonds, 338 residues, 1 model selected > select up 5222 atoms, 4677 bonds, 1245 residues, 1 model selected > hide sel atoms > show sel atoms > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 43 atoms, 46 bonds, 1 residue, 1 model selected > select up 1356 atoms, 1195 bonds, 338 residues, 1 model selected > select up 5222 atoms, 4677 bonds, 1245 residues, 1 model selected > select down 1356 atoms, 1195 bonds, 338 residues, 1 model selected > select down 43 atoms, 46 bonds, 1 residue, 1 model selected > select up 45 atoms, 47 bonds, 2 residues, 1 model selected > select up 86 atoms, 92 bonds, 2 residues, 1 model selected > select up 88 atoms, 93 bonds, 3 residues, 1 model selected > select up 129 atoms, 138 bonds, 3 residues, 1 model selected > select up 131 atoms, 139 bonds, 4 residues, 1 model selected > select up 172 atoms, 184 bonds, 4 residues, 1 model selected > select ~sel & ##selected 5050 atoms, 4493 bonds, 10 pseudobonds, 1241 residues, 2 models selected > select ~sel 9118 atoms, 9312 bonds, 36 pseudobonds, 1212 residues, 5 models selected > select ~sel 5050 atoms, 4493 bonds, 1241 residues, 1 model selected > hide sel atoms > select ~sel 9118 atoms, 9312 bonds, 36 pseudobonds, 1212 residues, 5 models selected > combine sel Remapping chain ID 'A' in T Deoxy Hemoglobin.pdb #2 to 'E' Remapping chain ID 'B' in T Deoxy Hemoglobin.pdb #2 to 'F' Remapping chain ID 'C' in T Deoxy Hemoglobin.pdb #2 to 'G' Remapping chain ID 'D' in T Deoxy Hemoglobin.pdb #2 to 'H' Remapping chain ID 'A' in Morph - R OXY Hemoglobin.pdb #3 to 'I' Remapping chain ID 'B' in Morph - R OXY Hemoglobin.pdb #3 to 'J' Remapping chain ID 'C' in Morph - R OXY Hemoglobin.pdb #3 to 'K' Remapping chain ID 'D' in Morph - R OXY Hemoglobin.pdb #3 to 'L' > close #4 > select ~sel 13996 atoms, 13621 bonds, 20 pseudobonds, 2449 residues, 4 models selected > hide sel & #!1 atoms > select ~sel 172 atoms, 184 bonds, 16 pseudobonds, 4 residues, 2 models selected > combine sel > hide #!1 models > select add #1 5222 atoms, 4677 bonds, 26 pseudobonds, 1245 residues, 2 models selected > show #!2 models > select subtract #1 Nothing selected > select add #2 4612 atoms, 4684 bonds, 20 pseudobonds, 634 residues, 2 models selected > hide #!4 models > style sel stick Changed 4612 atom styles > style sel stick Changed 4612 atom styles > style sel sphere Changed 4612 atom styles > style sel stick Changed 4612 atom styles > show sel atoms > morph #4,2 hideModels false frames 124 rate sinusoidal Computed 125 frame morph #5 > coordset #5 1,125 > hide #!2 models > select subtract #2 Nothing selected > show #!4 models > hide #!4 models > select add #5 4334 atoms, 4444 bonds, 574 residues, 1 model selected > select ~sel 19390 atoms, 18482 bonds, 72 pseudobonds, 3698 residues, 7 models selected > select subtract #1 14168 atoms, 13805 bonds, 46 pseudobonds, 2453 residues, 5 models selected > select subtract #2 9556 atoms, 9121 bonds, 26 pseudobonds, 1819 residues, 3 models selected > select subtract #3 5222 atoms, 4677 bonds, 26 pseudobonds, 1245 residues, 2 models selected > select subtract #4 Nothing selected > select #5/D:132 9 atoms, 8 bonds, 1 residue, 1 model selected > select clear > select #5/D:132 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 136 atoms, 137 bonds, 20 residues, 1 model selected > select up 1102 atoms, 1129 bonds, 146 residues, 1 model selected > select up 4334 atoms, 4444 bonds, 574 residues, 1 model selected > select up 23724 atoms, 22926 bonds, 4272 residues, 5 models selected > show #!4 models > hide #!4 models > select add #4 23724 atoms, 22926 bonds, 26 pseudobonds, 4272 residues, 6 models selected > select subtract #3 19390 atoms, 18482 bonds, 26 pseudobonds, 3698 residues, 5 models selected > select subtract #4 14168 atoms, 13805 bonds, 2453 residues, 3 models selected > select add #2 14168 atoms, 13805 bonds, 20 pseudobonds, 2453 residues, 4 models selected > select add #1 14168 atoms, 13805 bonds, 46 pseudobonds, 2453 residues, 5 models selected > select subtract #2 9556 atoms, 9121 bonds, 26 pseudobonds, 1819 residues, 3 models selected > select subtract #1 4334 atoms, 4444 bonds, 574 residues, 1 model selected > show sel atoms > hide sel atoms > select ::name=""HEM"" 516 atoms, 552 bonds, 48 pseudobonds, 12 residues, 6 models selected > select add #4 5566 atoms, 5045 bonds, 58 pseudobonds, 1253 residues, 6 models selected > select subtract #4 344 atoms, 368 bonds, 32 pseudobonds, 8 residues, 4 models selected > hide #!5 models > select add #2 4784 atoms, 4868 bonds, 36 pseudobonds, 638 residues, 4 models selected > select subtract #2 172 atoms, 184 bonds, 16 pseudobonds, 4 residues, 2 models selected > select add #1 5222 atoms, 4677 bonds, 26 pseudobonds, 1245 residues, 2 models selected > select subtract #1 Nothing selected > show #!1 models > hide #!1 models > show #!2 models > select #2/C:61 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 137 atoms, 137 bonds, 20 residues, 1 model selected > select up 1069 atoms, 1097 bonds, 141 residues, 1 model selected > select up 1113 atoms, 1143 bonds, 143 residues, 1 model selected > select up 4612 atoms, 4684 bonds, 634 residues, 1 model selected > select up 8946 atoms, 9128 bonds, 1208 residues, 2 models selected > hide sel & #!2 atoms > show sel & #!2 atoms > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 43 atoms, 46 bonds, 1 residue, 1 model selected > select up 45 atoms, 47 bonds, 2 residues, 1 model selected > select up 86 atoms, 92 bonds, 2 residues, 1 model selected > select up 88 atoms, 93 bonds, 3 residues, 1 model selected > select up 129 atoms, 138 bonds, 3 residues, 1 model selected > select up 131 atoms, 139 bonds, 4 residues, 1 model selected > select up 172 atoms, 184 bonds, 4 residues, 1 model selected > select ~sel & ##selected 4440 atoms, 4500 bonds, 4 pseudobonds, 630 residues, 2 models selected > hide sel atoms > select ~sel & ##selected 172 atoms, 184 bonds, 16 pseudobonds, 4 residues, 2 models selected > combine sel > select add #2 4612 atoms, 4684 bonds, 20 pseudobonds, 634 residues, 2 models selected > select subtract #2 Nothing selected Cell requested for row 3 is out of bounds for table with 7 rows! Resizing table model. > hide #!6 models > hide #!2 models > show #!6 models > show #!5 models > hide #!6 models > close #5 > rename #6 id #5 > morph #4,5 hideModels false frames 124 rate sinusoidal Computed 125 frame morph #6 > coordset #6 1,125 > defattr r HEM Missing or invalid ""fileName"" argument: File 'r' does not exist > setattr r HEM color red Expected a keyword > setattr r HEM color blue Expected a keyword > setattr r HEM color Assigning HEM attribute to 4906 items Not creating attribute 'HEM'; use 'create true' to override > hide #!6 models > hide #!5 models > show #!6 models > show #!5 models > show #!4 models > hide #!4 models > hide #!5 models > hide #!6 models > show #!4 models > show #!5 models > hide #!5 models > hide #!4 models > show #!6 models > select #6/C:78 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 36 atoms, 36 bonds, 5 residues, 1 model selected > select up 1069 atoms, 1097 bonds, 141 residues, 1 model selected > select up 4334 atoms, 4444 bonds, 574 residues, 1 model selected > select ~sel & ##selected Nothing selected > hide #!6 atoms > show #!6 atoms > hide #!6 atoms > color #6 red > undo > select 28336 atoms, 27610 bonds, 92 pseudobonds, 4906 residues, 10 models selected > select clear > select ::name=""HEM"" 688 atoms, 736 bonds, 64 pseudobonds, 16 residues, 8 models selected > view sel > nucleotides #6 fill > select ::name=""HEM"" 688 atoms, 736 bonds, 64 pseudobonds, 16 residues, 8 models selected > hide #!6 models > show #!5 models > select up 19668 atoms, 18722 bonds, 64 pseudobonds, 3758 residues, 8 models selected > select add #4 19668 atoms, 18722 bonds, 74 pseudobonds, 3758 residues, 8 models selected > select subtract #4 14446 atoms, 14045 bonds, 48 pseudobonds, 2513 residues, 6 models selected > combine sel Remapping chain ID 'A' in T Deoxy Hemoglobin.pdb #2 to 'E' Remapping chain ID 'B' in T Deoxy Hemoglobin.pdb #2 to 'F' Remapping chain ID 'C' in T Deoxy Hemoglobin.pdb #2 to 'G' Remapping chain ID 'D' in T Deoxy Hemoglobin.pdb #2 to 'H' Remapping chain ID 'A' in copy of T Deoxy Hemoglobin.pdb #5 to 'I' Remapping chain ID 'B' in copy of T Deoxy Hemoglobin.pdb #5 to 'J' Remapping chain ID 'C' in copy of T Deoxy Hemoglobin.pdb #5 to 'K' Remapping chain ID 'D' in copy of T Deoxy Hemoglobin.pdb #5 to 'L' Called accessibilityLabel on invalid object: 2157867720 > hide #!5 models > select add #5 14446 atoms, 14045 bonds, 52 pseudobonds, 2513 residues, 6 models selected > select subtract #5 9834 atoms, 9361 bonds, 32 pseudobonds, 1879 residues, 4 models selected > hide #!7 models > show #!7 models > undo > close #7 > select add #2 9834 atoms, 9361 bonds, 36 pseudobonds, 1879 residues, 4 models selected > select add #1 9834 atoms, 9361 bonds, 46 pseudobonds, 1879 residues, 4 models selected > select subtract #2 5222 atoms, 4677 bonds, 26 pseudobonds, 1245 residues, 2 models selected > select subtract #1 Nothing selected > show #!5 models > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 43 atoms, 46 bonds, 1 residue, 1 model selected > select up 1167 atoms, 1199 bonds, 148 residues, 1 model selected > select up 4612 atoms, 4684 bonds, 634 residues, 1 model selected > select up 28336 atoms, 27610 bonds, 4906 residues, 6 models selected > select down 4612 atoms, 4684 bonds, 634 residues, 1 model selected > select up 4612 atoms, 4684 bonds, 634 residues, 1 model selected > select up 28336 atoms, 27610 bonds, 4906 residues, 6 models selected > select down 4612 atoms, 4684 bonds, 634 residues, 1 model selected > select up 4612 atoms, 4684 bonds, 634 residues, 1 model selected Drag select of 21 residues > select subtract #5/A:82 157 atoms, 20 residues, 1 model selected > select up 533 atoms, 542 bonds, 70 residues, 1 model selected > select up 2192 atoms, 2250 bonds, 287 residues, 1 model selected > select up 2309 atoms, 2342 bonds, 320 residues, 1 model selected > select up 4612 atoms, 4684 bonds, 634 residues, 1 model selected > select up 4612 atoms, 4684 bonds, 634 residues, 1 model selected > select up 4612 atoms, 4684 bonds, 634 residues, 1 model selected > combine sel > hide #!7 models > hide #!5 models > show #!7 models > select add #5 4612 atoms, 4684 bonds, 20 pseudobonds, 634 residues, 2 models selected > select subtract #5 Nothing selected > show #!3 models > hide #!7 models > hide #!3 models > show #!6 models > hide #!6 models > show #!4 models > select #4/D:87 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 89 atoms, 90 bonds, 11 residues, 1 model selected > select up 1124 atoms, 1151 bonds, 146 residues, 1 model selected > select up 1366 atoms, 1198 bonds, 345 residues, 1 model selected > select up 5222 atoms, 4677 bonds, 1245 residues, 1 model selected > select up 32948 atoms, 32294 bonds, 5540 residues, 7 models selected > select down 5222 atoms, 4677 bonds, 1245 residues, 1 model selected > select up 5222 atoms, 4677 bonds, 1245 residues, 1 model selected > combine sel > hide #!4 models > select add #4 5222 atoms, 4677 bonds, 26 pseudobonds, 1245 residues, 2 models selected > select subtract #4 Nothing selected > show #!7 models > hide #!7 models > hide #!8 models > morph #7,8 hideModels false frames 124 rate sinusoidal Computed 125 frame morph #9 > coordset #9 1,125 > close #9 > show #!3 models > hide #!3 models > show #!3 models > select #3/B:34 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 99 atoms, 99 bonds, 14 residues, 1 model selected > select up 1098 atoms, 1125 bonds, 146 residues, 1 model selected > select up 4334 atoms, 4444 bonds, 574 residues, 1 model selected > select up 38170 atoms, 36971 bonds, 6785 residues, 8 models selected > select down 4334 atoms, 4444 bonds, 574 residues, 1 model selected > hide sel atoms > hide #!3 models > select subtract #3 Nothing selected > save ""/Users/zachpilon/Desktop/ZackPilon W25/Hemoglobin red blue all parts > move no hem.cxs"" > show #!8 models > show #!7 models > hide #!7 models > show #!7 models > ui tool show ""Render/Select by Attribute"" > toolshed show > select ::name=""HEM"" 1032 atoms, 1104 bonds, 96 pseudobonds, 24 residues, 12 models selected > select add #5 5472 atoms, 5604 bonds, 100 pseudobonds, 654 residues, 12 models selected > select subtract #5 860 atoms, 920 bonds, 80 pseudobonds, 20 residues, 10 models selected > select add #4 5910 atoms, 5413 bonds, 90 pseudobonds, 1261 residues, 10 models selected > select subtract #4 688 atoms, 736 bonds, 64 pseudobonds, 16 residues, 8 models selected > select add #2 5128 atoms, 5236 bonds, 68 pseudobonds, 646 residues, 8 models selected > select subtract #2 516 atoms, 552 bonds, 48 pseudobonds, 12 residues, 6 models selected > select add #1 5566 atoms, 5045 bonds, 58 pseudobonds, 1253 residues, 6 models selected > select subtract #1 344 atoms, 368 bonds, 32 pseudobonds, 8 residues, 4 models selected > show #!4 models > show #!5 models > hide #!7 models > hide #!8 models > hide #!5 models > show #!5 models > hide #!5 models > close #7 > close #8 > show #!3 models > hide #!3 models > show #!5 models > hide #!5 models > hide #!4 models > show #!6 models > morph #4,5 frames 124 rate sinusoidal Computed 125 frame morph #7 > coordset #7 1,125 > hide #!6 models > hide #!7 models > save ""/Users/zachpilon/Desktop/ZackPilon W25/Hemoglobin red blue all parts > move no hem.cxs"" ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-23.0.22 OpenGL renderer: Intel(R) UHD Graphics 630 OpenGL vendor: Intel Inc. Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: Mac mini Model Identifier: Macmini8,1 Processor Name: 6-Core Intel Core i5 Processor Speed: 3 GHz Number of Processors: 1 Total Number of Cores: 6 L2 Cache (per Core): 256 KB L3 Cache: 9 MB Memory: 8 GB System Firmware Version: 2069.40.2.0.0 (iBridge: 22.16.11072.0.0,0) OS Loader Version: 582~2132 Software: System Software Overview: System Version: macOS 15.1 (24B83) Kernel Version: Darwin 24.1.0 Time since boot: 5 days, 4 hours, 36 minutes Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0000 Metal Support: Metal 3 Displays: VG270: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: TEGAA003851S Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Adapter Type: DVI or HDMI Adapter Firmware Version: 2.19 Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 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: 2.3 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: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 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: 1.4.1 ChimeraX-Hbonds: 2.5 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: 1.2.1 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: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 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-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 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 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: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 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: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 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: 1.18.1 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 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: 1.41 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: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 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: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 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: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Core can't reproduce Tom Goddard Greg Couch all ChimeraX