id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16347 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.6.1-arm64-arm-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. I have a bunch of programs open, I was working on a different one when ChimeraX crashed. Fatal Python error: Segmentation fault Current thread 0x00000001f8474f40 (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.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 57) {""app_name"":""ChimeraX"",""timestamp"":""2024-11-20 12:57:49.00 -0800"",""app_version"":""1.8.0"",""slice_uuid"":""17982d98-65bc-3327-8526-577ec996453c"",""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 14.6.1 (23G93)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""48D858B6-3694-4F29-A68B-FA057519E96C""} { ""uptime"" : 820000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""Mac15,10"", ""coalitionID"" : 75879, ""osVersion"" : { ""train"" : ""macOS 14.6.1"", ""build"" : ""23G93"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2024-11-20 12:57:42.0176 -0800"", ""codeSigningMonitor"" : 1, ""incident"" : ""48D858B6-3694-4F29-A68B-FA057519E96C"", ""pid"" : 98195, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2024-11-18 14:25:58.9385 -0800"", ""procStartAbsTime"" : 18559191883898, ""procExitAbsTime"" : 19767044176037, ""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"":""E86FC26C-28CC-5EEB-A07C-067736B39E4C"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""757FF526-C3CD-C48D-1A97-DEC7F6A548D6"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""instructionByteStream"" : {""beforePC"":""fyMD1f17v6n9AwCRd+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A=="",""atPC"":""AwEAVH8jA9X9e7+p\/QMAkWzg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g==""}, ""wakeTime"" : 11697, ""sleepWakeUUID"" : ""826F9A8A-CBA9-4BA1-BA63-7DD9BAD0C892"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x3b95400ca528 is not in any region. 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unallocated=7.7G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 512K 4 \nActivity Tracing 256K 1 \nCG image 1744K 78 \nColorSync 656K 31 \nCoreAnimation 4416K 252 \nCoreGraphics 96K 6 \nCoreServices 624K 2 \nCoreUI image data 5888K 62 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 6.8G 200 \nMALLOC guard page 192K 12 \nMALLOC_LARGE (reserved) 122.0M 1 reserved VM address space (unallocated)\nMach message 64K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 816K 51 \nStack 162.3M 52 \nStack Guard 56.0M 1 \nVM_ALLOCATE 358.8M 415 \nVM_ALLOCATE (reserved) 320.0M 4 reserved VM address space (unallocated)\n__AUTH 2210K 407 \n__AUTH_CONST 31.9M 626 \n__CTF 824 1 \n__DATA 21.9M 771 \n__DATA_CONST 42.5M 782 \n__DATA_DIRTY 2032K 234 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 554.0M 151 \n__OBJC_RO 71.9M 1 \n__OBJC_RW 2200K 1 \n__TEXT 939.3M 799 \ndyld private memory 272K 2 \nmapped file 595.6M 121 \nshared memory 3280K 33 \n=========== ======= ======= \nTOTAL 10.0G 5113 \nTOTAL, minus reserved VM space 9.6G 5113 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""dc33f7fa6a1e3bcffcdfeaa4db4e8813ced7b940"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""642da32dea3b2418c750f848"", ""factorPackIds"" : { }, ""deploymentId"" : 240000004 }, { ""rolloutId"" : ""648a2601f74c42732876cb5b"", ""factorPackIds"" : { ""SIRI_TEXT_TO_SPEECH"" : ""6733fcb357a33f0bf26912cf"" }, ""deploymentId"" : 240000272 } ], ""experiments"" : [ { ""treatmentId"" : ""45f4e2a5-551b-4bc2-a2dc-19c244dda8f8"", ""experimentId"" : ""6643969b3099cf28e049862f"", ""deploymentId"" : 400000007 } ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/will/Documents/Marletta_Lab/Houghton/Kim_Paper/Kim_Work/Open/Cyc_Open_Files/Ms_sGC_BC122S_Ext_85pix.mrc Opened Ms_sGC_BC122S_Ext_85pix.mrc as #1, grid size 320,320,320, pixel 0.85, shown at level 0.091, step 2, values float32 > 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 white > set bgColor white > volume #1 color #00efff98 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #1 step 1 > volume #1 level 0.1879 > volume #1 level 0.4786 > open > /Users/will/Documents/Marletta_Lab/Houghton/Kim_Paper/Kim_Work/Closed/Unliganded_Closed_Files/J85_J92_combined.mrc Opened J85_J92_combined.mrc as #2, grid size 320,320,320, pixel 0.942, shown at level 0.00381, step 2, values float32 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #2 step 1 > volume #2 level 0.9596 > volume #2 color #ff14f199 > open > /Users/will/Documents/Marletta_Lab/Crystallography/XRD/Phenix/Ms_sGC_C122S_cyc_20240415/RealSpaceRefine_8/KAH_Tinker_SM_C122S_Ext_Fit_Unsharpened_85px- > Backbone_Trace_Done-coot-3_real_space_refined_008.pdb Chain information for KAH_Tinker_SM_C122S_Ext_Fit_Unsharpened_85px- Backbone_Trace_Done-coot-3_real_space_refined_008.pdb #3 --- Chain | Description A | No description available B | No description available > open > /Users/will/Documents/Marletta_Lab/Crystallography/XRD/Phenix/Ms_sGC_C122S_20231023/RealSpaceRefine_53/HNOX_C122S-WCTedits3_real_space_refined_053-coot-0.pdb Chain information for HNOX_C122S-WCTedits3_real_space_refined_053-coot-0.pdb #4 --- Chain | Description A | No description available B | No description available > save > /Users/will/Documents/Marletta_Lab/Presentations/Group_Meeting/20241121_meeting/Grpmeeting_maps.cxs > hide #!3 models > show #!3 models > hide #!4 models > hide #!3 models > volume #1 level 0.5087 > volume #1 level 0.4786 > save > /Users/will/Documents/Marletta_Lab/Presentations/Group_Meeting/20241121_meeting/active_J287.png > width 1111 height 786 supersample 3 > hide #!1 models > show #!4 models > hide #!4 models > show #!2 models > save > /Users/will/Documents/Marletta_Lab/Presentations/Group_Meeting/20241121_meeting/Chimera_Images/inactive.png > width 1111 height 786 supersample 3 > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!1 models > hide #!2 models > show #!3 models > volume #1 level 0.4886 > close #4 > open > /Users/will/Documents/Marletta_Lab/Crystallography/XRD/Phenix/Ms_sGC_C122S_cyc_20240415/RealSpaceRefine_8/KAH_Tinker_SM_C122S_Ext_Fit_Unsharpened_85px- > Backbone_Trace_Done-coot-4.pdb Chain information for KAH_Tinker_SM_C122S_Ext_Fit_Unsharpened_85px- Backbone_Trace_Done-coot-4.pdb #4 --- Chain | Description A | No description available B | No description available > open > /Users/will/Documents/Marletta_Lab/Crystallography/XRD/Phenix/Ms_sGC_C122S_20231023/RealSpaceRefine_53/HNOX_C122S-WCTedits3_real_space_refined_053-coot-0.pdb Chain information for HNOX_C122S-WCTedits3_real_space_refined_053-coot-0.pdb #5 --- Chain | Description A | No description available B | No description available > open > /Users/will/Documents/Marletta_Lab/Crystallography/XRD/Phenix/Ms_sGC_C122S_cyc_20240415/RealSpaceRefine_8/KAH_Tinker_SM_C122S_Ext_Fit_Unsharpened_85px- > Backbone_Trace_Done-coot-4.pdb Chain information for KAH_Tinker_SM_C122S_Ext_Fit_Unsharpened_85px- Backbone_Trace_Done-coot-4.pdb #6 --- Chain | Description A | No description available B | No description available > hide #!5 models > show #!5 models > hide #!5 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!3 models > hide #!4 models > show #!4 models > close #6 > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > close #3 > hide #!1 models > select #4/C 32 atoms, 34 bonds, 1 residue, 1 model selected > color sel forest green > color sel byhetero > ui mousemode right select > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 56 atoms, 60 bonds, 1 residue, 1 model selected > color sel purple > color sel byhetero > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 43 atoms, 46 bonds, 1 residue, 1 model selected > color sel dark gray > color sel byhetero > select clear > save > /Users/will/Documents/Marletta_Lab/Presentations/Group_Meeting/20241121_meeting/Grpmeeting_maps.cxs > show #!2 models > hide #!2 models > show #!1 models > hide #!1 models > select clear > select #4/C and #4/B:601-602 Expected a keyword > select #4/C or #4/B:601-602 Expected a keyword > select #4/C or /B:601-602 Expected a keyword > select #4/C or select #4/B:601-602 Expected a keyword > select #4/C,#4/B:601-602 Expected an objects specifier or a keyword > select #4/C/B:601-602 131 atoms, 140 bonds, 4 pseudobonds, 3 residues, 2 models selected > name frozen ligands sel > show #!1 models > ui tool show ""Color Zone"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > color zone #1 near #4 distance 5.1 > color single #1 > color zone #1 near sel distance 5.1 > color zone #1 near sel distance 1.25 > color zone #1 near sel distance 1.23 > color zone #1 near sel distance 1.21 > color zone #1 near sel distance 1.23 > volume #1 level 0.5925 > color zone #1 near sel distance 1.24 > color zone #1 near sel distance 2.84 > volume splitbyzone #1 Opened Ms_sGC_BC122S_Ext_85pix.mrc 0 as #3.1, grid size 320,320,320, pixel 0.85, shown at level 0.592, step 1, values float32 Opened Ms_sGC_BC122S_Ext_85pix.mrc 1 as #3.2, grid size 320,320,320, pixel 0.85, shown at level 0.592, step 1, values float32 Opened Ms_sGC_BC122S_Ext_85pix.mrc 2 as #3.3, grid size 320,320,320, pixel 0.85, shown at level 0.592, step 1, values float32 Opened Ms_sGC_BC122S_Ext_85pix.mrc 3 as #3.4, grid size 320,320,320, pixel 0.85, shown at level 0.592, step 1, values float32 Opened Ms_sGC_BC122S_Ext_85pix.mrc 4 as #3.5, grid size 320,320,320, pixel 0.85, shown at level 0.592, step 1, values float32 Opened Ms_sGC_BC122S_Ext_85pix.mrc 5 as #3.6, grid size 320,320,320, pixel 0.85, shown at level 0.592, step 1, values float32 Opened Ms_sGC_BC122S_Ext_85pix.mrc 6 as #3.7, grid size 320,320,320, pixel 0.85, shown at level 0.592, step 1, values float32 Opened Ms_sGC_BC122S_Ext_85pix.mrc 7 as #3.8, grid size 320,320,320, pixel 0.85, shown at level 0.592, step 1, values float32 Opened Ms_sGC_BC122S_Ext_85pix.mrc 8 as #3.9, grid size 320,320,320, pixel 0.85, shown at level 0.592, step 1, values float32 Opened Ms_sGC_BC122S_Ext_85pix.mrc 9 as #3.10, grid size 320,320,320, pixel 0.85, shown at level 0.592, step 1, values float32 > close #3.10 > close #3.8 > close #3.7 > close #3.6 > close #3.5 > close #3.4 > close #3.3 > close #3.9 > close #3 > show #!1 models > color single #1 > hide #!1 models > select clear > select #4/B:601@CBD 1 atom, 1 residue, 1 model selected > select #4/B:601@CBD 1 atom, 1 residue, 1 model selected > select up 43 atoms, 46 bonds, 1 residue, 1 model selected > select up 4459 atoms, 4553 bonds, 560 residues, 1 model selected > color sel gray > undo > select down 43 atoms, 46 bonds, 1 residue, 1 model selected > color sel gray > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 56 atoms, 60 bonds, 1 residue, 1 model selected > color sel purple > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 32 atoms, 34 bonds, 1 residue, 1 model selected > color sel forest green > select #4/C/B:601-602 131 atoms, 140 bonds, 4 pseudobonds, 3 residues, 2 models selected > show #!1 models > color zone #1 near sel distance 2.84 > color zone #1 near sel distance 2.94 > color zone #1 near sel distance 2.84 > color zone #1 near sel distance 2.8 > color zone #1 near sel distance 2.85 > color zone #1 near sel distance 2.8 > color zone #1 near sel distance 2.86 > volume splitbyzone #1 Opened Ms_sGC_BC122S_Ext_85pix.mrc 0 as #3.1, grid size 320,320,320, pixel 0.85, shown at level 0.592, step 1, values float32 Opened Ms_sGC_BC122S_Ext_85pix.mrc 1 as #3.2, grid size 320,320,320, pixel 0.85, shown at level 0.592, step 1, values float32 Opened Ms_sGC_BC122S_Ext_85pix.mrc 2 as #3.3, grid size 320,320,320, pixel 0.85, shown at level 0.592, step 1, values float32 Opened Ms_sGC_BC122S_Ext_85pix.mrc 3 as #3.4, grid size 320,320,320, pixel 0.85, shown at level 0.592, step 1, values float32 > select clear > transparency #4#3.2-4#!3 60 > color #4#3.2-4#!3 byhetero > save > /Users/will/Documents/Marletta_Lab/Presentations/Group_Meeting/20241121_meeting/Grpmeeting_maps.cxs > includeMaps true > save > /Users/will/Documents/Marletta_Lab/Presentations/Group_Meeting/20241121_meeting/Chimera_Images/active_G2P.png > width 1136 height 786 supersample 3 > hide #!3.3 models > save > /Users/will/Documents/Marletta_Lab/Presentations/Group_Meeting/20241121_meeting/Chimera_Images/inactive_heme.png > width 1136 height 786 supersample 3 > show #!3.3 models > hide #!3.2 models > save > /Users/will/Documents/Marletta_Lab/Presentations/Group_Meeting/20241121_meeting/Chimera_Images/inactive_cyc.png > width 1136 height 786 supersample 3 > save > /Users/will/Documents/Marletta_Lab/Presentations/Group_Meeting/20241121_meeting/Chimera_Images/inactive_cyc2.png > width 1136 height 786 supersample 3 > save > /Users/will/Documents/Marletta_Lab/Presentations/Group_Meeting/20241121_meeting/Chimera_Images/inactive_cyc3.png > width 1136 height 786 supersample 3 > show #!1 models > hide #!3.3 models > hide #!3 models > hide #!3.4 models > hide #!4 models > show #!4 models > show #!3.4 models > hide #!3.4 models > show #!3.3 models > hide #!3.3 models > hide #!3 models > hide #!1 models > show #!1 models > color single #1 > volume #1 level 0.441 > save > /Users/will/Documents/Marletta_Lab/Presentations/Group_Meeting/20241121_meeting/Chimera_Images/inactive_with_model.png > width 1136 height 786 supersample 3 > show #!3.4 models > volume #1 level 0.5384 > volume #3.4 level 0.4535 > volume #3.1 level 0.7548 > volume #3.1 level 0.4626 > volume #3.1 level 0.5275 > volume #1 level 0.6249 > save > /Users/will/Documents/Marletta_Lab/Presentations/Group_Meeting/20241121_meeting/Chimera_Images/active_G2P_over.png > width 1136 height 786 supersample 3 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > open > /Users/will/Documents/Marletta_Lab/SAXS/10_24/Marletta_10_02_24/Ms_sGC_bin2/DENSS/C122S_nolig/C122S_nolig_refine_aligned.mrc Opened C122S_nolig_refine_aligned.mrc as #6, grid size 64,64,64, pixel 6.33, shown at level 0.000834, step 1, values float32 > open > /Users/will/Documents/Marletta_Lab/SAXS/10_24/Marletta_10_02_24/Ms_sGC_bin2/DENSS/C122S_nolig/8hbe_centered.pdb Chain information for 8hbe_centered.pdb #7 --- Chain | Description A | No description available B | No description available > volume #6 color #b2ffb2aa > volume #6 color #b2ffb2ab > volume #6 level 0.006581 > open > /Users/will/Documents/Marletta_Lab/SAXS/10_24/Marletta_10_02_24/Ms_sGC_bin2/DENSS/C122S_cyc/C122S_cyc_refine_aligned.mrc Opened C122S_cyc_refine_aligned.mrc as #8, grid size 64,64,64, pixel 6.33, shown at level 0.000719, step 1, values float32 > volume #8 level 0.005941 > volume #8 color #e5bf99a8 > volume #6 level 0.0153 > volume #8 level 0.007477 > select add #8 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #8,-0.39844,0.90908,0.12177,14.843,0.89861,0.36032,0.25034,-7.65,0.1837,0.20916,-0.96047,-13.123 > view matrix models > #8,0.55373,0.76355,0.33222,4.7091,0.67378,-0.64529,0.36003,-1.0228,0.48928,0.024486,-0.87178,-15.813 > view matrix models > #8,-0.35769,0.9313,-0.068832,13.28,0.88889,0.36214,0.28058,-7.3795,0.28623,0.039175,-0.95736,-13.81 > view matrix models > #8,0.14553,0.98158,0.12378,7.93,0.93262,-0.17786,0.31399,-5.9744,0.33023,0.069741,-0.94132,-14.368 > ui mousemode right ""translate selected models"" > view matrix models > #8,0.14553,0.98158,0.12378,2.1043,0.93262,-0.17786,0.31399,-11.166,0.33023,0.069741,-0.94132,-0.96409 > view matrix models > #8,0.14553,0.98158,0.12378,-0.35155,0.93262,-0.17786,0.31399,-15.366,0.33023,0.069741,-0.94132,0.5689 > view matrix models > #8,0.14553,0.98158,0.12378,0.2831,0.93262,-0.17786,0.31399,-6.1745,0.33023,0.069741,-0.94132,-2.0622 > view matrix models > #8,0.14553,0.98158,0.12378,0.39841,0.93262,-0.17786,0.31399,-3.703,0.33023,0.069741,-0.94132,-8.6659 > select subtract #8 Nothing selected > show #!3.1 models > hide #!3.1 models > hide #!1 models > show #!2 models > hide #!3.4 models > show #!3.4 models > hide #!3.4 models > hide #!4 models > hide #!6 models > hide #!7 models > hide #!8 models > show #!4 models > hide #!4 models > show #!5 models > color #5 #15fd1fff > color #5 #3ae9fdff > save > /Users/will/Documents/Marletta_Lab/Presentations/Group_Meeting/20241121_meeting/Chimera_Images/inactive_with_model.png > width 1136 height 786 supersample 3 > ui mousemode right clip > ui mousemode right zone > ui tool show ""Side View"" > save > /Users/will/Documents/Marletta_Lab/Presentations/Group_Meeting/20241121_meeting/Chimera_Images/inactive_empty_basket.png > width 1136 height 786 supersample 3 > select #5/C/B:601 75 atoms, 78 bonds, 4 pseudobonds, 1 residue, 2 models selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > ui tool show ""Surface Color"" > color (#!5 & sel) gray > ui tool show ""Surface Color"" > ui tool show ""Surface Zone"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > surface zone #2 nearAtoms #5 distance 5.65 > surface zone #2 nearAtoms sel distance 5.65 > surface zone #2 nearAtoms sel distance 4.45 > surface zone #2 nearAtoms sel distance 1.95 > color (#!5 & sel) gray > surface unzone #2 > surface zone #2 nearAtoms sel distance 1.95 > surface unzone #2 > ui tool show ""Surface Zone"" > ui tool show ""Surface Color"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > ui tool show ""Color Zone"" > color zone #2 near #5 distance 1.8 > color single #2 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > color zone #2 near sel distance 1.8 > volume splitbyzone #2 Opened J85_J92_combined.mrc 0 as #9.1, grid size 320,320,320, pixel 0.942, shown at level 0.96, step 1, values float32 Opened J85_J92_combined.mrc 1 as #9.2, grid size 320,320,320, pixel 0.942, shown at level 0.96, step 1, values float32 > hide #!9.2 models > show #!9.2 models > hide #!9.1 models > show #!9.1 models > color (#!5 & sel) forest green > color (#!5 & sel) byhetero > color #9 #b2b2b293 models > color #9 #b2b2b294 models > hide #!9.1 models > show #!9.1 models > color #9 #b2b2b2ff models > color #9.1 #ff00f9ff models > color #9.1 #ff00f998 models > color #9.1 #ff00f980 models > color #9.2 #80808098 models > color #9.2 #80808099 models > hide #!9.1 models > select clear > color #5#9.2#!3,9 byhetero > save > /Users/will/Documents/Marletta_Lab/Presentations/Group_Meeting/20241121_meeting/Chimera_Images/inactive_heme.png > width 905 height 786 supersample 3 > show #!7 models > show #!6 models > show #!8 models > open > /Users/will/Documents/Marletta_Lab/SAXS/10_24/Marletta_10_02_24/Ms_sGC_bin2/DENSS/C122S_G2P_cyc_BIFT/C122S_G2P_cyc2_refine_aligned.mrc Opened C122S_G2P_cyc2_refine_aligned.mrc as #10, grid size 64,64,64, pixel 8.73, shown at level 2.46e-05, step 1, values float32 > volume #10 level 0.004475 > volume #10 color #b2b2b2b0 > hide #!7 models > show #!7 models > hide #!6 models > hide #!5 models > hide #!8 models > select add #10 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #10,-0.83853,-0.54423,0.026125,2.3156,-0.54441,0.83882,0.00026625,0.69237,-0.022059,-0.013999,-0.99966,1.8163 > view matrix models > #10,-0.94876,0.049305,0.31212,-0.88255,0.032066,0.99768,-0.06013,0.070151,-0.31436,-0.047041,-0.94814,1.8792 > view matrix models > #10,-0.99341,0.11247,-0.022269,-0.90955,0.11405,0.98927,-0.091359,0.15437,0.011755,-0.093297,-0.99557,2.2101 > view matrix models > #10,-0.98932,0.13523,-0.054441,-0.99286,0.13998,0.98551,-0.095802,0.18167,0.040697,-0.1024,-0.99391,2.259 > open /Users/will/Documents/Marletta_Lab/sGC/Msexta_sGC/PDB_Files/8hbf.pdb 8hbf.pdb title: Structure of human soluble guanylate cyclase In the No+rio state At 3.1 angstrom [more info...] Chain information for 8hbf.pdb #11 --- Chain | Description | UniProt A | guanylate cyclase soluble subunit α-1 | GCYA1_HUMAN 1-690 B | guanylate cyclase soluble subunit β-1 | GCYB1_HUMAN 1-619 Non-standard residues in 8hbf.pdb #11 --- G2P — phosphomethylphosphonic acid guanylate ester GZO — methyl ~{N}-[4,6-bis(azanyl)-2-[1-[(2-fluorophenyl)methyl]pyrazolo[3,4-B]pyridin-3-yl]pyrimidin-5-yl]-~{N}-methyl- carbamate HEM — protoporphyrin IX containing Fe (HEME) MG — magnesium ion NO — nitric oxide (nitrogen monoxide) 2 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > select add #11 8446 atoms, 8614 bonds, 25 pseudobonds, 1101 residues, 5 models selected > select subtract #10 8446 atoms, 8614 bonds, 25 pseudobonds, 1101 residues, 3 models selected > view matrix models > #11,-0.63869,0.66485,-0.38737,189.88,0.70973,0.70349,0.037211,-62.878,0.29725,-0.25116,-0.92117,260.87 > ui mousemode right ""translate selected models"" > view matrix models > #11,-0.63869,0.66485,-0.38737,187.72,0.70973,0.70349,0.037211,-192.52,0.29725,-0.25116,-0.92117,99.205 > view matrix models > #11,-0.63869,0.66485,-0.38737,57.146,0.70973,0.70349,0.037211,-179.24,0.29725,-0.25116,-0.92117,123.08 > ui mousemode right ""rotate selected models"" > view matrix models > #11,-0.80429,-0.59423,0.00041531,184.55,-0.52833,0.71541,0.45722,-73.435,-0.272,0.36752,-0.88935,116.65 > view matrix models > #11,0.85758,0.06966,-0.50962,-51.109,0.25894,-0.91455,0.31073,47.886,-0.44442,-0.39844,-0.80233,224.61 > view matrix models > #11,0.96296,0.22257,-0.15219,-134.65,0.26528,-0.88302,0.38717,32.341,-0.048215,-0.41321,-0.90936,188.3 > ui mousemode right ""translate selected models"" > view matrix models > #11,0.96296,0.22257,-0.15219,-133.9,0.26528,-0.88302,0.38717,26.842,-0.048215,-0.41321,-0.90936,183.82 > volume #10 level 0.007047 > view matrix models > #11,0.96296,0.22257,-0.15219,-129.78,0.26528,-0.88302,0.38717,13.912,-0.048215,-0.41321,-0.90936,169.98 > ui mousemode right ""rotate selected models"" > view matrix models > #11,0.94568,-0.30285,-0.11821,-65.669,-0.21364,-0.85297,0.47623,61.895,-0.24506,-0.4251,-0.87134,192.58 > view matrix models > #11,0.97242,0.23321,-0.0034054,-153.22,0.18478,-0.76141,0.62138,-23.477,0.14232,-0.60487,-0.7835,151.08 > select subtract #11 Nothing selected > hide #!11 models > show #!11 models > hide #!11 models > show #!8 models > hide #!10 models > ui tool show ""Fit in Map"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > hide #!7 models > show #!7 models The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > show #!6 models > hide #!8 models > hide #!6 models > show #!6 models > volume #6 level 0.01061 Opened 8hbe_centered.pdb map 5 as #12, grid size 56,68,101, pixel 1.67, shown at level 0.1, step 1, values float32 > fitmap #7 inMap #6 resolution 5 Fit map 8hbe_centered.pdb map 5 in map C122S_nolig_refine_aligned.mrc using 32943 points correlation = 0.7722, correlation about mean = 0.02628, overlap = 284.2 steps = 68, shift = 3.96, angle = 5.47 degrees Position of 8hbe_centered.pdb map 5 (#12) relative to C122S_nolig_refine_aligned.mrc (#6) coordinates: Matrix rotation and translation 0.99821929 -0.05963242 -0.00148866 1.98975524 0.05957753 0.99544092 0.07448421 -0.23286547 -0.00295980 -0.07444027 0.99722108 3.41000515 Axis -0.78066563 0.00771176 0.62490136 Axis point 0.00000000 40.76298503 5.68103763 Rotation angle (degrees) 5.47336510 Shift along axis 0.57578752 Average map value = 0.02434 for 8610 atoms, 1297 outside contour > hide #!7 models > show #!7 models > show #!8 models > fitmap #8 inMap #12 Fit map C122S_cyc_refine_aligned.mrc in map 8hbe_centered.pdb map 5 using 1800 points correlation = 0.5271, correlation about mean = 0.1255, overlap = 4.607 steps = 164, shift = 5.96, angle = 14.9 degrees Position of C122S_cyc_refine_aligned.mrc (#8) relative to 8hbe_centered.pdb map 5 (#12) coordinates: Matrix rotation and translation 0.00119032 0.99985513 -0.01697929 0.58507699 0.90747006 0.00605324 0.42007314 -2.49405624 0.42011507 -0.01590822 -0.90733139 -6.83424330 Axis -0.69842784 -0.70021082 -0.14799786 Axis point 2.27774967 0.00000000 -2.89915643 Rotation angle (degrees) 161.81318786 Shift along axis 2.34918445 > hide #!6 models > show #!11 models > hide #!11 models > show #!11 models > ui mousemode right ""move picked models"" > select add #11 8446 atoms, 8614 bonds, 25 pseudobonds, 1101 residues, 3 models selected > view matrix models > #11,0.97242,0.23321,-0.0034054,-149.98,0.18478,-0.76141,0.62138,-26.343,0.14232,-0.60487,-0.7835,165.66 > ui mousemode right ""rotate selected models"" > view matrix models > #11,0.42126,-0.85269,0.30896,17.774,-0.90474,-0.41881,0.077733,152.55,0.063113,-0.31227,-0.94789,162.24 > view matrix models > #11,0.95358,0.26424,0.14446,-172.08,0.13751,-0.80882,0.57176,-7.0489,0.26793,-0.52535,-0.8076,142.11 > view matrix models > #11,0.10425,-0.98861,-0.10856,135.97,-0.99454,-0.10414,-0.0067043,136.56,-0.0046779,0.10866,-0.99407,124.48 > view matrix models > #11,0.98331,-0.17011,-0.064475,-91.811,-0.16072,-0.97838,0.13016,116.26,-0.085222,-0.11762,-0.98939,163.3 > ui mousemode right ""translate selected models"" > view matrix models > #11,0.98331,-0.17011,-0.064475,-91.758,-0.16072,-0.97838,0.13016,132.58,-0.085222,-0.11762,-0.98939,176.91 > ui mousemode right ""rotate selected models"" > view matrix models > #11,0.98334,-0.16998,-0.064396,-91.788,-0.16066,-0.97847,0.12955,132.67,-0.08503,-0.11704,-0.98948,176.82 Opened 8hbf.pdb map 5 as #13, grid size 50,76,101, pixel 1.67, shown at level 0.101, step 1, values float32 Opened 8hbf.pdb map 5 as #14, grid size 50,76,101, pixel 1.67, shown at level 0.101, step 1, values float32 > fitmap #11 inMap #12 resolution 5 Fit map 8hbf.pdb map 5 in map 8hbe_centered.pdb map 5 using 32157 points correlation = 0.6743, correlation about mean = 0.1197, overlap = 2513 steps = 2000, shift = 13.3, angle = 36.1 degrees Position of 8hbf.pdb map 5 (#14) relative to 8hbe_centered.pdb map 5 (#12) coordinates: Matrix rotation and translation 0.75669742 -0.62005543 -0.20722035 16.04564334 -0.65034173 -0.74631724 -0.14165523 215.62017722 -0.06681803 0.24195419 -0.96798426 116.30544316 Axis 0.93650708 -0.34276471 -0.07393805 Axis point 0.00000000 104.59522449 69.42301043 Rotation angle (degrees) 168.18170472 Shift along axis -67.47952656 Average map value = 0.2319 for 8381 atoms, 3371 outside contour > show #!10 models > select subtract #11 Nothing selected > fitmap #10 inMap #14 Fit map C122S_G2P_cyc2_refine_aligned.mrc in map 8hbf.pdb map 5 using 650 points correlation = 0.6168, correlation about mean = 0.3939, overlap = 2.12 steps = 136, shift = 2.16, angle = 4.56 degrees Position of C122S_G2P_cyc2_refine_aligned.mrc (#10) relative to 8hbf.pdb map 5 (#14) coordinates: Matrix rotation and translation -0.90689824 -0.42099990 0.01716624 134.62497110 0.40917528 -0.88968597 -0.20256965 142.85406676 0.10055437 -0.17668606 0.97911739 147.19850089 Axis 0.03100745 -0.09989544 0.99451468 Axis point 47.81607757 93.15540942 0.00000000 Rotation angle (degrees) 155.33090072 Shift along axis 136.29497662 > fitmap #10 inMap #14 Fit map C122S_G2P_cyc2_refine_aligned.mrc in map 8hbf.pdb map 5 using 650 points correlation = 0.6171, correlation about mean = 0.3947, overlap = 2.12 steps = 48, shift = 0.0346, angle = 0.11 degrees Position of C122S_G2P_cyc2_refine_aligned.mrc (#10) relative to 8hbf.pdb map 5 (#14) coordinates: Matrix rotation and translation -0.90767371 -0.41934549 0.01666709 134.59443001 0.40760914 -0.89033394 -0.20287992 142.84223340 0.09991605 -0.17735511 0.97906177 147.18821727 Axis 0.03069633 -0.10011586 0.99450216 Axis point 47.89583841 93.10618147 0.00000000 Rotation angle (degrees) 155.43261737 Shift along axis 136.20978240 > ui mousemode right ""translate selected atoms"" > ui mousemode right ""rotate selected models"" > hide #!9 models > show #!9 models > hide #!7 models > show #!7 models > hide #!8 models > hide #!7 models > select add #10 2 models selected > view matrix models > #10,-0.97412,0.14087,-0.17677,1.3205,0.15374,0.98621,-0.06133,0.17319,0.1657,-0.086921,-0.98234,2.7739 > view matrix models > #10,-0.6427,0.76177,-0.081537,-2.0193,0.76476,0.63158,-0.12752,2.3102,-0.045641,-0.14431,-0.98848,3.0308 > view matrix models > #10,-0.95319,-0.075577,-0.29277,2.6348,-0.023658,0.98393,-0.17697,0.29687,0.30144,-0.16176,-0.93966,3.1489 > view matrix models > #10,-0.96246,0.19276,-0.19111,1.0677,0.22951,0.95382,-0.1938,0.54738,0.14493,-0.23038,-0.96225,3.5026 > view matrix models > #10,-0.93158,-0.24336,-0.27006,3.5004,-0.2036,0.96471,-0.16699,0.33729,0.30117,-0.10058,-0.94825,2.8357 > view matrix models > #10,-0.53102,0.83766,-0.12781,-2.329,0.8354,0.49229,-0.24445,3.2294,-0.14184,-0.23658,-0.9612,3.4577 > view matrix models > #10,-0.91978,0.071964,-0.38578,1.988,0.22423,0.90314,-0.36614,1.0519,0.32206,-0.42327,-0.84683,4.4155 > ui mousemode right ""translate selected models"" > view matrix models > #10,-0.91978,0.071964,-0.38578,5.8895,0.22423,0.90314,-0.36614,9.7635,0.32206,-0.42327,-0.84683,16.104 > fitmap #10 inMap #14 Fit map C122S_G2P_cyc2_refine_aligned.mrc in map 8hbf.pdb map 5 using 650 points correlation = 0.6479, correlation about mean = 0.3999, overlap = 2.351 steps = 96, shift = 2.99, angle = 10.9 degrees Position of C122S_G2P_cyc2_refine_aligned.mrc (#10) relative to 8hbf.pdb map 5 (#14) coordinates: Matrix rotation and translation -0.94725477 -0.32039190 -0.00757898 132.76811198 0.31141233 -0.92577745 0.21437930 135.61392817 -0.07570184 0.20071163 0.97672108 128.72113254 Axis -0.02150313 0.10717660 0.99400744 Axis point 57.87617404 72.00846116 0.00000000 Rotation angle (degrees) 161.46967157 Shift along axis 139.62947275 > select subtract #10 Nothing selected > show #!2 models The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > select add #2 2 models selected > ui tool show ""Selection Inspector"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > view orient > view sel > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!9 models > hide #!3 models > show #!4 models > hide #!4 models > show #!5 models > select #4/B:122 6 atoms, 5 bonds, 1 residue, 1 model selected > hide #!9.2 models > show #!9.2 models > hide #!9 models > hide #!9.2 models > show #!9.2 models > hide #!9.2 models > color #2 #ff50ec99 models > color #2 #ff40e899 models > color #2 #ff44dd99 models > color #2 #ff00faff models > color #2 #ff00fa9b models > color #2 #ff00fa99 models > color #2 #ff00fa80 models > color #2 #ff00fa9a models > color #2 #ff00fa99 models > select #4/B:122 6 atoms, 5 bonds, 1 residue, 1 model selected > view sel No displayed objects specified. > view sel No displayed objects specified. > view matrix models #4,1,0,0,-0.13721,0,1,0,-0.076784,0,0,1,-2.4285 > view matrix models #4,1,0,0,0.013151,0,1,0,3.4421,0,0,1,2.4784 > select add #4 7309 atoms, 7470 bonds, 11 pseudobonds, 922 residues, 3 models selected > select subtract #4 Nothing selected > select #5/B:122 11 atoms, 10 bonds, 1 residue, 1 model selected > view sel > show (sel-residues & sidechain) target ab > volume #2 level 0.6175 > ui tool show ""Side View"" > select H 9056 atoms, 1159 residues, 2 models selected > hide (#!5 & sel) target a > select clear > volume #2 color #ff00fa80 > volume #2 color #ff00fa73 > hide #!9 models > hide #!5 models > show #!5 models > save > /Users/will/Documents/Marletta_Lab/Presentations/Group_Meeting/20241121_meeting/Chimera_Images/inactive_c122s.png > width 753 height 805 supersample 3 ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet 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 - 88.1 OpenGL renderer: Apple M3 Max 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 Pro Model Identifier: Mac15,10 Model Number: MRX53LL/A Chip: Apple M3 Max Total Number of Cores: 14 (10 performance and 4 efficiency) Memory: 36 GB System Firmware Version: 10151.140.19 OS Loader Version: 10151.140.19 Software: System Software Overview: System Version: macOS 14.6.1 (23G93) Kernel Version: Darwin 23.6.0 Time since boot: 36 days, 2 hours, 14 minutes Graphics/Displays: Apple M3 Max: Chipset Model: Apple M3 Max Type: GPU Bus: Built-In Total Number of Cores: 30 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Acer S232HL: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported 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-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-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 Window Toolkit duplicate all ChimeraX