id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17269 Crash on Mac waking from sleep psrini7@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.3.2-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. Fatal Python error: Segmentation fault Current thread 0x00000001fc574840 (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, 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 (total: 59) {""app_name"":""ChimeraX"",""timestamp"":""2025-04-01 18:03:48.00 -0700"",""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 15.3.2 (24D81)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""D25CBCCD-4498-44EF-BDE7-E1F9F05F530A""} { ""uptime"" : 450000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""Mac14,5"", ""coalitionID"" : 21145, ""osVersion"" : { ""train"" : ""macOS 15.3.2"", ""build"" : ""24D81"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2025-04-01 18:03:45.1577 -0700"", ""codeSigningMonitor"" : 1, ""incident"" : ""D25CBCCD-4498-44EF-BDE7-E1F9F05F530A"", ""pid"" : 49198, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2025-04-01 11:19:55.3861 -0700"", ""procStartAbsTime"" : 10600421643542, ""procExitAbsTime"" : 10962382130276, ""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"":""8130645D-BEAB-5776-BE53-C039A7FAE8AE"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""34646E04-77D9-22C8-5CBA-A82BA218D2EA"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""instructionByteStream"" : {""beforePC"":""fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A=="",""atPC"":""AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g==""}, ""bootSessionUUID"" : ""0C17CBEB-30D5-476A-8EB6-962600B7C5A8"", ""wakeTime"" : 239, ""sleepWakeUUID"" : ""7FE8AB52-28D8-4CFD-884E-5FE70CFE36B3"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0 is not in any region. 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""com.apple.main-thread"" } }, ""logWritingSignature"" : ""51ddcda665aa31d492c5dd85695960599a4082a4"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""642da32dea3b2418c750f848"", ""factorPackIds"" : { ""VISUAL_INTELLIGENCE_VICTORIA"" : ""66d8b2f77cd4b62688efd2cf"" }, ""deploymentId"" : 240000004 }, { ""rolloutId"" : ""6425c75e4327780c10cc4252"", ""factorPackIds"" : { ""SIRI_HOME_AUTOMATION_INTENT_SELECTION_CACHE"" : ""642600a457e7664b1698eb32"" }, ""deploymentId"" : 240000004 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/poojasrinivas/Library/CloudStorage/OneDrive- > UW/Desktop/umbtoxin_paper2/models_lectindomains.cxs Log from Mon Mar 31 14:02:19 2025 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/poojasrinivas/Library/CloudStorage/OneDrive- > UW/Desktop/umbtoxin_paper2/lectindomainstructures/TrypsinLectinStructures/SP+inTrypsin+5BPF-4+CBM_4_9_MER7108863.pdb Chain information for SP+inTrypsin+5BPF-4+CBM_4_9_MER7108863.pdb #1 --- Chain | Description A | No description available > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > lighting soft > open /Users/poojasrinivas/Library/CloudStorage/OneDrive- > UW/Desktop/umbtoxin_paper2/lectindomainstructures/TrypsinLectinStructures/SP+inTrypsin+6BPF-1+6BPF-1_MFD5149162.pdb Chain information for SP+inTrypsin+6BPF-1+6BPF-1_MFD5149162.pdb #2 --- Chain | Description A | No description available > matchmaker #2 to #1 Parameters --- Chain pairing | bb 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 SP+inTrypsin+5BPF-4+CBM_4_9_MER7108863.pdb, chain A (#1) with SP+inTrypsin+6BPF-1+6BPF-1_MFD5149162.pdb, chain A (#2), sequence alignment score = 827.2 RMSD between 185 pruned atom pairs is 0.728 angstroms; (across all 574 pairs: 25.783) > hide #1 models > show #1 models > open /Users/poojasrinivas/Library/CloudStorage/OneDrive- > UW/Desktop/umbtoxin_paper2/lectindomainstructures/TrypsinLectinStructures/SP+7BPF-7+BPA- > Ig+5BPF-11_MER8041134.cif Chain information for SP+7BPF-7+BPA-Ig+5BPF-11_MER8041134.cif #3 --- Chain | Description A | . > matchmaker #3 to #1 Parameters --- Chain pairing | bb 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 SP+inTrypsin+5BPF-4+CBM_4_9_MER7108863.pdb, chain A (#1) with SP+7BPF-7+BPA-Ig+5BPF-11_MER8041134.cif, chain A (#3), sequence alignment score = 447.9 RMSD between 6 pruned atom pairs is 1.424 angstroms; (across all 454 pairs: 30.481) > open /Users/poojasrinivas/Library/CloudStorage/OneDrive- > UW/Desktop/umbtoxin_paper2/lectindomainstructures/TrypsinLectinStructures/ALF_accessory+inTrypsin+RicinB-2+RicinB-2_ALO06367.pdb Chain information for ALF_accessory+inTrypsin+RicinB-2+RicinB-2_ALO06367.pdb #4 --- Chain | Description A | No description available > matchmaker #4 to #1 Parameters --- Chain pairing | bb 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 SP+inTrypsin+5BPF-4+CBM_4_9_MER7108863.pdb, chain A (#1) with ALF_accessory+inTrypsin+RicinB-2+RicinB-2_ALO06367.pdb, chain A (#4), sequence alignment score = 684 RMSD between 181 pruned atom pairs is 0.827 angstroms; (across all 474 pairs: 28.058) > open /Users/poojasrinivas/Library/CloudStorage/OneDrive- > UW/Desktop/umbtoxin_paper2/lectindomainstructures/TrypsinLectinStructures/ALF_accessory+inTrypsin+Jellyroll- > like+Jellyroll-like+Jellyroll-like_MCU7825302.pdb Chain information for ALF_accessory+inTrypsin+Jellyroll-like+Jellyroll- like+Jellyroll-like_MCU7825302.pdb #5 --- Chain | Description A | No description available > matchmaker #5 to #1 Parameters --- Chain pairing | bb 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 SP+inTrypsin+5BPF-4+CBM_4_9_MER7108863.pdb, chain A (#1) with ALF_accessory+inTrypsin+Jellyroll-like+Jellyroll-like+Jellyroll- like_MCU7825302.pdb, chain A (#5), sequence alignment score = 684.8 RMSD between 174 pruned atom pairs is 0.841 angstroms; (across all 575 pairs: 34.961) > open /Users/poojasrinivas/Library/CloudStorage/OneDrive- > UW/Desktop/umbtoxin_paper2/lectindomainstructures/TrypsinLectinStructures/SP+inTrypsin+TAC4_MER7568781.pdb Chain information for SP+inTrypsin+TAC4_MER7568781.pdb #6 --- Chain | Description A | No description available > matchmaker #6to #1 Missing or invalid ""matchAtoms"" argument: only initial part ""#6"" of atom specifier valid > matchmaker #6 to #1 Parameters --- Chain pairing | bb 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 SP+inTrypsin+5BPF-4+CBM_4_9_MER7108863.pdb, chain A (#1) with SP+inTrypsin+TAC4_MER7568781.pdb, chain A (#6), sequence alignment score = 684.5 RMSD between 198 pruned atom pairs is 0.726 angstroms; (across all 357 pairs: 19.803) > open /Users/poojasrinivas/Library/CloudStorage/OneDrive- > UW/Desktop/umbtoxin_paper2/lectindomainstructures/TrypsinLectinStructures/SP+inTrypsin+Bulb- > lectin+Bulb-lectin+RicinB-6_BAU81346.pdb Chain information for SP+inTrypsin+Bulb-lectin+Bulb- lectin+RicinB-6_BAU81346.pdb #7 --- Chain | Description A | No description available > matchmaker #7 to #1 Parameters --- Chain pairing | bb 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 SP+inTrypsin+5BPF-4+CBM_4_9_MER7108863.pdb, chain A (#1) with SP+inTrypsin+Bulb-lectin+Bulb-lectin+RicinB-6_BAU81346.pdb, chain A (#7), sequence alignment score = 827.6 RMSD between 180 pruned atom pairs is 0.755 angstroms; (across all 556 pairs: 29.281) > open /Users/poojasrinivas/Library/CloudStorage/OneDrive- > UW/Desktop/umbtoxin_paper2/lectindomainstructures/TrypsinLectinStructures/SP+inTrypsin+Bulb- > lectin+Bulb-lectin+5BPF-6_MER7730173.pdb Chain information for SP+inTrypsin+Bulb-lectin+Bulb- lectin+5BPF-6_MER7730173.pdb #8 --- Chain | Description A | No description available > color white > hide #8 models > hide #7 models > hide #6 models > hide #5 models > hide #4 models > hide #3 models > hide #2 models > tile 1 model tiled > show #1-8 > show #1-8 cartoons > show #2 models > show #3 models > show #8 models > show #7 models > show #5 models > show #4 models > show #6 models > tile 8 models tiled > select #1-8 :1-25 1397 atoms, 1412 bonds, 200 residues, 8 models selected > ui mousemode right select Drag select of 27 residues Drag select of 29 residues > delete sel Drag select of 25 residues Drag select of 33 residues Drag select of 31 residues > delete sel Drag select of 19 residues > delete sel Drag select of 14 residues > delete sel Drag select of 7 residues > delete sel Drag select of 18 residues > delete sel Drag select of 46 residues > delete sel Drag select of 30 residues > delete sel Drag select of 2 residues > delete sel Drag select of 19 residues > delete sel Drag select of 12 residues > delete sel > lighting soft > hide #2-8 cartoons > select #1 :256-504 1824 atoms, 1868 bonds, 249 residues, 1 model selected > select #1 :256-501 1795 atoms, 1837 bonds, 246 residues, 1 model selected > color sel dodgerblue > select #1 :505-644 1044 atoms, 1061 bonds, 140 residues, 1 model selected > color sel tan > select clear [Repeated 2 time(s)]Drag select of 39 residues > select clear > hide #1 models > show #2/catoons > show #2 cartoons > select #2:251-819 4123 atoms, 4215 bonds, 569 residues, 1 model selected > color sel pueple Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color sel lavendar Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color sel lavender > color sel plum > select clear > hide #3 models > show #3 models > hide #2 models > show #1 models > show #2 models Drag select of 34 residues > select clear > show #3 cartoons > select #3 :49-367 2352 atoms, 2397 bonds, 319 residues, 1 model selected > select #3 :41-367 2409 atoms, 2457 bonds, 327 residues, 1 model selected > color sel lime > color pale green > color sel pale green > select #3 :368-489 924 atoms, 951 bonds, 122 residues, 1 model selected > select #3 :368-488 917 atoms, 943 bonds, 121 residues, 1 model selected > color sel forestgreen > select #3 :487-700 1596 atoms, 1635 bonds, 214 residues, 1 model selected > select #3 :487-900 1998 atoms, 2051 bonds, 265 residues, 1 model selected > color sel dodger blue > select clear > open > /Users/poojasrinivas/Downloads/fold_meu0719199_1/fold_meu0719199_1_model_0.cif Chain information for fold_meu0719199_1_model_0.cif #9 --- Chain | Description A | . > matchmaker #9 to #1 Parameters --- Chain pairing | bb 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 SP+inTrypsin+5BPF-4+CBM_4_9_MER7108863.pdb, chain A (#1) with fold_meu0719199_1_model_0.cif, chain A (#9), sequence alignment score = 3063 RMSD between 249 pruned atom pairs is 0.509 angstroms; (across all 615 pairs: 17.385) > hide #1 models > show #1 models > hide #9 models > show #4 cartoons > select #4 :342..477 Expected a keyword > select #4 :342-477 1032 atoms, 1052 bonds, 136 residues, 1 model selected > select #4 :342-800 2103 atoms, 2146 bonds, 277 residues, 1 model selected > color sel orange > color sel gold Drag select of 141 residues > select clear > hide #4 models > show #4 models > hide #5 models > show #5 models > show #5 cartoons > select #5 :402-766 2615 atoms, 2678 bonds, 365 residues, 1 model selected > color sel magenta > color sel medium violet red > select clear > show #6 cartoons > select clear > select #6:274-401 910 atoms, 927 bonds, 128 residues, 1 model selected > color sel pink > select clear > show #7 cartoons > select #7 :246-370 927 atoms, 947 bonds, 125 residues, 1 model selected > select #7 :246-370,371-485 1823 atoms, 1867 bonds, 240 residues, 1 model selected > color sel magenta > select #7 :485-606 887 atoms, 903 bonds, 121 residues, 1 model selected > color sel orange > select clear > show #8 cartoons > select #8 :250-368 869 atoms, 887 bonds, 119 residues, 1 model selected > select #8 :247-368 893 atoms, 911 bonds, 122 residues, 1 model selected > color sel magenta > select #8 :247-491 1812 atoms, 1855 bonds, 245 residues, 1 model selected > color sel magenta > select #8 :492-774 2090 atoms, 2139 bonds, 283 residues, 1 model selected > color sel dodger blue > select clear Drag select of 76 residues > select clear > close #9 > open > /Users/poojasrinivas/Downloads/fold_meu6965693_1/fold_meu6965693_1_model_0.cif Chain information for fold_meu6965693_1_model_0.cif #9 --- Chain | Description A | . > tile 9 models tiled > hide #8 models > hide #7 models > hide #6 models > hide #5 models > hide #4 models > hide #3 models > hide #2 models > hide #1 models > lighting soft > select #9:1-40 262 atoms, 265 bonds, 40 residues, 1 model selected > delete sel > color #9 white > select #9 :378-900 grey Expected a keyword > select #9 :378-900 3258 atoms, 3331 bonds, 435 residues, 1 model selected > color sel grey > select clear > show #8 models > show #7 models > show #6 models > show #5 models > show #3 models > show #4 models > show #2 models > show #1 models > save /Users/poojasrinivas/Library/CloudStorage/OneDrive- > UW/Desktop/umbtoxin_paper2/models_lectindomains.cxs ——— End of log from Mon Mar 31 14:02:19 2025 ——— opened ChimeraX session > hide #9 models > hide #8 models > hide #7 models > hide #6 models > hide #5 models > hide #4 models > hide #3 models > hide #2 models > ui tool show ""Side View"" > ui mousemode right select Drag select of 172 residues > color sel white > select clear > color #1 :255-501 #192F8A Drag select of 13 residues > select clear > ui mousemode right translate > preset ""overall look"" ""publication 2 (depth-cued)"" Using preset: Overall Look / Publication 2 (Depth-Cued) Preset expands to these ChimeraX commands: set bg white graphics silhouettes f lighting depthCue t > graphics silhouettes true > color #1 white > ui mousemode right select Drag select of 143 residues > color #1 #B5A688 > color sel #B5A688 > select clear Drag select of 3 residues > color sel #B5A688 > select clear > save > /Users/poojasrinivas/Desktop/umbtoxin_paper2/chimeraXscreenshots/CBM_4_MER71088631.png > width 1800 height 1800 supersample 4 transparentBackground true > hide #1 models > show #2 models > open /Users/poojasrinivas/Library/CloudStorage/OneDrive- > UW/Desktop/umbtoxin_paper2/lectindomainstructures/TrypsinLectinStructures/SP+inTrypsin+6BPF-2_MET7413469.cif Chain information for SP+inTrypsin+6BPF-2_MET7413469.cif #10 --- Chain | Description A | . Drag select of 24 residues > delete sel Drag select of 3 residues > delete sel > select clear > hide #2 models Drag select of 217 residues > color sel white > select ~sel 46124 atoms, 47132 bonds, 6307 residues, 10 models selected > color sel #BD8FC1 > select clear Drag select of 72 residues > color sel white > select clear > save > /Users/poojasrinivas/Desktop/umbtoxin_paper2/chimeraXscreenshots/6BPF-2_MET7413469.png > width 1800 height 1800 supersample 4 transparentBackground true > hide #10 models > show #3 models Drag select of 711 residues > color sel white > select clear > select #3 :1-370 2428 atoms, 2477 bonds, 330 residues, 1 model selected > color sel #A7D073 > select clear > select #3/A:113 8 atoms, 7 bonds, 1 residue, 1 model selected > save > /Users/poojasrinivas/Desktop/umbtoxin_paper2/chimeraXscreenshots/7bpf-7_MER8041134.png > width 1800 height 1800 supersample 4 transparentBackground true > select clear > save > /Users/poojasrinivas/Desktop/umbtoxin_paper2/chimeraXscreenshots/7bpf-7_MER8041134.png > width 1800 height 1800 supersample 4 transparentBackground true > color #1 white > color #3 white Drag select of 2 residues > ui mousemode right translate > color #3:369-484 #3BB092 > ui mousemode right select > select clear > save /Users/poojasrinivas/Desktop/umbtoxin_paper2/chimeraXscreenshots/bpa- > ig_MER8041134.png width 1800 height 1800 supersample 4 transparentBackground > true Drag select of 401 residues > color sel white > select clear > ui mousemode right translate > ui mousemode right select Drag select of 266 residues > color sel #48B4ED > select clear Drag select of 7 residues > select clear > save > /Users/poojasrinivas/Desktop/umbtoxin_paper2/chimeraXscreenshots/5bpf11_MER8041134.png > width 1800 height 1800 supersample 4 transparentBackground true > hide #3 models > show #4 models > select add #4 4507 atoms, 4590 bonds, 618 residues, 1 model selected > color sel white > select clear Drag select of 135 residues > color sel #E64216 Drag select of 63 residues > color sel #E64216 Drag select of 126 residues > color sel #E64216 Drag select of 20 residues > color sel #E64216 Drag select of 3 residues > color sel #E64216 > select clear > select #4/A:480 7 atoms, 7 bonds, 1 residue, 1 model selected > select clear > save > /Users/poojasrinivas/Desktop/umbtoxin_paper2/chimeraXscreenshots/ricinb2_alo06367.png > width 1800 height 1800 supersample 4 transparentBackground true > hide #4 models > show #5 models Drag select of 748 residues > color sel white > select clear > select #5 :402-766 2615 atoms, 2678 bonds, 365 residues, 1 model selected > color sel #D165A5 > select #5/A:413 11 atoms, 10 bonds, 1 residue, 1 model selected > select clear > save > /Users/poojasrinivas/Desktop/umbtoxin_paper2/chimeraXscreenshots/jellyrolllike_mcu7825302.png > width 1800 height 1800 supersample 4 transparentBackground true > hide #5 models > show #6 models > color #6 white > select clear Drag select of 126 residues > color #6 #EFA0C6 > color sel #EFA0C6 > select clear > save > /Users/poojasrinivas/Desktop/umbtoxin_paper2/chimeraXscreenshots/tac4_mer7568781.png > width 1800 height 1800 supersample 4 transparentBackground true > hide #6 models > show #7 models > color #7 white > color #7 :246-485 #DE007B > select #7/A:246 11 atoms, 10 bonds, 1 residue, 1 model selected > select clear > select #7/A:485 6 atoms, 5 bonds, 1 residue, 1 model selected > color #7/A :246-485 #D19EC8 > select clear > save > /Users/poojasrinivas/Desktop/umbtoxin_paper2/chimeraXscreenshots/bulblectins.png > width 1800 height 1800 supersample 4 transparentBackground true > hide #7 models > show #1 models > color #1 white Drag select of 144 residues Drag select of 2 residues > select add #1/A:559 1087 atoms, 8 bonds, 145 residues, 1 model selected > color sel $B7D123 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color sel #B7D123 > select clear > save > /Users/poojasrinivas/Desktop/umbtoxin_paper2/chimeraXscreenshots/cmb4.png > width 1800 height 1800 supersample 4 transparentBackground true > color #1/white > color #1 white Drag select of 250 residues Drag select of 2 residues > select subtract #1/A:503 1817 atoms, 249 residues, 1 model selected Drag select of 2 residues Drag select of 4 residues > select subtract #1/A:250 1799 atoms, 246 residues, 1 model selected Drag select of 3 residues > color sel #65C2EE > select clear > save > /Users/poojasrinivas/Desktop/umbtoxin_paper2/chimeraXscreenshots/5bpf.png > width 1800 height 1800 supersample 4 transparentBackground true > hide #1 models > show #2 models > color #2 white Drag select of 572 residues Drag select of 1 residues > color sel #E266A3 > select clear > select #2/A:673 6 atoms, 5 bonds, 1 residue, 1 model selected > save > /Users/poojasrinivas/Desktop/umbtoxin_paper2/chimeraXscreenshots/6bpf.png > width 1800 height 1800 supersample 4 transparentBackground true > select clear > show #3 models > hide #2 models > color #3/white > color #3 white > color #3 :369-484 #3BB092 > save > /Users/poojasrinivas/Desktop/umbtoxin_paper2/chimeraXscreenshots/BPAig.png > width 1800 height 1800 supersample 4 transparentBackground true > hide #3 models > show #4 models > select clear Drag select of 104 residues Drag select of 171 residues > select #4 :342-900 2103 atoms, 2146 bonds, 277 residues, 1 model selected > color sel BF371B Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color sel #BF371B > select clear > save > /Users/poojasrinivas/Desktop/umbtoxin_paper2/chimeraXscreenshots/ricinb2.png > width 1800 height 1800 supersample 4 transparentBackground true > hide #4 models > show #5 models > color #5/A :402-900 > select #5/A :402-900 2615 atoms, 2678 bonds, 365 residues, 1 model selected > color sel #3280C7 > select clear > save > /Users/poojasrinivas/Desktop/umbtoxin_paper2/chimeraXscreenshots/jellyroll.png > width 1800 height 1800 supersample 4 transparentBackground true > hide #5 models > show #6 models Drag select of 121 residues Drag select of 119 residues Drag select of 126 residues > color sel #9A4193 > select clear > save > /Users/poojasrinivas/Desktop/umbtoxin_paper2/chimeraXscreenshots/tac4.png > width 1800 height 1800 supersample 4 transparentBackground true > hide #6 models > show #7 models > hide #7 models > show #8 models > show #3 models > hide #8 models > color #3 white > select clear > color #3 :1-366 > color #3 :1-366 #DE939C > save > /Users/poojasrinivas/Desktop/umbtoxin_paper2/chimeraXscreenshots/7bpf7.png > width 1800 height 1800 supersample 4 transparentBackground true > hide #3 models > show #9 models > hide #9 models > show #9 models > color #9 :378-812 #F69F29 > color #9 1_376 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #9 1-376 white Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #9 :1-376 white > save > /Users/poojasrinivas/Desktop/umbtoxin_paper2/chimeraXscreenshots/lameling.png > width 1800 height 1800 supersample 4 transparentBackground true ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/poojasrinivas/Library/CloudStorage/OneDrive- > UW/Desktop/umbtoxin_paper2/models_lectindomains.cxs Log from Mon Mar 31 14:02:19 2025 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/poojasrinivas/Library/CloudStorage/OneDrive- > UW/Desktop/umbtoxin_paper2/lectindomainstructures/TrypsinLectinStructures/SP+inTrypsin+5BPF-4+CBM_4_9_MER7108863.pdb Chain information for SP+inTrypsin+5BPF-4+CBM_4_9_MER7108863.pdb #1 --- Chain | Description A | No description available > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > lighting soft > open /Users/poojasrinivas/Library/CloudStorage/OneDrive- > UW/Desktop/umbtoxin_paper2/lectindomainstructures/TrypsinLectinStructures/SP+inTrypsin+6BPF-1+6BPF-1_MFD5149162.pdb Chain information for SP+inTrypsin+6BPF-1+6BPF-1_MFD5149162.pdb #2 --- Chain | Description A | No description available > matchmaker #2 to #1 Parameters --- Chain pairing | bb 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 SP+inTrypsin+5BPF-4+CBM_4_9_MER7108863.pdb, chain A (#1) with SP+inTrypsin+6BPF-1+6BPF-1_MFD5149162.pdb, chain A (#2), sequence alignment score = 827.2 RMSD between 185 pruned atom pairs is 0.728 angstroms; (across all 574 pairs: 25.783) > hide #1 models > show #1 models > open /Users/poojasrinivas/Library/CloudStorage/OneDrive- > UW/Desktop/umbtoxin_paper2/lectindomainstructures/TrypsinLectinStructures/SP+7BPF-7+BPA- > Ig+5BPF-11_MER8041134.cif Chain information for SP+7BPF-7+BPA-Ig+5BPF-11_MER8041134.cif #3 --- Chain | Description A | . > matchmaker #3 to #1 Parameters --- Chain pairing | bb 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 SP+inTrypsin+5BPF-4+CBM_4_9_MER7108863.pdb, chain A (#1) with SP+7BPF-7+BPA-Ig+5BPF-11_MER8041134.cif, chain A (#3), sequence alignment score = 447.9 RMSD between 6 pruned atom pairs is 1.424 angstroms; (across all 454 pairs: 30.481) > open /Users/poojasrinivas/Library/CloudStorage/OneDrive- > UW/Desktop/umbtoxin_paper2/lectindomainstructures/TrypsinLectinStructures/ALF_accessory+inTrypsin+RicinB-2+RicinB-2_ALO06367.pdb Chain information for ALF_accessory+inTrypsin+RicinB-2+RicinB-2_ALO06367.pdb #4 --- Chain | Description A | No description available > matchmaker #4 to #1 Parameters --- Chain pairing | bb 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 SP+inTrypsin+5BPF-4+CBM_4_9_MER7108863.pdb, chain A (#1) with ALF_accessory+inTrypsin+RicinB-2+RicinB-2_ALO06367.pdb, chain A (#4), sequence alignment score = 684 RMSD between 181 pruned atom pairs is 0.827 angstroms; (across all 474 pairs: 28.058) > open /Users/poojasrinivas/Library/CloudStorage/OneDrive- > UW/Desktop/umbtoxin_paper2/lectindomainstructures/TrypsinLectinStructures/ALF_accessory+inTrypsin+Jellyroll- > like+Jellyroll-like+Jellyroll-like_MCU7825302.pdb Chain information for ALF_accessory+inTrypsin+Jellyroll-like+Jellyroll- like+Jellyroll-like_MCU7825302.pdb #5 --- Chain | Description A | No description available > matchmaker #5 to #1 Parameters --- Chain pairing | bb 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 SP+inTrypsin+5BPF-4+CBM_4_9_MER7108863.pdb, chain A (#1) with ALF_accessory+inTrypsin+Jellyroll-like+Jellyroll-like+Jellyroll- like_MCU7825302.pdb, chain A (#5), sequence alignment score = 684.8 RMSD between 174 pruned atom pairs is 0.841 angstroms; (across all 575 pairs: 34.961) > open /Users/poojasrinivas/Library/CloudStorage/OneDrive- > UW/Desktop/umbtoxin_paper2/lectindomainstructures/TrypsinLectinStructures/SP+inTrypsin+TAC4_MER7568781.pdb Chain information for SP+inTrypsin+TAC4_MER7568781.pdb #6 --- Chain | Description A | No description available > matchmaker #6to #1 Missing or invalid ""matchAtoms"" argument: only initial part ""#6"" of atom specifier valid > matchmaker #6 to #1 Parameters --- Chain pairing | bb 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 SP+inTrypsin+5BPF-4+CBM_4_9_MER7108863.pdb, chain A (#1) with SP+inTrypsin+TAC4_MER7568781.pdb, chain A (#6), sequence alignment score = 684.5 RMSD between 198 pruned atom pairs is 0.726 angstroms; (across all 357 pairs: 19.803) > open /Users/poojasrinivas/Library/CloudStorage/OneDrive- > UW/Desktop/umbtoxin_paper2/lectindomainstructures/TrypsinLectinStructures/SP+inTrypsin+Bulb- > lectin+Bulb-lectin+RicinB-6_BAU81346.pdb Chain information for SP+inTrypsin+Bulb-lectin+Bulb- lectin+RicinB-6_BAU81346.pdb #7 --- Chain | Description A | No description available > matchmaker #7 to #1 Parameters --- Chain pairing | bb 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 SP+inTrypsin+5BPF-4+CBM_4_9_MER7108863.pdb, chain A (#1) with SP+inTrypsin+Bulb-lectin+Bulb-lectin+RicinB-6_BAU81346.pdb, chain A (#7), sequence alignment score = 827.6 RMSD between 180 pruned atom pairs is 0.755 angstroms; (across all 556 pairs: 29.281) > open /Users/poojasrinivas/Library/CloudStorage/OneDrive- > UW/Desktop/umbtoxin_paper2/lectindomainstructures/TrypsinLectinStructures/SP+inTrypsin+Bulb- > lectin+Bulb-lectin+5BPF-6_MER7730173.pdb Chain information for SP+inTrypsin+Bulb-lectin+Bulb- lectin+5BPF-6_MER7730173.pdb #8 --- Chain | Description A | No description available > color white > hide #8 models > hide #7 models > hide #6 models > hide #5 models > hide #4 models > hide #3 models > hide #2 models > tile 1 model tiled > show #1-8 > show #1-8 cartoons > show #2 models > show #3 models > show #8 models > show #7 models > show #5 models > show #4 models > show #6 models > tile 8 models tiled > select #1-8 :1-25 1397 atoms, 1412 bonds, 200 residues, 8 models selected > ui mousemode right select Drag select of 27 residues Drag select of 29 residues > delete sel Drag select of 25 residues Drag select of 33 residues Drag select of 31 residues > delete sel Drag select of 19 residues > delete sel Drag select of 14 residues > delete sel Drag select of 7 residues > delete sel Drag select of 18 residues > delete sel Drag select of 46 residues > delete sel Drag select of 30 residues > delete sel Drag select of 2 residues > delete sel Drag select of 19 residues > delete sel Drag select of 12 residues > delete sel > lighting soft > hide #2-8 cartoons > select #1 :256-504 1824 atoms, 1868 bonds, 249 residues, 1 model selected > select #1 :256-501 1795 atoms, 1837 bonds, 246 residues, 1 model selected > color sel dodgerblue > select #1 :505-644 1044 atoms, 1061 bonds, 140 residues, 1 model selected > color sel tan > select clear [Repeated 2 time(s)]Drag select of 39 residues > select clear > hide #1 models > show #2/catoons > show #2 cartoons > select #2:251-819 4123 atoms, 4215 bonds, 569 residues, 1 model selected > color sel pueple Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color sel lavendar Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color sel lavender > color sel plum > select clear > hide #3 models > show #3 models > hide #2 models > show #1 models > show #2 models Drag select of 34 residues > select clear > show #3 cartoons > select #3 :49-367 2352 atoms, 2397 bonds, 319 residues, 1 model selected > select #3 :41-367 2409 atoms, 2457 bonds, 327 residues, 1 model selected > color sel lime > color pale green > color sel pale green > select #3 :368-489 924 atoms, 951 bonds, 122 residues, 1 model selected > select #3 :368-488 917 atoms, 943 bonds, 121 residues, 1 model selected > color sel forestgreen > select #3 :487-700 1596 atoms, 1635 bonds, 214 residues, 1 model selected > select #3 :487-900 1998 atoms, 2051 bonds, 265 residues, 1 model selected > color sel dodger blue > select clear > open > /Users/poojasrinivas/Downloads/fold_meu0719199_1/fold_meu0719199_1_model_0.cif Chain information for fold_meu0719199_1_model_0.cif #9 --- Chain | Description A | . > matchmaker #9 to #1 Parameters --- Chain pairing | bb 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 SP+inTrypsin+5BPF-4+CBM_4_9_MER7108863.pdb, chain A (#1) with fold_meu0719199_1_model_0.cif, chain A (#9), sequence alignment score = 3063 RMSD between 249 pruned atom pairs is 0.509 angstroms; (across all 615 pairs: 17.385) > hide #1 models > show #1 models > hide #9 models > show #4 cartoons > select #4 :342..477 Expected a keyword > select #4 :342-477 1032 atoms, 1052 bonds, 136 residues, 1 model selected > select #4 :342-800 2103 atoms, 2146 bonds, 277 residues, 1 model selected > color sel orange > color sel gold Drag select of 141 residues > select clear > hide #4 models > show #4 models > hide #5 models > show #5 models > show #5 cartoons > select #5 :402-766 2615 atoms, 2678 bonds, 365 residues, 1 model selected > color sel magenta > color sel medium violet red > select clear > show #6 cartoons > select clear > select #6:274-401 910 atoms, 927 bonds, 128 residues, 1 model selected > color sel pink > select clear > show #7 cartoons > select #7 :246-370 927 atoms, 947 bonds, 125 residues, 1 model selected > select #7 :246-370,371-485 1823 atoms, 1867 bonds, 240 residues, 1 model selected > color sel magenta > select #7 :485-606 887 atoms, 903 bonds, 121 residues, 1 model selected > color sel orange > select clear > show #8 cartoons > select #8 :250-368 869 atoms, 887 bonds, 119 residues, 1 model selected > select #8 :247-368 893 atoms, 911 bonds, 122 residues, 1 model selected > color sel magenta > select #8 :247-491 1812 atoms, 1855 bonds, 245 residues, 1 model selected > color sel magenta > select #8 :492-774 2090 atoms, 2139 bonds, 283 residues, 1 model selected > color sel dodger blue > select clear Drag select of 76 residues > select clear > close #9 > open > /Users/poojasrinivas/Downloads/fold_meu6965693_1/fold_meu6965693_1_model_0.cif Chain information for fold_meu6965693_1_model_0.cif #9 --- Chain | Description A | . > tile 9 models tiled > hide #8 models > hide #7 models > hide #6 models > hide #5 models > hide #4 models > hide #3 models > hide #2 models > hide #1 models > lighting soft > select #9:1-40 262 atoms, 265 bonds, 40 residues, 1 model selected > delete sel > color #9 white > select #9 :378-900 grey Expected a keyword > select #9 :378-900 3258 atoms, 3331 bonds, 435 residues, 1 model selected > color sel grey > select clear > show #8 models > show #7 models > show #6 models > show #5 models > show #3 models > show #4 models > show #2 models > show #1 models > save /Users/poojasrinivas/Library/CloudStorage/OneDrive- > UW/Desktop/umbtoxin_paper2/models_lectindomains.cxs ——— End of log from Mon Mar 31 14:02:19 2025 ——— opened ChimeraX session OpenGL version: 4.1 Metal - 89.3 OpenGL renderer: Apple M2 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: Mac14,5 Model Number: MPHG3LL/A Chip: Apple M2 Max Total Number of Cores: 12 (8 performance and 4 efficiency) Memory: 32 GB System Firmware Version: 11881.81.4 OS Loader Version: 11881.81.4 Software: System Software Overview: System Version: macOS 15.3.2 (24D81) Kernel Version: Darwin 24.3.0 Time since boot: 16 days, 18 hours, 28 minutes Graphics/Displays: Apple M2 Max: Chipset Model: Apple M2 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 DELL P2721Q: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra 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