id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18374 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.5-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 0x00000001ef6adf00 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, PIL._imagingmath, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 54) {""app_name"":""ChimeraX"",""timestamp"":""2025-08-04 10:29:11.00 -0400"",""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 15.5 (24F74)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""9DE56445-1212-4386-BCAB-65F0C70B179D""} { ""uptime"" : 240000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""Mac15,6"", ""coalitionID"" : 3262, ""osVersion"" : { ""train"" : ""macOS 15.5"", ""build"" : ""24F74"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2025-08-04 10:26:29.3507 -0400"", ""codeSigningMonitor"" : 1, ""incident"" : ""9DE56445-1212-4386-BCAB-65F0C70B179D"", ""pid"" : 10185, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2025-08-04 08:57:36.2901 -0400"", ""procStartAbsTime"" : 5857684427410, ""procExitAbsTime"" : 5985677471420, ""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"":""8A0DEBBA-E629-56FE-A554-9DB986703AD3"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""999B5ACF-7899-A575-EB8B-89F6BAD982ED"", ""appleIntelligenceStatus"" : {""state"":""available""}, ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""codeSigningAuxiliaryInfo"" : 0, ""instructionByteStream"" : {""beforePC"":""fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A=="",""atPC"":""AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g==""}, ""bootSessionUUID"" : ""825016ED-E003-4E43-BEB2-75E8C899CDF8"", ""wakeTime"" : 7636, ""sleepWakeUUID"" : ""624B0FE6-7E62-4F83-897F-E2F2B55FD0EF"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x2815b0a418c8 is not in any region. 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: 240000016 } ], ""experiments"" : [ ] } } ===== 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/ehecatlga/work/Fitted_tutorial/1hkw_docking/1hkw_cluster_40ns_docking/rep.c0.pdb > format pdb Chain information for rep.c0.pdb #1 --- Chain | Description ? | No description available > select add #1 13310 atoms, 13435 bonds, 891 residues, 1 model selected > show sel surfaces > ui mousemode right select > select clear > select /?:448 19 atoms, 18 bonds, 1 residue, 1 model selected > select clear > select /?:447 17 atoms, 16 bonds, 1 residue, 1 model selected > hide sel atoms > hide sel cartoons > select clear > select /?:448 19 atoms, 18 bonds, 1 residue, 1 model selected > hide sel cartoons > select clear The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > color cornflower blue > color byhetero > undo > color byhetero > undo > hide surfaces > color byhetero > show surfaces > color byhetero > color bychain > undo > hide surfaces > undo > show surfaces > color byhetero > hide #!1 models > show #!1 models > color #1 #0096ffff > color #1 #0433ffff > color #1 #011993ff > color #1 #0096ffff > color #1 #009193ff > color #1 #009051ff > select #1/?: UNL 48 atoms, 48 bonds, 1 residue, 1 model selected > color sel byhetero > select clear > color light sea green > color cornflower blue > select #1/?: UNL 48 atoms, 48 bonds, 1 residue, 1 model selected > color sel byhetero > select clear > select #1/? 13310 atoms, 13435 bonds, 891 residues, 1 model selected > transparency 60 > transparency 40 > tranparency 70 Unknown command: tranparency 70 > transparency 70 > select up 13310 atoms, 13435 bonds, 891 residues, 2 models selected > select up 13310 atoms, 13435 bonds, 891 residues, 2 models selected > select up 13310 atoms, 13435 bonds, 891 residues, 2 models selected > select up 13310 atoms, 13435 bonds, 891 residues, 2 models selected > select #1/?: UNL 48 atoms, 48 bonds, 1 residue, 1 model selected > color sel orange > color sel byhetero > color sel #f1fff4ff > color sel #f0fff4ff > color sel #eefff4ff > color sel #eafff5ff > color sel #e7fff5ff > color sel #e3fff5ff > color sel #e1fff5ff > color sel #dffff5ff > color sel #ddfff5ff > color sel #dafff5ff > color sel #d6fff5ff > color sel #d0fff5ff > color sel #c9fff5ff > color sel #c1fff5ff > color sel #bbfff5ff > color sel #b5fff5ff > color sel #affff5ff > color sel #abfff5ff > color sel #a5fff5ff > color sel #9ffff6ff > color sel #9afff7ff > color sel #95fff9ff > color sel #90fffaff > color sel #8bfffcff > color sel #86fffeff > color sel #80fdffff > color sel #7bfaffff > color sel #76f7ffff > color sel #71f4ffff > color sel #6df1ffff > color sel #69efffff > color sel #67edffff > color sel #66ecffff > color sel #6eefffff > color sel #7ef5ffff > color sel #94fcffff > color sel #acfffaff > color sel #c4fff3ff > color sel #d8ffebff > color sel #e2ffe1ff > color sel #f1ffe0ff > color sel #fbffd9ff > color sel #fffcd2ff > color sel #fff8ccff > color sel #fff4c7ff > color sel #fff1c2ff > color sel #ffeebdff > color sel #ffebb8ff > color sel #ffe7b3ff > color sel #ffe3aeff > color sel #ffdfa8ff > color sel #ffdaa2ff > color sel #ffd59cff > color sel #ffd097ff > color sel #ffcb91ff > color sel #ffc68bff > color sel #ffc286ff > color sel #ffbe80ff > color sel #ffba7bff > color sel #ffb776ff > color sel #ffb371ff > color sel #ffb06cff > color sel #ffad67ff > color sel #ffab64ff > color sel #ffaa61ff > color sel #ffaa60ff > color sel #ffa95fff > color sel #ffa95eff > color sel #ffa95cff > color sel #ffa859ff > color sel #ffa756ff > color sel #ffa653ff > color sel #ffa54fff > color sel #ffa34cff > color sel #ffa349ff > color sel #ffa247ff > color sel #ffa146ff > color sel #ffa145ff > color sel #ffa042ff > color sel #ff9f3fff > color sel #ff9f3dff > color sel #ff9f3aff > color sel #ff9f39ff > color sel #ffa037ff > color sel #ffa236ff > color sel #ffa335ff > color sel #ffa533ff > color sel #ffa632ff > color sel #ffa731ff > color sel #ffa830ff > color sel #ffa930ff > color sel #ffab2fff > color sel #ffad2fff > color sel #ffae2eff > color sel #ffaf2eff > color sel #ffb02dff > color sel #ffb12dff > color sel #ffb22dff > color sel #ffb32cff > color sel #ffb42bff > color sel #ffb62aff > color sel #ffb728ff > color sel #ffb927ff > color sel #ffba25ff > color sel #ffbb24ff > color sel #ffbb23ff > color sel #ffbc21ff > color sel #ffbd20ff > color sel #ffbe1fff > color sel #ffbf1dff > color sel #ffbf1cff > color sel #ffbf1bff > color sel #ffbf1aff > color sel #ffbe19ff > color sel #ffbd18ff > color sel #ffbc17ff > color sel #ffba15ff > color sel #ffb912ff > color sel #ffb710ff > color sel #ffb40eff > color sel #ffb30dff > color sel #ffb10cff > color sel #ffb00bff > color sel #ffaf0aff > color sel #ffae09ff > color sel #ffac09ff > color sel #ffaa09ff > color sel #ffa808ff > color sel #ffa609ff > color sel #ffa309ff > color sel #ffa109ff > color sel #ffa00aff > color sel #ff9e0aff > color sel #ff9d0aff > color sel #ff9d0bff > color sel #ff9c0cff > color sel #ff9b0dff > color sel #ff9a0eff > color sel #ff990fff > color sel #ff9810ff > color sel #ff9811ff > color sel #ff9713ff > color sel #ff9714ff > color sel #ff9715ff > color sel #ff9617ff > color sel #ff9618ff > color sel #ff9619ff > color sel #ff951aff > color sel #ff951bff > color sel #ff951dff > color sel #ff941fff > color sel #ff9420ff > color sel #ff9322ff > color sel #ff9224ff > color sel #ff9126ff > color sel #ff9027ff > color sel #ff8f28ff > color sel #ff8e29ff > color sel #ff8d2aff > color sel #ff8c2bff > color sel #ff8a2cff > color sel #ff882dff > color sel #ff872fff > color sel #ff8530ff > color sel #ff8331ff > color sel #ff8131ff > color sel #ff7f31ff > color sel #ff7e31ff > color sel #ff7d30ff > color sel #ff7d31ff > color sel #ff7d32ff > color sel #ff7e32ff > color sel #ff7e33ff > color sel #ff7f34ff > color sel #ff8036ff > color sel #ff8238ff > color sel #ff833bff > color sel #ff843dff > color sel #ff863eff > color sel #ff863fff > color sel #ff8640ff > color sel #ff8740ff > color sel #ff8741ff > color sel #ff8842ff > color sel #ff8843ff > color sel #ff8a45ff > color sel #ff8b47ff > color sel #ff8d49ff > color sel #ff8e4bff > color sel #ff8e4cff > color sel #ff8f4dff > color sel #ff904dff > color sel #ff904cff > color sel #ff914cff > color sel #ff924cff > color sel #ff934dff > color sel #ff954eff > color sel #ff984fff > color sel #ff9a50ff > color sel #ff9c51ff > color sel #ff9e51ff > color sel #ff9f52ff > color sel #ffa052ff > color sel #ffa153ff > color sel #ffa253ff > color sel #ffa454ff > color sel #ffa554ff > color sel #ffa755ff > color sel #ffa855ff > color sel #ffa956ff > color sel #ffaa56ff > color sel #ffab57ff > color sel #ffac57ff > color sel #ffae58ff > color sel #ffb058ff > color sel #ffb259ff > color sel #ffb45aff > color sel #ffb75bff > color sel #ffb95cff > color sel #ffbb5dff > color sel #ffbc5dff > color sel #ffbe5eff > color sel #ffc05fff > color sel #ffc260ff > color sel #ffc361ff > color sel #ffc562ff > color sel #ffc763ff > color sel #ffc863ff > color sel #ffc964ff > color sel #ffca64ff > color sel #ffcb64ff > color sel #ffcc64ff > color sel #ffcd65ff > color sel #ffce65ff > color sel #ffcf66ff > color sel #ffd066ff > color sel #ffd167ff > color sel #ffd267ff > color sel #ffd368ff > color sel #ffd468ff > color sel #ffd568ff > color sel #ffd668ff > color sel #ffd769ff > color sel #ffd969ff > color sel #ffda69ff > color sel #ffdb68ff > color sel #ffdc68ff > color sel #ffde67ff > color sel #ffdf67ff > color sel #ffe166ff > color sel #ffe265ff > color sel #ffe464ff > color sel #ffe563ff > color sel #ffe662ff > color sel #ffe760ff > color sel #ffe95eff > color sel #ffea5dff > color sel #ffeb5bff > color sel #ffec59ff > color sel #ffed57ff > color sel #ffee55ff > color sel #ffef53ff > color sel #fff052ff > color sel #fff150ff > color sel #fff14eff > color sel #fff24cff > color sel #fff24aff > color sel #fff347ff > color sel #fff445ff > color sel #fff444ff > color sel #fff442ff > color sel #fff542ff > color sel #fff541ff > color sel #fff641ff > color sel #fff742ff > color sel #fff944ff > color sel #fffa46ff > color sel #fffb4aff > color sel #fffc4eff > color sel #fffd51ff > color sel #fffd54ff > color sel #fffd56ff > color sel #fffd58ff > color sel #fffc5aff > color sel #fffc5cff > color sel #fffc5eff > color sel #fffb61ff > color sel #fffb64ff > color sel #fffc66ff > color sel #fffb69ff > color sel #fffb6aff > color sel #fffb6cff > color sel #fffb6eff > color sel #fffb6fff > color sel #fffc71ff > color sel #fffd74ff > color sel #fffd76ff > color sel #fffe78ff > color sel #ffff7bff > color sel #ffff7dff > color sel #feff7fff > color sel #fdff81ff > color sel #fdff84ff > color sel #fdff87ff > color sel #fcff8aff > color sel #fcff8dff > color sel #fdff90ff > color sel #fdff92ff > color sel #fdff94ff > color sel #fdff95ff > color sel #feff97ff > color sel #feff99ff > color sel #feff9aff > color sel #feff9cff > color sel #feff9dff > color sel #ffff9eff > color sel #ffffa0ff > color sel #ffffa1ff > color sel #ffffa2ff > color sel #ffffa3ff > color sel #fffea4ff > color sel #fffea5ff > color sel #fffea6ff > color sel #fffea7ff > color sel #fffda8ff > color sel #fffca7ff > color sel #fffba7ff > color sel #fffaa6ff > color sel #fff9a5ff > color sel #fff8a5ff > color sel #fff6a4ff > color sel #fff4a4ff > color sel #fff2a3ff > color sel #fff0a2ff > color sel #ffeda1ff > color sel #ffeaa1ff > color sel #ffe8a0ff > color sel #ffe59fff > color sel #ffe39fff > color sel #ffe09eff > color sel #ffde9eff > color sel #ffda9dff > color sel #ffd89dff > color sel #ffd79cff > color sel #ffd59bff > color sel #ffd39bff > color sel #ffd199ff > color sel #ffcf98ff > color sel #ffcd97ff > color sel #ffcb96ff > color sel #ffc995ff > color sel #ffc894ff > color sel #ffc792ff > color sel #ffc490ff > color sel #ffc18eff > color sel #ffbf8cff > color sel #ffbc89ff > color sel #ffba88ff > color sel #ffb987ff > color sel #ffb786ff > color sel #ffb785ff > color sel #ffb685ff > color sel #ffb684ff > color sel #ffb583ff > color sel #ffb482ff > color sel #ffb381ff > color sel #ffb280ff > color sel #ffb07eff > color sel #ffae7cff > color sel #ffac7bff > color sel #ffaa79ff > color sel #ffa977ff > color sel #ffa776ff > color sel #ffa573ff > color sel #ffa270ff > color sel #ff9f6dff > color sel #ff9c6aff > color sel #ff9a67ff > color sel #ff9864ff > color sel #ff9663ff > color sel #ff9561ff > color sel #ff9460ff > color sel #ff935fff > color sel #ff935eff > color sel #ff925dff > color sel #ff905cff > color sel #ff8f5bff > color sel #ff8e59ff > color sel #ff8c57ff > color sel #ff8b55ff > color sel #ff8a54ff > color sel #ff8852ff > color sel #ff8751ff > color sel #ff8650ff > color sel #ff8550ff > color sel #ff854fff > color sel #ff844eff > color sel #ff834dff > color sel #ff824cff > color sel #ff814bff > color sel #ff7f4aff > color sel #ff7e48ff > color sel #ff7d47ff > color sel #ff7b46ff > color sel #ff7a44ff > color sel #ff7943ff > color sel #ff7842ff > color sel #ff7741ff > color sel #ff7640ff > color sel #ff7540ff > color sel #ff753fff > color sel #ff743eff > color sel #ff733dff > color sel #ff703bff > color sel #ff6e38ff > color sel #ff6b36ff > color sel #ff6a34ff > color sel #ff6833ff > color sel #ff6732ff > color sel #ff6731ff > color sel #ff6631ff > color sel #ff6630ff > color sel #ff642eff > color sel #ff632cff > color sel #ff612aff > color sel #ff6028ff > color sel #ff5f26ff > color sel #ff5e25ff > color sel #ff5e23ff > color sel #ff5e20ff > color sel #ff5e1eff > color sel #ff5e1bff > color sel #ff5f19ff > color sel #ff6016ff > color sel #ff6014ff > color sel #ff6213ff > color sel #ff6312ff > color sel #ff6410ff > color sel #ff640fff > color sel #ff650dff > color sel #ff650bff > color sel #ff650aff > color sel #ff6509ff > color sel #ff6508ff > color sel #ff6406ff > color sel #ff6404ff > color sel #ff6201ff > color sel #ff6200ff > color sel #ff6001ff > color sel #ff5f00ff > color sel #ff5d00ff > color sel #ff5b00ff > color sel #ff5700ff > color sel #ff5500ff > color sel #ff5200ff > color sel #ff4e00ff > color sel #ff4b00ff > color sel #ff4800ff > color sel #ff4600ff > color sel #ff4300ff > color sel #ff4100ff > color sel #ff3f00ff > color sel #ff3c00ff > color sel #ff3900ff > color sel #ff3500ff > color sel #ff3000ff > color sel #ff2b00ff > color sel #ff2600ff > color sel #ff2400ff > color sel #ff1f00ff > color sel #ff1a00ff > color sel #ff1800ff > color sel #ff1500ff > color sel #ff1300ff > color sel #ff1100ff > color sel #ff0e00ff > color sel #ff0c00ff > color sel #ff0a00ff > color sel #ff0700ff > color sel #ff0500ff > color sel #ff0200ff > color sel #ff0000ff > color sel #ff0002ff > color sel #ff0005ff > color sel #ff0002ff > color sel #ff0000ff > color sel #ff0500ff > color sel #ff0700ff > color sel #ff0a00ff > color sel #ff0e00ff > color sel #ff1100ff > color sel #ff1300ff > color sel #ff1800ff > color sel #ff1a00ff > color sel #ff1d00ff > color sel #ff1f00ff > color sel #ff2200ff > color sel #ff2600ff > color sel #ff2900ff > color sel #ff2d00ff > color sel #ff3200ff > color sel #ff3700ff > color sel #ff3901ff > color sel #ff3e04ff > color sel #ff4306ff > color sel #ff4809ff > color sel #ff4d0cff > color sel #ff5310ff > color sel #ff5814ff > color sel #ff5d16ff > color sel #ff6119ff > color sel #ff661cff > color sel #ff6a1fff > color sel #ff6e21ff > color sel #ff7225ff > color sel #ff7729ff > color sel #ff7d2eff > color sel #ff8433ff > color sel #ff8937ff > color sel #ff8d3aff > color sel #ff903cff > color sel #ff923eff > color sel #ff9440ff > color sel #ff9743ff > color sel #ff9a46ff > color sel #ff9d4aff > color sel #ffa04dff > color sel #ffa150ff > color sel #ffa353ff > color sel #ffa456ff > color sel #ffa558ff > color sel #ffa65aff > color sel #ffa75cff > color sel #ffa85eff > color sel #ffa960ff > color sel #ffaa61ff > color sel #ffab63ff > color sel #ffac65ff > color sel #ffae68ff > color sel #ffb06aff > color sel #ffb26dff > color sel #ffb46fff > color sel #ffb671ff > color sel #ffb773ff > color sel #ffb974ff > color sel #ffba76ff > color sel #ffbc78ff > color sel #ffbd79ff > color sel #ffbf7bff > color sel #ffc07cff > color sel #ffc27eff > color sel #ffc37fff > color sel #ffc580ff > color sel #ffc682ff > color sel #ffc783ff > color sel #ffc883ff > color sel #ffc884ff > color sel #ffc984ff > color sel #ffca85ff > color sel #ffcb86ff > color sel #ffcb87ff > color sel #ffcc87ff > color sel #ffcb86ff > color sel #ffca85ff > color sel #ffc884ff > color sel #ffc782ff > color sel #ffc480ff > color sel #ffc37dff > color sel #ffc17bff > color sel #ffc079ff > color sel #ffbe76ff > color sel #ffbc74ff > color sel #ffba70ff > color sel #ffb86cff > color sel #ffb668ff > color sel #ffb364ff > color sel #ffb160ff > color sel #ffae5dff > color sel #ffac5aff > color sel #ffab58ff > color sel #ffaa56ff > color sel #ffa955ff > color sel #ffa854ff > color sel #ffa753ff > color sel #ffa651ff > color sel #ffa550ff > color sel #ffa44eff > color sel #ffa34cff > color sel #ffa24bff > color sel #ffa14aff > color sel #ffa149ff > color sel #ffa048ff > color sel #ff9f47ff > color sel #ff9f46ff > color sel #ff9e45ff > color sel #ff9d44ff > color sel #ff9d43ff > color sel #ff9c42ff > color sel #ff9b41ff > color sel #ff9a40ff > color sel #ff9a3fff > color sel #ff993eff > color sel #ff983cff > color sel #ff973bff > color sel #ff963aff > color sel #ff9538ff > color sel #ff9437ff > color sel #ff9336ff > color sel #ff9235ff > color sel #ff9234ff > color sel #ff9133ff > color sel #ff9132ff > color sel #ff9031ff > color sel #ff8f30ff > color sel #ff8f2fff > color sel #ff8e2eff > color sel #ff8d2cff > color sel #ff8c2bff > color sel #ff8b2aff > color sel #ff8a28ff > color sel #ff8927ff > color sel #ff8826ff > color sel #ff8724ff > color sel #ff8623ff > color sel #ff8521ff > color sel #ff8420ff > color sel #ff841fff > color sel #ff8420ff > color sel #ff8421ff > color sel #ff8322ff > color sel #ff8323ff > color sel #ff8324ff > color sel #ff8325ff > color sel #ff8227ff > color sel #ff8229ff > color sel #ff812bff > color sel #ff812dff > color sel #ff802fff > color sel #ff8030ff > color sel #ff7f31ff > color sel #ff7f32ff > color sel #ff7f33ff > color sel #ff8035ff > color sel #ff8539ff > color sel #ff8d42ff > color sel #ff9b52ff > color sel #ffae68ff > color sel #ffc383ff > color sel #ffdaa1ff > color sel #fff0c0ff > color sel #f9ffdfff > color sel #e5ffefff > color sel #cefffdff > color sel #b6f6ffff > color sel #a1edffff > color sel #8fe6ffff > color sel #80e1ffff > color sel #6fdcffff > color sel #60d8ffff > color sel #51d4ffff > color sel #44d1ffff > color sel #39cfffff > color sel #31cdffff > color sel #2bcdffff > color sel #28cdffff > color sel #26cdffff > color sel #25cdffff > color sel #25ceffff > color sel #24cfffff > color sel #24d3ffff > color sel #25d8ffff > color sel #24ddffff > color sel #23e3ffff > color sel #22e7ffff > color sel #21ebffff > color sel #20efffff > color sel #1ef1ffff > color sel #1cf4ffff > color sel #19f5ffff > color sel #17f7ffff > color sel #15f8ffff > color sel #13f8ffff > color sel #13f9ffff > color sel #16faffff > color sel #1ffcffff > color sel #32ffffff > color sel #4dfffcff > color sel #6ffff8ff > color sel #99fff3ff > color sel #c2ffedff > color sel #e0ffe1ff > color sel #fffad6ff > color sel #ffe0b9ff > color sel #ffcea5ff > color sel #ffc298ff > color sel #ffb88eff > color sel #ffb187ff > color sel #ffad83ff > color sel #ffaa80ff > color sel #ffa87eff > color sel #ffa67cff > color sel #ffa379ff > color sel #ffa076ff > color sel #ff9b72ff > color sel #ff976dff > color sel #ff9168ff > color sel #ff8c63ff > color sel #ff865eff > color sel #ff815aff > color sel #ff7d57ff > color sel #ff7853ff > color sel #ff7350ff > color sel #ff6f4dff > color sel #ff6a4aff > color sel #ff6748ff > color sel #ff6346ff > color sel #ff5f43ff > color sel #ff5c41ff > color sel #ff583fff > color sel #ff553dff > color sel #ff513aff > color sel #ff4e39ff > color sel #ff4b37ff > color sel #ff4835ff > color sel #ff4532ff > color sel #ff4230ff > color sel #ff3e2dff > color sel #ff392aff > color sel #ff3527ff > color sel #ff3124ff > color sel #ff2d21ff > color sel #ff2a1eff > color sel #ff271bff > color sel #ff2519ff > color sel #ff2318ff > color sel #ff2216ff > color sel #ff2015ff > color sel #ff1e13ff > color sel #ff1b10ff > color sel #ff180eff > color sel #ff160cff > color sel #ff1309ff > color sel #ff1108ff > color sel #ff0f06ff > color sel #ff0e05ff > color sel #ff0c04ff > color sel #ff0c03ff > color sel #ff0c04ff > color sel #ff0e06ff > color sel #ff120aff > color sel #ff1910ff > color sel #ff2017ff > color sel #ff271eff > color sel #ff2f25ff > color sel #ff352cff > color sel #ff3b31ff > color sel #ff4037ff > color sel #ff453bff > color sel #ff493fff > color sel #ff4c42ff > color sel #ff4e44ff > color sel #ff5146ff > color sel #ff5348ff > color sel #ff564bff > color sel #ff594eff > color sel #ff5d51ff > color sel #ff6054ff > color sel #ff6356ff > color sel #ff6659ff > color sel #ff695bff > color sel #ff6b5eff > color sel #ff6e61ff > color sel #ff7163ff > color sel #ff7365ff > color sel #ff7566ff > color sel #ff7667ff > color sel #ff7767ff > color sel #ff7868ff > color sel #ff7869ff > color sel #ff7969ff > color sel #ff7a6aff > color sel #ff7a6bff > color sel #ff7a6aff > color sel #ff796aff > color sel #ff7969ff > color sel #ff7869ff > color sel #ff7868ff > color sel #ff7767ff > color sel #ff7667ff > color sel #ff7666ff > color sel #ff7665ff > color sel #ff7565ff > color sel #ff7564ff > color sel #ff7463ff > color sel #ff7362ff > color sel #ff7262ff > color sel #ff7261ff > color sel #ff7161ff > color sel #ff7160ff > color sel #ff7060ff > color sel #ff705fff > color sel #ff6f5eff > color sel #ff6e5eff > color sel #ff6e5dff > color sel #ff6d5cff > color sel byhetero > select clear > hide atoms > select #1/?: UNL 48 atoms, 48 bonds, 1 residue, 1 model selected > show sel atoms > select clear > set bgColor white > select #1/?: Expected an objects specifier or a keyword > select #1/? 13310 atoms, 13435 bonds, 891 residues, 1 model selected > transparency 0 > select clear > lighting full > lighting shadows false > graphics silhouettes true > graphics silhouettes false > select clear > open /Users/ehecatlga/work/clusters_trial/cluster_400ns/rep.c1.pdb Chain information for rep.c1.pdb #2 --- Chain | Description ? | No description available > ui tool show Matchmaker The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > matchmaker #2 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 rep.c0.pdb, chain (blank) (#1) with rep.c1.pdb, chain (blank) (#2), sequence alignment score = 4262.5 RMSD between 724 pruned atom pairs is 1.058 angstroms; (across all 890 pairs: 1.810) > hide #!1 models > hide #2 atoms > select #2/? 13310 atoms, 13435 bonds, 891 residues, 1 model selected > show sel surfaces > color (#!2 & sel) byhetero > undo > color (#!2 & sel) #ff6e5eff > color (#!2 & sel) #ff665fff > color (#!2 & sel) #ff5f61ff > color (#!2 & sel) #ff5f6aff > color (#!2 & sel) #ff606eff > color (#!2 & sel) #ff6176ff > color (#!2 & sel) #ff617aff > color (#!2 & sel) #ff617eff > color (#!2 & sel) #ff6282ff > color (#!2 & sel) #ff6387ff > color (#!2 & sel) #ff638aff > color (#!2 & sel) #ff648fff > color (#!2 & sel) #ff6491ff > color (#!2 & sel) #ff6492ff > color (#!2 & sel) #ff6497ff > color (#!2 & sel) #ff649cff > color (#!2 & sel) #ff64a0ff > color (#!2 & sel) #ff64a6ff > color (#!2 & sel) #ff64aaff > color (#!2 & sel) #ff63b2ff > color (#!2 & sel) #ff62b7ff > color (#!2 & sel) #ff61bbff > color (#!2 & sel) #ff61bfff > color (#!2 & sel) #ff60c3ff > color (#!2 & sel) #ff61cbff > color (#!2 & sel) #ff60ceff > color (#!2 & sel) #ff60cfff > color (#!2 & sel) #ff65cdff > color (#!2 & sel) #ff71c9ff > color (#!2 & sel) #ff7ec5ff > color (#!2 & sel) #ff8ac2ff > color (#!2 & sel) #ff8ebfff > color (#!2 & sel) #ff94bbff > color (#!2 & sel) #ff98b9ff > color (#!2 & sel) #ff9cb6ff > color (#!2 & sel) #ffa2b3ff > color (#!2 & sel) #ffaab2ff > color (#!2 & sel) #ffafb0ff > color (#!2 & sel) #ffb2b0ff > color (#!2 & sel) #ffb5b1ff > color (#!2 & sel) #ffbab0ff > color (#!2 & sel) #ffbfaeff > color (#!2 & sel) #ffc0abff 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sel #93ff7bff > color sel #95ff7cff > color sel #98ff7cff > color sel #9dff7eff > color sel #9fff7eff > color sel #a1ff7eff > color sel #a2ff7fff > color sel #a4ff80ff > color sel #a7ff82ff > color sel #adff87ff > color sel #b0ff8aff > color sel #b3ff8eff > color sel #b9ff96ff > color sel #bbff9aff > color sel #bdff9dff > color sel #bfffa0ff > color sel #c1ffa2ff > color sel #c2ffa5ff > color sel #c4ffa7ff > color sel #c5ffa9ff > color sel #c9ffadff > color sel #caffaeff > color sel #cbffafff > color sel #cbffaeff > color sel #caffadff > color sel #c9ffadff > color sel #c8ffabff > color sel #c6ffa9ff > color sel #c4ffa7ff > color sel #c2ffa4ff > color sel #bfffa2ff > color sel #bdff9fff > color sel #bbff9bff > color sel #b9ff98ff > color sel #b7ff95ff > color sel #b3ff90ff > color sel #b1ff8dff > color sel #afff8aff > color sel #aeff88ff > color sel #acff86ff > color sel #abff83ff > color sel #a9ff80ff > color sel #a8ff7dff > color sel #a5ff77ff > color sel #a3ff74ff > color sel #a2ff72ff > color sel #a1ff70ff > color sel #a1ff6fff > color sel #a0ff6eff > color sel #9fff6dff > color sel #9fff6cff > color sel #a0ff6bff > color sel #a0ff6cff > color sel #a1ff6dff > color sel #a0ff6dff > color sel #9fff6dff > color sel #9eff6dff > color sel #9eff6eff > color sel #9dff6eff > color sel #9dff6fff > color sel #9dff70ff > color sel byhetero > select clear > select #2/?: UNL 48 atoms, 48 bonds, 1 residue, 1 model selected > color sel #f1ffa5ff > color sel #f2ffa5ff > color sel #f3ffa4ff > color sel #f7ffa3ff > color sel #fcffa7ff > color sel #ffffaaff > color sel #fff9b4ff > color sel #fff3bfff > color sel #ffefc5ff > color sel #ffeacbff > color sel #ffe8cdff > color sel #ffe7ceff > color sel #ffe6cfff > color sel #ffe7d0ff > color sel #ffe7d2ff > color sel #ffe7d5ff > color sel #ffe8d7ff > color sel #ffe8d9ff > color sel #ffe8dbff > color sel #ffe8dcff > color sel #ffeadbff > color sel #f1ddcfff > color sel #f0dcceff > color sel #efdbcdff > color sel #ead7c9ff > color sel #e6d3c6ff > color sel #e4d1c4ff > color sel #e2cfc2ff > color sel #deccbfff > color sel #d3c2b6ff > color sel #d0beb2ff > color sel #c8b8acff > color sel #c5b4a9ff > color sel #c1b1a6ff > color sel #bdada2ff > color sel #bbaca1ff > color sel #bbaba1ff > color sel #bbaba0ff > color sel #bcaca1ff > color sel #bfafa4ff > color sel #c5b4a9ff > color sel #cebdb1ff > color sel #d8c6baff > color sel #edd9ccff > color sel #f5e1d3ff > color sel #fce7d9ff > color sel #ffeadbff > color sel #ffe7d4ff > color sel #ffe8d3ff > color sel #fff0d2ff > color sel #fff6d3ff > color sel #fffcd4ff > color sel #f1ffd0ff > color sel #e9ffceff > color sel #e1ffc9ff > color sel #d8ffc4ff > color sel #c9ffbaff > color sel #c3ffb5ff > color sel #baffaeff > color sel #b7ffacff > color sel #b5ffabff > color sel #b3ffa9ff > color sel #aeffa5ff > color sel #acffa3ff > color sel #a5ff9eff > color sel #a2ff9cff > color sel #9dff97ff > color sel #98ff93ff > color sel #96ff92ff > color sel #95ff90ff > color sel #94ff8fff > color sel #93ff8eff > color sel #93fe8eff > color sel #8bf187ff > color sel #89ee85ff > color sel #87ea83ff > color sel #83e47fff > color sel #81e07dff > color sel #7ed979ff > color sel #7bd677ff > color sel #79d275ff > color sel #77ce73ff > color sel #75cb71ff > color sel #71c46eff > color sel #6ebf6aff > color sel #6cbc69ff > color sel #6bb967ff > color sel #68b364ff > color sel #66b163ff > color sel #65af62ff > color sel #64ae61ff > color sel #63ac60ff > color sel #62aa5fff > color sel #61a85eff > color sel #60a65dff > color sel #5fa55cff > color sel #5ea35bff > color sel #5da25aff > color sel #5da15aff > color sel #5c9f59ff > color sel #5b9e58ff > color sel #5a9d57ff > color sel #5a9c57ff > color sel #599b56ff > color sel #599a56ff > color sel #599956ff > color sel #589955ff > color sel #599956ff > color sel #599a56ff > color sel #5a9c57ff > color sel #5a9d57ff > color sel #5b9d58ff > color sel #5ea35bff > color sel #61a85eff > color sel #69b665ff > color sel #6dbc69ff > color sel #73c86fff > color sel #76cc72ff > color sel #79d275ff > color sel #7ad476ff > color sel #7bd577ff > color sel #7bd677ff > color sel #7cd778ff > color sel #7cd878ff > color sel #7dd979ff > color sel #7fdb7aff > color sel #7fdc7bff > color sel #80de7cff > color sel #85e680ff > color sel #87eb83ff > color sel #8af086ff > color sel #8df589ff > color sel #91fa8cff > color sel #93ff8eff > color sel forest green > color sel byhetero > select clear > select #2/?:447 17 atoms, 16 bonds, 1 residue, 1 model selected > hide sel cartoons > select #2/?:448 19 atoms, 18 bonds, 1 residue, 1 model selected > hide sel cartoons > select clear > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > ui tool show ""Side View"" > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models ===== 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 > open ""/Volumes/TOSHIBA > EXT/Rorqual_July_2025/filtering_eigthround/filtered_poses.sdf"" > hide #1.1-124 target m > show #1.1 models > hide #1.1 models > show #1.2 models > show #1.1 models > hide #1.2 models > select add #1.1 43 atoms, 44 bonds, 1 residue, 1 model selected > select subtract #1.1 Nothing selected > hide #1.1 models > show #1.3 models > hide #1.3 models > show #1.4 models > hide #1.4 models > show #1.5 models > hide #1.5 models > show #1.1 models > hide #1.1 models > show #1.37 models > hide #1.37 models > show #1.49 models > hide #1.49 models > show #1.53 models > hide #1.53 models > show #1.95 models > hide #1.95 models > show #1.2 models > open > /Users/ehecatlga/work/Fitted_tutorial/1hkw_docking/1hkw_cluster_40ns_docking/1hkw1_cluster1_process_prepare/cluster_c1_correct_dummy_pro.mol2 Chain information for cluster_c1_correct_dummy_pro.mol2 #2 --- Chain | Description ? | No description available Opened cluster_c1_correct_dummy_pro.mol2 containing 1 structure (13335 atoms, 13456 bonds) > hide #1.2 models > show #1.1 models > select add #1.1 43 atoms, 44 bonds, 1 residue, 1 model selected > select sel @< 5 5907 atoms, 6144 bonds, 146 residues, 125 models selected > show sel & #2#1.1 atoms > ui mousemode right select > select clear OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M3 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.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: Mac15,6 Model Number: MRX33LL/A Chip: Apple M3 Pro Total Number of Cores: 11 (5 performance and 6 efficiency) Memory: 18 GB System Firmware Version: 11881.121.1 OS Loader Version: 11881.121.1 Software: System Software Overview: System Version: macOS 15.5 (24F74) Kernel Version: Darwin 24.5.0 Time since boot: 23 days, 56 minutes Graphics/Displays: Apple M3 Pro: Chipset Model: Apple M3 Pro Type: GPU Bus: Built-In Total Number of Cores: 14 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 S2409W: 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