id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15760 Crash on Mac waking from sleep hannesludewig@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.1-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. Fatal Python error: Segmentation fault Current thread 0x00000001e2db9ec0 (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.pdb_lib._load_libs, openmm._openmm, openmm.app.internal.compiled, 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.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, chimerax.atom_search.ast, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PIL._webp (total: 66) {""app_name"":""ChimeraX"",""timestamp"":""2024-08-13 15:11:53.00 -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 14.1 (23B74)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""EFB1616F-F637-4038-B3E6-6B72BD52BE7B""} { ""uptime"" : 150000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""Mac14,5"", ""coalitionID"" : 4393, ""osVersion"" : { ""train"" : ""macOS 14.1"", ""build"" : ""23B74"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2024-08-13 15:11:49.2148 -0400"", ""codeSigningMonitor"" : 1, ""incident"" : ""EFB1616F-F637-4038-B3E6-6B72BD52BE7B"", ""pid"" : 19620, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2024-08-12 18:37:07.9729 -0400"", ""procStartAbsTime"" : 3168971316022, ""procExitAbsTime"" : 3681925374739, ""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"":""BCFC189E-F43E-5EBE-9E96-04E464046690"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""99BD7651-6EDA-2D82-7078-BC72DBC083D3"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""instructionByteStream"" : {""beforePC"":""fyMD1f17v6n9AwCRXOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A=="",""atPC"":""AwEAVH8jA9X9e7+p\/QMAkVHg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g==""}, ""sleepWakeUUID"" : ""12F3D603-8258-41C8-A4F6-218B48EB152A"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x613bd5ee5978 is not in any region. 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\nTOTAL, minus reserved VM space 5.4G 5187 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""9139c9e4937f07eab0698b5148eee028f1057b71"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""64628732bf2f5257dedc8988"", ""factorPackIds"" : { }, ""deploymentId"" : 240000001 }, { ""rolloutId"" : ""5fb4245a1bbfe8005e33a1e1"", ""factorPackIds"" : { }, ""deploymentId"" : 240000021 } ], ""experiments"" : [ { ""treatmentId"" : ""c47ab4cc-c9c3-4b5d-a87c-e2433ce02597"", ""experimentId"" : ""6639bc6ba73d460582162323"", ""deploymentId"" : 400000006 }, { ""treatmentId"" : ""45f4e2a5-551b-4bc2-a2dc-19c244dda8f8"", ""experimentId"" : ""6643969b3099cf28e049862f"", ""deploymentId"" : 400000007 } ] } } ===== 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/hannesludewig/Desktop/ANC2_AflAdk_MgADP_AF3_V4M_comparison.cxs Log from Fri Aug 9 11:08:10 2024 > graphics silhouettes true > lighting shadows true > lighting flat > lighting full > lighting soft > color name goldHL #cc9900 Color 'goldHL' is opaque: rgb(80%, 60%, 0%) hex: #cc9900 > color name lightblueHL #66ccff Color 'lightblueHL' is opaque: rgb(40%, 80%, 100%) hex: #66ccff > color name greenHL #009966 Color 'greenHL' is opaque: rgb(0%, 60%, 40%) hex: #009966 > color name yellowHL #cccc33 Color 'yellowHL' is opaque: rgb(80%, 80%, 20%) hex: #cccc33 > color name blueHL #006699 Color 'blueHL' is opaque: rgb(0%, 40%, 60%) hex: #006699 > color name orangeHL #cc6600 Color 'orangeHL' is opaque: rgb(80%, 40%, 0%) hex: #cc6600 > color name pinkHL #cc6699 Color 'pinkHL' is opaque: rgb(80%, 40%, 60%) hex: #cc6699 > color name darkblueHL #003478 Color 'darkblueHL' is opaque: rgb(0%, 20.4%, 47.1%) hex: #003478 > color name blueGRC #93A9D7 Color 'blueGRC' is opaque: rgb(57.6%, 66.3%, 84.3%) hex: #93a9d7 > color name lightblueGRC #DBE2F1 Color 'lightblueGRC' is opaque: rgb(85.9%, 88.6%, 94.5%) hex: #dbe2f1 > color name orangeGRC #EAB48A Color 'orangeGRC' is opaque: rgb(91.8%, 70.6%, 54.1%) hex: #eab48a > color name lightorangeGRC #F7E6D7 Color 'lightorangeGRC' is opaque: rgb(96.9%, 90.2%, 84.3%) hex: #f7e6d7 > color name greenGRC #B0CF94 Color 'greenGRC' is opaque: rgb(69%, 81.2%, 58%) hex: #b0cf94 > color name lightgreenGRC #E4EFDB Color 'lightgreenGRC' is opaque: rgb(89.4%, 93.7%, 85.9%) hex: #e4efdb 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/hannesludewig/Downloads/ANC2/wt_MgADP/fold_2024_05_09_20_49_model_0.cif Chain information for fold_2024_05_09_20_49_model_0.cif #1 --- Chain | Description A | . > open > /Users/hannesludewig/Downloads/AF/AF_wt_MgADP/fold_2024_05_09_20_53_model_0.cif Chain information for fold_2024_05_09_20_53_model_0.cif #2 --- Chain | Description A | . > mmaker #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 fold_2024_05_09_20_49_model_0.cif, chain A (#1) with fold_2024_05_09_20_53_model_0.cif, chain A (#2), sequence alignment score = 891.7 RMSD between 204 pruned atom pairs is 0.799 angstroms; (across all 217 pairs: 2.301) > lighting soft > hide atoms > select ::name=""ADP"" 108 atoms, 116 bonds, 4 residues, 2 models selected > show sel atoms > select ::name=""MG"" 2 atoms, 2 residues, 2 models selected > show sel atoms > select clear > select :4 15 atoms, 13 bonds, 2 residues, 2 models selected > show sel atoms > select clear > color #1 #006699ff > color #2 #cc6600ff > color byhetero > select #2 1735 atoms, 1760 bonds, 220 residues, 1 model selected > color sel goldHL > color sel byhetero > select clear > select :28-31 62 atoms, 62 bonds, 8 residues, 2 models selected > color sel light grey > select :42-51 141 atoms, 139 bonds, 20 residues, 2 models selected > color sel light grey > select :58-63 92 atoms, 92 bonds, 12 residues, 2 models selected > color sel light grey > select :71-80 154 atoms, 153 bonds, 20 residues, 2 models selected > color sel light grey > select :114-120 115 atoms, 114 bonds, 14 residues, 2 models selected > color sel light grey > select :123-125 52 atoms, 50 bonds, 6 residues, 2 models selected > color sel light grey > select :161-165 77 atoms, 75 bonds, 10 residues, 2 models selected > color sel light grey > select :176-182 112 atoms, 112 bonds, 14 residues, 2 models selected > color sel light grey > select clear > select #2/A:4@CG2 1 atom, 1 residue, 1 model selected > select up 7 atoms, 6 bonds, 1 residue, 1 model selected > contacts sel restrict #2 select true reveal true 12 contacts > select up 72 atoms, 68 bonds, 9 residues, 1 model selected > show sel atoms > color sel byhetero > select clear > undo > color sel orangeHL > color sel byhetero > select #2/A:4@CG2 1 atom, 1 residue, 1 model selected > undo > style sel sphere Changed 72 atom styles > style sel stick Changed 72 atom styles > hide #1 models > select #2/A:83@CD2 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > contacts sel restrict #2 select true reveal true 13 contacts > select #2/A:86@CZ 1 atom, 1 residue, 1 model selected > select up 11 atoms, 11 bonds, 1 residue, 1 model selected > contacts sel restrict #2 select true reveal true 26 contacts > select #2/A:6@SD 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 39 atoms, 38 bonds, 5 residues, 1 model selected > select down 8 atoms, 7 bonds, 1 residue, 1 model selected > contacts sel restrict #2 select true reveal true 16 contacts > select clear > select #2:166 5 atoms, 4 bonds, 1 residue, 1 model selected > select #2/A:83@CG 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:6@CE 1 atom, 1 residue, 1 model selected > save /Users/hannesludewig/Desktop/ANC2_AflAdk_MgADP_AF3_V4M_comparison.cxs ——— End of log from Fri Aug 9 11:08:10 2024 ——— opened ChimeraX session > select #2/A:4@CG2 1 atom, 1 residue, 1 model selected > select up 7 atoms, 6 bonds, 1 residue, 1 model selected > style sel ball Changed 7 atom styles > select clear > select #2/A:6@CE 1 atom, 1 residue, 1 model selected > select #2/A:182@CG 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > contacts sel restrict #2 select true 16 contacts > select clear > select #2/A:186@CG 1 atom, 1 residue, 1 model selected > select up 12 atoms, 12 bonds, 1 residue, 1 model selected > hide sel atoms > select #2/A:112@CB 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select #2/A:183@CG 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select #2/A:111@CA 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select #2/A:110@CB 1 atom, 1 residue, 1 model selected > select up 7 atoms, 6 bonds, 1 residue, 1 model selected > hide sel atoms > select #2/A:30 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/A:29@CD1 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > contacts sel restrict #2 select true 13 contacts > select #2/A:81@CZ 1 atom, 1 residue, 1 model selected > select down 1 atom, 1 residue, 1 model selected > select up 11 atoms, 11 bonds, 1 residue, 1 model selected > hide sel atoms > select #2/A:29@CD1 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > contacts sel restrict #2 select true 13 contacts > select #2/A:3 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select #2/A:107@CB 1 atom, 1 residue, 1 model selected > hide sel atoms > select #2/A:5 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 39 atoms, 38 bonds, 5 residues, 1 model selected > select clear > select #2/A:107@CG2 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select clear > select #2/A:31@CG2 1 atom, 1 residue, 1 model selected > select up 7 atoms, 6 bonds, 1 residue, 1 model selected > contacts sel restrict #2 select true 12 contacts > select clear > select #2/A:96 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select #2/A:92 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #2/A:29@CB 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > style sel ball Changed 8 atom styles > select clear > select #2/A:31@CB 1 atom, 1 residue, 1 model selected > select up 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 85 atoms, 85 bonds, 11 residues, 1 model selected > style sel ball Changed 85 atom styles > select #2/A:182@CG 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > style sel ball Changed 8 atom styles > select clear > hide #2.1 models > select #2/A:64 7 atoms, 6 bonds, 1 residue, 1 model selected > hide sel atoms > select clear > select #2/A:68 7 atoms, 6 bonds, 1 residue, 1 model selected > hide sel atoms > select clear > ui tool show ""Side View"" > select #2/A:13@CD 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel atoms > select clear > save > /Users/hannesludewig/Desktop/ANC2_AflAdk_MgADP_AF3_V4M_comparison_cut_Afl.cxs > hide #!2 models > show #1 models > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > style sel ball Changed 8 atom styles > select clear > select #1/A:4@CG1 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 40 atoms, 39 bonds, 5 residues, 1 model selected > select down 8 atoms, 7 bonds, 1 residue, 1 model selected > contacts sel restrict #1 select true 14 contacts > contacts sel restrict #1 select true reveal true 30 contacts > select up 114 atoms, 106 bonds, 14 residues, 1 model selected > color sel lightblueHL > color sel byhetero > select clear > show #!2 models > hide #!1 models > hide #!2 models > show #!1 models > show #!2 models > hide #!1 models > hide #!2 models > show #!1 models > select #1/A:4@CD1 1 atom, 1 residue, 1 model selected > hide #!1 models > show #!2 models > open > /Users/hannesludewig/Downloads/AF_AF3/AFwt_V4M_MgADP_AF3/fold_2024_08_09_08_30_model_0.cif Chain information for fold_2024_08_09_08_30_model_0.cif #3 --- Chain | Description A | . > mmaker #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 fold_2024_05_09_20_49_model_0.cif, chain A (#1) with fold_2024_08_09_08_30_model_0.cif, chain A (#3), sequence alignment score = 893.3 RMSD between 204 pruned atom pairs is 0.746 angstroms; (across all 217 pairs: 2.228) > hide #!2 models > select #3/A:5 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:4 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3/A:4@CE 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > contacts sel restrict #3 reveal true select true 17 contacts > show #!2 models > hide #!2 models > hide #!3 models > show #!2 models > show #!1 models > hide #!2 models > show #!3 models > show #!2 models > hide #!1 models > show #!1 models > hide #!3 models > hide #!2 models > select #1/A:4@CB 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > contacts sel restrict #1 reveal true select true 14 contacts > select up 82 atoms, 77 bonds, 10 residues, 1 model selected > contacts sel restrict #1 reveal true select true 109 contacts > hide #1.1 models > select clear > select #1/A:182@CG 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > style sel ball Changed 8 atom styles > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > style sel ball Changed 2 atom styles > select clear > select #1/A:4@CG1 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > contacts sel restrict #1 reveal true select true 14 contacts > select up 82 atoms, 77 bonds, 10 residues, 1 model selected > contacts sel restrict #1 reveal true select true 109 contacts > select up 301 atoms, 286 bonds, 36 residues, 1 model selected > hide sel atoms > select #1/A:5 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:4 8 atoms, 7 bonds, 1 residue, 1 model selected > contacts sel restrict #1 reveal true select true 14 contacts > select up 82 atoms, 77 bonds, 10 residues, 1 model selected > select #1/A:29 8 atoms, 7 bonds, 1 residue, 1 model selected > show #!2 models > hide #!2 models > show sel atoms > style sel ball Changed 8 atom styles > show #!2 models > hide #!2 models > select #1/A:182 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select #1/A:29@CB 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 24 atoms, 24 bonds, 3 residues, 1 model selected > select down 8 atoms, 7 bonds, 1 residue, 1 model selected > contacts sel restrict #1 reveal true select true 13 contacts > select clear > undo > select up 2 atoms, 1 bond, 1 residue, 1 model selected > hide sel atoms > select clear > select #1/A:72@CD2 1 atom, 1 residue, 1 model selected > hide sel atoms > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select #1/A:28@CB 1 atom, 1 residue, 1 model selected > select up 10 atoms, 10 bonds, 1 residue, 1 model selected > hide sel atoms > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 11 atoms, 10 bonds, 1 residue, 1 model selected > hide sel atoms > select #1/A:29@CD1 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > contacts sel restrict #1 select true 13 contacts > select #1/A:182@CB 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > contacts sel restrict #1 select true 26 contacts > select clear > select #1/A:100 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel blueHL > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select #1/A:110@CB 1 atom, 1 residue, 1 model selected > select up 7 atoms, 6 bonds, 1 residue, 1 model selected > hide sel atoms > select #1/A:107@CG 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select clear > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > save /Users/hannesludewig/Desktop/ANC2_AflAdk_X4M_hinge_network.cxs > save /Users/hannesludewig/Desktop/ANC2_X4M_hinge_network.tif width 2000 > height 1265 supersample 4 transparentBackground true > show #!2 models > hide #!1 models > save /Users/hannesludewig/Desktop/AflAdk_X4M_hinge_network.tif width 2000 > height 1265 supersample 4 transparentBackground true > show #!1 models > hide #!2 models > save /Users/hannesludewig/Desktop/ANC2_X4M_hinge_network_normal_pose.tif > width 2000 height 1265 supersample 4 transparentBackground true > show #!2 models > hide #!1 models > save /Users/hannesludewig/Desktop/AflAdk_X4M_hinge_network_normal_pose.tif > width 2000 height 1265 supersample 4 transparentBackground true > hide #!2 models > show #!1 models > rename Missing or invalid ""models"" argument: empty atom specifier > rename #1 ANC2_WT_MgADP > rename #1 AF3_ANC2-MgADP > rename #2 AF3_AflAdk-MgADP > show #!3 models > hide #!1 models > rename #3 AF3_ANC2:I4M-MgADP > open > /Users/hannesludewig/Downloads/AF_AF3/AFwt_V4M_MgADP_AF3/fold_2024_08_09_08_30_model_0.cif Chain information for fold_2024_08_09_08_30_model_0.cif #4 --- Chain | Description A | . > rename #4 AF3_AflAdk:V4M-MgADP > mmaker #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 AF3_ANC2-MgADP, chain A (#1) with AF3_AflAdk:V4M-MgADP, chain A (#4), sequence alignment score = 893.3 RMSD between 204 pruned atom pairs is 0.746 angstroms; (across all 217 pairs: 2.228) > hide #!3 models > show #!1 models > hide #4 models > color #3 #006699ff > color #4 orangeHL > color #4 goldHL > select #4 1736 atoms, 1761 bonds, 220 residues, 1 model selected > colorsel Unknown command: colorsel > select 6950 atoms, 7051 bonds, 55 pseudobonds, 880 residues, 7 models selected > color sel byhetero > select clear > show #4 models > hide #4 models > show #!3 models > hide #3.1 models > show #4 models > hide #4 models > hide #!3 models > hide #!1 models > select #3:28-32 35 atoms, 35 bonds, 5 residues, 1 model selected > color sel light grey > select #4:28-32 35 atoms, 35 bonds, 5 residues, 1 model selected > color sel light grey > select #3:42-51 69 atoms, 68 bonds, 10 residues, 1 model selected > color sel light grey > select #4:42-51 69 atoms, 68 bonds, 10 residues, 1 model selected > color sel light grey > select #3:58-63 46 atoms, 46 bonds, 6 residues, 1 model selected > color sel light grey > select #4:58-63 46 atoms, 46 bonds, 6 residues, 1 model selected > color sel light grey > select #3:71-80 77 atoms, 76 bonds, 10 residues, 1 model selected > color sel light grey > select #4:71-80 77 atoms, 76 bonds, 10 residues, 1 model selected > color sel light grey > select #3:114-120 55 atoms, 54 bonds, 7 residues, 1 model selected > color sel light grey > select #4:114-120 55 atoms, 54 bonds, 7 residues, 1 model selected > color sel light grey > select #3:123-125 26 atoms, 25 bonds, 3 residues, 1 model selected > color sel light grey > select #4:114-120 55 atoms, 54 bonds, 7 residues, 1 model selected > color sel light grey > select #3:161-165 38 atoms, 37 bonds, 5 residues, 1 model selected > color sel light grey > select #4:161-165 38 atoms, 37 bonds, 5 residues, 1 model selected > color sel light grey > select #3:176-182 55 atoms, 55 bonds, 7 residues, 1 model selected > color sel light grey > select #4:176-182 55 atoms, 55 bonds, 7 residues, 1 model selected > color sel light grey > show #!3 models > show #4 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > select clear > show #!2 models > hide #4 models > open ""/Users/hannesludewig/Downloads/ANC2 > 2/wt_MgADP/fold_2024_05_09_20_49_model_0.cif"" Chain information for fold_2024_05_09_20_49_model_0.cif #5 --- Chain | Description A | . > rename #5 AF3_ANC2-MgADP_sel_winners > color #5 lightgrey > hide #!2 models > select clear > open ""/Users/hannesludewig/Downloads/AF > 2/AF_wt_MgADP/fold_2024_05_09_20_53_model_0.cif"" Chain information for fold_2024_05_09_20_53_model_0.cif #6 --- Chain | Description A | . > mmaker #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 AF3_ANC2-MgADP, chain A (#1) with AF3_ANC2-MgADP_sel_winners, chain A (#5), sequence alignment score = 1130.2 RMSD between 217 pruned atom pairs is 0.000 angstroms; (across all 217 pairs: 0.000) > mmaker #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 AF3_ANC2-MgADP, chain A (#1) with fold_2024_05_09_20_53_model_0.cif, chain A (#6), sequence alignment score = 891.7 RMSD between 204 pruned atom pairs is 0.799 angstroms; (across all 217 pairs: 2.301) > select 10428 atoms, 10580 bonds, 55 pseudobonds, 1320 residues, 9 models selected > color sel byhetero > select clear > hide #6 models > select #3:28-32 35 atoms, 35 bonds, 5 residues, 1 model selected > color sel blueHL > select #4:28-32 35 atoms, 35 bonds, 5 residues, 1 model selected > color sel goldHL > select #3:42-51 69 atoms, 68 bonds, 10 residues, 1 model selected > color sel blueHL > select #4:42-51 69 atoms, 68 bonds, 10 residues, 1 model selected > color sel goldHL > select #3:58-63 46 atoms, 46 bonds, 6 residues, 1 model selected > color sel blueHL > select #4:58-63 46 atoms, 46 bonds, 6 residues, 1 model selected > color sel goldHL > select #3:71-80 77 atoms, 76 bonds, 10 residues, 1 model selected > color sel blueHL > select #4:71-80 77 atoms, 76 bonds, 10 residues, 1 model selected > color sel goldHL > select #3:114-120 55 atoms, 54 bonds, 7 residues, 1 model selected > color sel blueHL > select #4:114-120 55 atoms, 54 bonds, 7 residues, 1 model selected > color sel goldHL > select #3:123-125 26 atoms, 25 bonds, 3 residues, 1 model selected > color sel lblueHL Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > select #4:114-120 55 atoms, 54 bonds, 7 residues, 1 model selected > color sel goldHL > select #3:161-165 38 atoms, 37 bonds, 5 residues, 1 model selected > color sel lblueHL Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > select #4:161-165 38 atoms, 37 bonds, 5 residues, 1 model selected > color sel goldHL > select #3:176-182 55 atoms, 55 bonds, 7 residues, 1 model selected > color sel blueHL > select #4:176-182 55 atoms, 55 bonds, 7 residues, 1 model selected > color sel goldHL > select clear > select #3:28-32 35 atoms, 35 bonds, 5 residues, 1 model selected > color sel light grey > select #4:28-32 35 atoms, 35 bonds, 5 residues, 1 model selected > color sel light grey > select #3:42-51 69 atoms, 68 bonds, 10 residues, 1 model selected > color sel light grey > select #4:42-51 69 atoms, 68 bonds, 10 residues, 1 model selected > color sel light grey > select #3:58-63 46 atoms, 46 bonds, 6 residues, 1 model selected > color sel light grey > select #4:58-63 46 atoms, 46 bonds, 6 residues, 1 model selected > color sel light grey > select #3:71-80 77 atoms, 76 bonds, 10 residues, 1 model selected > color sel light grey > select #4:71-80 77 atoms, 76 bonds, 10 residues, 1 model selected > color sel light grey > select #3:114-120 55 atoms, 54 bonds, 7 residues, 1 model selected > color sel light grey > select #4:114-120 55 atoms, 54 bonds, 7 residues, 1 model selected > color sel light grey > select #3:123-125 26 atoms, 25 bonds, 3 residues, 1 model selected > color sel light grey > select #4:114-120 55 atoms, 54 bonds, 7 residues, 1 model selected > color sel light grey > select #3:161-165 38 atoms, 37 bonds, 5 residues, 1 model selected > color sel light grey > select #4:161-165 38 atoms, 37 bonds, 5 residues, 1 model selected > color sel light grey > select #3:176-182 55 atoms, 55 bonds, 7 residues, 1 model selected > color sel light grey > select #4:176-182 55 atoms, 55 bonds, 7 residues, 1 model selected > color sel light grey > select clear > select #5:28-32 35 atoms, 35 bonds, 5 residues, 1 model selected > color sel light grey > select #6:28-32 35 atoms, 35 bonds, 5 residues, 1 model selected > color sel light grey > select #5:42-51 72 atoms, 71 bonds, 10 residues, 1 model selected > color sel light grey > select #6:42-51 69 atoms, 68 bonds, 10 residues, 1 model selected > color sel light grey > select #5:58-63 46 atoms, 46 bonds, 6 residues, 1 model selected > color sel light grey > select #6:58-63 46 atoms, 46 bonds, 6 residues, 1 model selected > color sel light grey > select #5:71-80 77 atoms, 77 bonds, 10 residues, 1 model selected > color sel light grey > select #6:71-80 77 atoms, 76 bonds, 10 residues, 1 model selected > color sel light grey > select #5:114-120 60 atoms, 60 bonds, 7 residues, 1 model selected > color sel light grey > select #6:114-120 55 atoms, 54 bonds, 7 residues, 1 model selected > color sel light grey > select #5:123-125 26 atoms, 25 bonds, 3 residues, 1 model selected > color sel light grey > select #6:114-120 55 atoms, 54 bonds, 7 residues, 1 model selected > color sel light grey > select #5:161-165 39 atoms, 38 bonds, 5 residues, 1 model selected > color sel light grey > select #6:161-165 38 atoms, 37 bonds, 5 residues, 1 model selected > color sel light grey > select #5:176-182 57 atoms, 57 bonds, 7 residues, 1 model selected > color sel light grey > select #6:176-182 55 atoms, 55 bonds, 7 residues, 1 model selected > color sel light grey > select clear > select #5:28-32 35 atoms, 35 bonds, 5 residues, 1 model selected > color sel light grey > select #6:28-32 35 atoms, 35 bonds, 5 residues, 1 model selected > color sel light grey > select #5:42-51 72 atoms, 71 bonds, 10 residues, 1 model selected > color sel light grey > select #6:42-51 69 atoms, 68 bonds, 10 residues, 1 model selected > color sel light grey > select #5:58-63 46 atoms, 46 bonds, 6 residues, 1 model selected > color sel light grey > select #6:58-63 46 atoms, 46 bonds, 6 residues, 1 model selected > color sel light grey > select #5:71-80 77 atoms, 77 bonds, 10 residues, 1 model selected > color sel light grey > select #6:71-80 77 atoms, 76 bonds, 10 residues, 1 model selected > color sel light grey > select #5:114-120 60 atoms, 60 bonds, 7 residues, 1 model selected > color sel light grey > select #6:114-120 55 atoms, 54 bonds, 7 residues, 1 model selected > color sel light grey > select #5:123-125 26 atoms, 25 bonds, 3 residues, 1 model selected > color sel light grey > select #6:114-120 55 atoms, 54 bonds, 7 residues, 1 model selected > color sel light grey > select #5:161-165 39 atoms, 38 bonds, 5 residues, 1 model selected > color sel light grey > select #6:161-165 38 atoms, 37 bonds, 5 residues, 1 model selected > color sel light grey > select #5:176-182 57 atoms, 57 bonds, 7 residues, 1 model selected > color sel light grey > select #6:176-182 55 atoms, 55 bonds, 7 residues, 1 model selected > color sel light grey > select clear > select #5:28-32 35 atoms, 35 bonds, 5 residues, 1 model selected > color sel blueHL > select #6:28-32 35 atoms, 35 bonds, 5 residues, 1 model selected > color sel goldHL > select #5:42-51 72 atoms, 71 bonds, 10 residues, 1 model selected > color sel blueHL > select #6:42-51 69 atoms, 68 bonds, 10 residues, 1 model selected > color sel goldHL > select #5:58-63 46 atoms, 46 bonds, 6 residues, 1 model selected > color sel blueHL > select #6:58-63 46 atoms, 46 bonds, 6 residues, 1 model selected > color sel goldHL > select #5:71-80 77 atoms, 77 bonds, 10 residues, 1 model selected > color sel blueHL > select #6:71-80 77 atoms, 76 bonds, 10 residues, 1 model selected > color sel goldHL > select #5:114-120 60 atoms, 60 bonds, 7 residues, 1 model selected > color sel blueHL > select #6:114-120 55 atoms, 54 bonds, 7 residues, 1 model selected > color sel goldHL > select #5:123-125 26 atoms, 25 bonds, 3 residues, 1 model selected > color sel blueHL > select #6:114-120 55 atoms, 54 bonds, 7 residues, 1 model selected > color sel goldHL > select #5:161-165 39 atoms, 38 bonds, 5 residues, 1 model selected > color sel blueHL > select #6:161-165 38 atoms, 37 bonds, 5 residues, 1 model selected > color sel goldHL > select #5:176-182 57 atoms, 57 bonds, 7 residues, 1 model selected > color sel blueHL > select #6:176-182 55 atoms, 55 bonds, 7 residues, 1 model selected > color sel goldHL > select clear > show #6 models > hide #6 models > hide #5 models > show #5 models > cartoon suppressBackboneDisplay false > select #5:4@ca 1 atom, 1 residue, 1 model selected > show sel balls Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > color sel red > select #5:4@ca 1 atom, 1 residue, 1 model selected > show sel atoms > style sel sphere Changed 1 atom style > select #5:4@ca 1 atom, 1 residue, 1 model selected > color sel red > hide sel atoms > select clear > hide #5 atoms > select clear > select #5/A:112 8 atoms, 7 bonds, 1 residue, 1 model selected > select #5/A:4 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel light grey > select clear > select ::name=""ADP"" 324 atoms, 348 bonds, 12 residues, 6 models selected > show sel & #5 atoms > select clear > select #5:203@ca 1 atom, 1 residue, 1 model selected > show sel atoms > style sel sphere Changed 1 atom style > color sel red > select #5:203@ca 1 atom, 1 residue, 1 model selected > show sel atoms > style sel sphere Changed 1 atom style > color sel darkblueHL. Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color sel darkblueHL > cartoon suppressBackboneDisplay false > select #5:203@ca 1 atom, 1 residue, 1 model selected > show sel atoms > style sel sphere Changed 1 atom style > color sel darkblueHL > select #5:166@ca 1 atom, 1 residue, 1 model selected > show sel atoms > style sel sphere Changed 1 atom style > color sel blueHL > select #5:4@ca 1 atom, 1 residue, 1 model selected > show sel atoms > style sel sphere Changed 1 atom style > color sel lightblueHL > select #5:6@ca 1 atom, 1 residue, 1 model selected > show sel atoms > style sel sphere Changed 1 atom style > color sel lightblueHL > select #5:23@ca 1 atom, 1 residue, 1 model selected > show sel atoms > style sel sphere Changed 1 atom style > color sel purple > select #5:79@ca 1 atom, 1 residue, 1 model selected > show sel atoms > style sel sphere Changed 1 atom style > color sel purple > select #6:4@ca 1 atom, 1 residue, 1 model selected > show sel atoms > style sel sphere Changed 1 atom style > color sel orangeHL > show #6 models > hide #5 models > select add #5 1744 atoms, 1769 bonds, 221 residues, 2 models selected > select subtract #5 1 atom, 1 residue, 1 model selected > hide #6 models > select add #6 1735 atoms, 1760 bonds, 220 residues, 1 model selected > show #6 models > hide sel atoms > select clear > select ::name=""ADP"" 324 atoms, 348 bonds, 12 residues, 6 models selected > show sel & #6 atoms > select ::name=""MG"" 6 atoms, 6 residues, 6 models selected > show sel & #6 atoms > select clear > select #6:4@ca 1 atom, 1 residue, 1 model selected > show sel atoms > style sel sphere Changed 1 atom style > color sel orangeHL > select clear > show #5 models > hide #6 models > select #5/A:182 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > open 3gmt Summary of feedback from opening 3gmt fetched from pdb --- note | Fetching compressed mmCIF 3gmt from http://files.rcsb.org/download/3gmt.cif 3gmt title: Crystal structure of adenylate kinase from burkholderia pseudomallei [more info...] Chain information for 3gmt #7 --- Chain | Description | UniProt A B | Adenylate kinase | KAD_BURP1 1-215 Non-standard residues in 3gmt #7 --- SO4 — sulfate ion 3gmt mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > mmaker #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 AF3_ANC2-MgADP, chain A (#1) with 3gmt, chain B (#7), sequence alignment score = 658.1 RMSD between 77 pruned atom pairs is 1.109 angstroms; (across all 192 pairs: 10.358) > hide #5 models > show #!1 models > select clear > hide #!1 models > select add #7 3320 atoms, 3157 bonds, 1 pseudobond, 623 residues, 2 models selected > rainbow sel > select #7/A 1706 atoms, 1601 bonds, 338 residues, 1 model selected > hide sel cartoons > hide sel atoms > select clear > select #7 3320 atoms, 3157 bonds, 1 pseudobond, 623 residues, 2 models selected > hide sel atoms > select clear > show #!1 models > select #7 3320 atoms, 3157 bonds, 1 pseudobond, 623 residues, 2 models selected > color sel light grey > select clear > select #7:28-32 68 atoms, 66 bonds, 10 residues, 1 model selected > color sel blueHL > select #7:28-32 68 atoms, 66 bonds, 10 residues, 1 model selected > color sel goldHL > select #7:42-51 134 atoms, 134 bonds, 20 residues, 1 model selected > color sel blueHL > select #7:42-51 134 atoms, 134 bonds, 20 residues, 1 model selected > color sel goldHL > select #7:58-63 88 atoms, 88 bonds, 12 residues, 1 model selected > color sel blueHL > select #7:58-63 88 atoms, 88 bonds, 12 residues, 1 model selected > color sel goldHL > select #7:71-80 146 atoms, 144 bonds, 20 residues, 1 model selected > color sel blueHL > select #7:71-80 146 atoms, 144 bonds, 20 residues, 1 model selected > color sel goldHL > select #7:114-120 118 atoms, 116 bonds, 14 residues, 1 model selected > color sel blueHL > select #7:114-120 118 atoms, 116 bonds, 14 residues, 1 model selected > color sel goldHL > select #7:123-125 58 atoms, 56 bonds, 6 residues, 1 model selected > color sel blueHL > select #7:114-120 118 atoms, 116 bonds, 14 residues, 1 model selected > color sel goldHL > select #7:161-165 82 atoms, 80 bonds, 10 residues, 1 model selected > color sel blueHL > select #7:161-165 82 atoms, 80 bonds, 10 residues, 1 model selected > color sel goldHL > select #7:176-182 122 atoms, 126 bonds, 14 residues, 1 model selected > color sel blueHL > select #7:176-182 122 atoms, 126 bonds, 14 residues, 1 model selected > color sel goldHL > select clear > show #6 models > hide #!1 models > hide #6 models > show #5 models > hide #!7 models > show #6 models > hide #5 models > save > /Users/hannesludewig/Desktop/Fig2_ANC2_AflAdk_sel_winner_hinges_plot.cxs > save /Users/hannesludewig/Desktop/Fig2_AflAdk_sel_winner_hinges_plot.tif > width 2000 height 1265 supersample 4 transparentBackground true > show #!7 models > hide #6 models > show #6 models > hide #6 models > select #7/B:123 11 atoms, 10 bonds, 1 residue, 1 model selected > select up 29 atoms, 28 bonds, 3 residues, 1 model selected > color sel lightgrey > select clear > hide #!7 models > show #6 models > show #5 models > hide #5 models > save /Users/hannesludewig/Desktop/Fig2_AflAdk_sel_winner_hinges_plot.tif > width 2000 height 1265 supersample 4 transparentBackground true > show #5 models > hide #6 models > save /Users/hannesludewig/Desktop/Fig2_ANC2_sel_winner_hinges_plot.tif width > 2000 height 1265 supersample 4 transparentBackground true The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > show #6 models > hide #5 models > select :157:213 88 atoms, 74 bonds, 14 residues, 7 models selected > select #6:157:213 12 atoms, 10 bonds, 2 residues, 1 model selected > select ~sel & ##selected 1723 atoms, 1750 bonds, 218 residues, 1 model selected > select ~sel & ##selected 12 atoms, 10 bonds, 2 residues, 1 model selected > select #6:20 8 atoms, 7 bonds, 1 residue, 1 model selected > select clear > hide #6 models > show #!1 models > show #!2 models > select #1:123 11 atoms, 10 bonds, 1 residue, 1 model selected > select clear > hide #!1 models > show #!1 models > hide #!2 models > show #!7 models > show #6 models > hide #!1 models > show #!2 models > show #4 models > hide #6 models > hide #!7 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > hide #4 models > show #!2 models > show #4 models > hide #4 models > show #4 models > hide #4 models > show #4 models > hide #4 models > show #4 models > hide #4 models > show #4 models > hide #4 models > show #4 models > hide #!2 models > select #4/A:4 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > show #!2 models > hide #4 models > hide #!2 models > show #6 models > show #5 models > hide #6 models > select #6:111 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #5:111 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > show #6 models > hide #5 models > select #6/A:111 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select #6:135 5 atoms, 4 bonds, 1 residue, 1 model selected > show sela toms Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show sel atoms > contacts sel restrict #6 reveal true select true 9 contacts ===== Log before crash end ===== Log: > graphics silhouettes true > lighting shadows true > lighting flat > lighting full > lighting soft > color name goldHL #cc9900 Color 'goldHL' is opaque: rgb(80%, 60%, 0%) hex: #cc9900 > color name lightblueHL #66ccff Color 'lightblueHL' is opaque: rgb(40%, 80%, 100%) hex: #66ccff > color name greenHL #009966 Color 'greenHL' is opaque: rgb(0%, 60%, 40%) hex: #009966 > color name yellowHL #cccc33 Color 'yellowHL' is opaque: rgb(80%, 80%, 20%) hex: #cccc33 > color name blueHL #006699 Color 'blueHL' is opaque: rgb(0%, 40%, 60%) hex: #006699 > color name orangeHL #cc6600 Color 'orangeHL' is opaque: rgb(80%, 40%, 0%) hex: #cc6600 > color name pinkHL #cc6699 Color 'pinkHL' is opaque: rgb(80%, 40%, 60%) hex: #cc6699 > color name darkblueHL #003478 Color 'darkblueHL' is opaque: rgb(0%, 20.4%, 47.1%) hex: #003478 > color name blueGRC #93A9D7 Color 'blueGRC' is opaque: rgb(57.6%, 66.3%, 84.3%) hex: #93a9d7 > color name lightblueGRC #DBE2F1 Color 'lightblueGRC' is opaque: rgb(85.9%, 88.6%, 94.5%) hex: #dbe2f1 > color name orangeGRC #EAB48A Color 'orangeGRC' is opaque: rgb(91.8%, 70.6%, 54.1%) hex: #eab48a > color name lightorangeGRC #F7E6D7 Color 'lightorangeGRC' is opaque: rgb(96.9%, 90.2%, 84.3%) hex: #f7e6d7 > color name greenGRC #B0CF94 Color 'greenGRC' is opaque: rgb(69%, 81.2%, 58%) hex: #b0cf94 > color name lightgreenGRC #E4EFDB Color 'lightgreenGRC' is opaque: rgb(89.4%, 93.7%, 85.9%) hex: #e4efdb 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 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: Z17J00164LL/A Chip: Apple M2 Max Total Number of Cores: 12 (8 performance and 4 efficiency) Memory: 96 GB System Firmware Version: 10151.41.12 OS Loader Version: 10151.41.12 Software: System Software Overview: System Version: macOS 14.1 (23B74) Kernel Version: Darwin 23.1.0 Time since boot: 52 minutes, 21 seconds Graphics/Displays: Apple M2 Max: Chipset Model: Apple M2 Max Type: GPU Bus: Built-In Total Number of Cores: 38 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 R240HY: 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-Clipper: 0.23.0 ChimeraX-clix: 0.1.5 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.8.dev0 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-PhenixUI: 1.3.2 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 MolecularDynamicsViewer: 1.4 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 Send2Trash: 1.8.2 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