id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15852 Crash moving window between screens chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.5-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 0x00000001fea8cc00 (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, 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 (total: 58) {""app_name"":""ChimeraX"",""timestamp"":""2024-08-30 14:17:53.00 +0200"",""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 14.5 (23F79)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""B318FB84-1AD3-46B6-A205-02606DFA04D8""} { ""uptime"" : 18000, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 502, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro18,3"", ""coalitionID"" : 1339, ""osVersion"" : { ""train"" : ""macOS 14.5"", ""build"" : ""23F79"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2024-08-30 14:17:51.0109 +0200"", ""codeSigningMonitor"" : 1, ""incident"" : ""B318FB84-1AD3-46B6-A205-02606DFA04D8"", ""pid"" : 6388, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2024-08-30 14:17:21.4682 +0200"", ""procStartAbsTime"" : 449563058059, ""procExitAbsTime"" : 450271490240, ""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"":""AFD4C665-57CF-5E66-939F-C1317475F940"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""30492E88-BE55-51F6-475C-E82A6DE93EED"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""instructionByteStream"" : {""beforePC"":""fyMD1f17v6n9AwCRW+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A=="",""atPC"":""AwEAVH8jA9X9e7+p\/QMAkVDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g==""}, ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x70c11ced9e48 is not in any region. 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\n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""efbf0ed2b4f3d2eb8009bef5d3bc6d051cdce3ed"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""62745b8e85854550ad70b6e4"", ""factorPackIds"" : { ""SIRI_TTS_DEVICE_TRAINING"" : ""6539d7f333b9b7499c6f1b63"" }, ""deploymentId"" : 240000073 }, { ""rolloutId"" : ""654439cdafbf5b61207873a9"", ""factorPackIds"" : { }, ""deploymentId"" : 240000004 } ], ""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/pfefferlab/Desktop/CM1_revision_1.cxs Opened run_class001 (1).mrc as #1, grid size 128,128,128, pixel 5.08, shown at level 0.278, step 1, values float32 Opened GCP23_CM1.pdb map 10 as #3, grid size 55,50,68, pixel 3.33, shown at level 0.0571, step 1, values float32 Opened copy of GCP23_CM1.pdb map 10 as #6, grid size 55,51,68, pixel 3.33, shown at level 0.0554, step 1, values float32 Opened run_class001 (1).mrc 0 as #9.1, grid size 128,128,128, pixel 5.08, shown at level 0.25, step 1, values float32 Opened run_class001 (1).mrc 1 as #9.2, grid size 128,128,128, pixel 5.08, shown at level 0.306, step 1, values float32 Opened run_class001 (1).mrc 2 as #9.3, grid size 128,128,128, pixel 5.08, shown at level 0.235, step 1, values float32 Opened run_class001 (1).mrc 3 as #9.4, grid size 128,128,128, pixel 5.08, shown at level 0.235, step 1, values float32 Opened run_class001 (1).mrc 4 as #9.5, grid size 128,128,128, pixel 5.08, shown at level 0.235, step 1, values float32 Opened run_class001 (1).mrc 5 as #9.6, grid size 128,128,128, pixel 5.08, shown at level 0.235, step 1, values float32 Log from Fri Aug 30 13:47:56 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/pfefferlab/Desktop/CM1_revision_1.cxs Opened run_class001 (1).mrc as #1, grid size 128,128,128, pixel 5.08, shown at level 0.235, step 1, values float32 Opened GCP23_CM1.pdb map 10 as #3, grid size 55,50,68, pixel 3.33, shown at level 0.0571, step 1, values float32 Opened copy of GCP23_CM1.pdb map 10 as #6, grid size 55,51,68, pixel 3.33, shown at level 0.0554, step 1, values float32 Opened run_class001 (1).mrc 0 as #9.1, grid size 128,128,128, pixel 5.08, shown at level 0.25, step 1, values float32 Opened run_class001 (1).mrc 1 as #9.2, grid size 128,128,128, pixel 5.08, shown at level 0.306, step 1, values float32 Opened run_class001 (1).mrc 2 as #9.3, grid size 128,128,128, pixel 5.08, shown at level 0.235, step 1, values float32 Opened run_class001 (1).mrc 3 as #9.4, grid size 128,128,128, pixel 5.08, shown at level 0.235, step 1, values float32 Opened run_class001 (1).mrc 4 as #9.5, grid size 128,128,128, pixel 5.08, shown at level 0.235, step 1, values float32 Opened run_class001 (1).mrc 5 as #9.6, grid size 128,128,128, pixel 5.08, shown at level 0.235, step 1, values float32 Log from Thu Aug 29 11:27:54 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/pfefferlab/Desktop/CM1_revision_1.cxs Opened run_class001 (1).mrc as #1, grid size 128,128,128, pixel 5.08, shown at level 0.235, step 1, values float32 Opened GCP23_CM1.pdb map 10 as #3, grid size 55,50,68, pixel 3.33, shown at level 0.0571, step 1, values float32 Opened copy of GCP23_CM1.pdb map 10 as #6, grid size 55,51,68, pixel 3.33, shown at level 0.0554, step 1, values float32 Opened run_class001 (1).mrc 0 as #8.1, grid size 128,128,128, pixel 5.08, shown at level 0.235, step 1, values float32 Opened run_class001 (1).mrc 1 as #8.2, grid size 128,128,128, pixel 5.08, shown at level 0.474, step 1, values float32 Opened run_class001 (1).mrc 2 as #8.3, grid size 128,128,128, pixel 5.08, shown at level 0.101, step 1, values float32 Opened run_class001 (1).mrc 3 as #8.4, grid size 128,128,128, pixel 5.08, shown at level 0.15, step 1, values float32 Opened run_class001 (1).mrc 4 as #8.5, grid size 128,128,128, pixel 5.08, shown at level 0.202, step 1, values float32 Opened run_class001 (1).mrc 5 as #8.6, grid size 128,128,128, pixel 5.08, shown at level 0.235, step 1, values float32 Log from Wed Aug 28 17:14:39 2024 Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle > alias af open alphafold:$1 UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/pfefferlab/Downloads/run_class001 (1).mrc"" Opened run_class001 (1).mrc as #1, grid size 128,128,128, pixel 5.08, shown at level 0.373, step 1, values float32 > volume #1 level 0.1361 > volume #1 level 0.2325 > open /Users/pfefferlab/Desktop/GCP23_CM1.pdb Chain information for GCP23_CM1.pdb #2 --- Chain | Description M | No description available S | No description available T | No description available V | No description available W | No description available m t | No description available Drag select of 13333 atoms, 48 pseudobonds, 60 bonds > hide sel atoms > show sel cartoons > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.86949,-0.35348,-0.34502,846.83,0.1861,0.4126,-0.8917,378.35,0.45755,-0.83953,-0.29297,480.89 > view matrix models > #2,-0.78527,-0.56003,0.26404,674.38,-0.44457,0.21318,-0.87001,640.2,0.43095,-0.80057,-0.41637,519.86 > view matrix models > #2,-0.96043,-0.22451,0.16486,679.17,-0.16443,-0.020716,-0.98617,642.58,0.22482,-0.97425,-0.01702,506.63 > view matrix models > #2,-0.9647,0.16981,-0.20128,696.39,0.25704,0.44094,-0.85994,336.27,-0.05728,-0.88133,-0.46902,725.86 > view matrix models > #2,-0.90481,0.18593,-0.38309,730.52,0.42549,0.43047,-0.79602,260.37,0.016905,-0.88325,-0.46861,700.72 > view matrix models > #2,-0.86151,0.21916,-0.458,731.24,0.50583,0.44863,-0.7368,208.82,0.043996,-0.86643,-0.49735,696.34 > view matrix models > #2,-0.90489,0.21239,-0.36887,719.03,0.42562,0.46125,-0.77852,246.62,0.0047893,-0.86147,-0.50778,711.9 > view matrix models > #2,-0.91725,0.12665,-0.37764,748.5,0.38415,0.5318,-0.75473,234.75,0.10524,-0.83735,-0.53645,680.36 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.91725,0.12665,-0.37764,688.87,0.38415,0.5318,-0.75473,314.08,0.10524,-0.83735,-0.53645,640.3 > view matrix models > #2,-0.91725,0.12665,-0.37764,715.39,0.38415,0.5318,-0.75473,335.8,0.10524,-0.83735,-0.53645,657.21 > hide #!1 models > select clear > select #2/t/m/T/M 12048 atoms, 12171 bonds, 38 pseudobonds, 1852 residues, 2 models selected > ui tool show ""Fit in Map"" Opened GCP23_CM1.pdb map 10 as #3, grid size 55,50,68, pixel 3.33, shown at level 0.0571, step 1, values float32 > fitmap sel inMap #1 resolution 10 metric correlation Fit map GCP23_CM1.pdb map 10 in map run_class001 (1).mrc using 9577 points correlation = 0.915, correlation about mean = 0.3624, overlap = 1607 steps = 56, shift = 9.82, angle = 13.2 degrees Position of GCP23_CM1.pdb map 10 (#3) relative to run_class001 (1).mrc (#1) coordinates: Matrix rotation and translation -0.89406490 -0.08233926 -0.44030468 781.59552794 0.35290364 0.47590538 -0.80558866 386.70852709 0.27587494 -0.87563366 -0.39643247 557.12731153 Axis -0.08328924 -0.85159609 0.51753938 Axis point 292.66446969 0.00000000 496.09849470 Rotation angle (degrees) 155.13431222 Shift along axis -106.08264302 Average map value = 0.788 for 12048 atoms, 4 outside contour > transparency #1 70 > set bgColor white > graphics silhouettes true > volume #1 level 0.2711 > volume #1 level 0.2601 > volume #1 level 0.2463 > volume #1 level 0.2353 > color #2/V hot pink > color #2/W aquamarine > select /W:102 5 atoms, 4 bonds, 1 residue, 1 model selected > select add /W:505 10 atoms, 8 bonds, 2 residues, 1 model selected > select add /W:11 15 atoms, 12 bonds, 3 residues, 1 model selected > select up 225 atoms, 222 bonds, 45 residues, 1 model selected > select up 240 atoms, 237 bonds, 48 residues, 1 model selected > select up 775 atoms, 766 bonds, 155 residues, 1 model selected > select down 240 atoms, 237 bonds, 48 residues, 1 model selected > color sel dark slate grey > hide pseudobonds > select clear > select /S:17 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 90 atoms, 89 bonds, 18 residues, 1 model selected > select up 95 atoms, 94 bonds, 19 residues, 1 model selected > select up 200 atoms, 198 bonds, 40 residues, 1 model selected > delete sel > select clear > color #2/M aquamarine > color #2/T cornfloweer Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #2/T cornflowerblue > color #2/t/m gold > select clear > select /W:110 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 60 atoms, 59 bonds, 12 residues, 1 model selected > select up 65 atoms, 64 bonds, 13 residues, 1 model selected > select up 775 atoms, 766 bonds, 155 residues, 1 model selected > select down 65 atoms, 64 bonds, 13 residues, 1 model selected > color sel aquamarine > select clear [Repeated 1 time(s)] > select /W:703 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 80 atoms, 79 bonds, 16 residues, 1 model selected > select up 85 atoms, 84 bonds, 17 residues, 1 model selected > select up 775 atoms, 766 bonds, 155 residues, 1 model selected > select down 85 atoms, 84 bonds, 17 residues, 1 model selected > color sel dark slate grey > select clear > show #!1 models > ui tool show ""Color Zone"" > color zone #1 near #2 distance 100 > color zone #1 near #2 distance 50 [Repeated 2 time(s)] > color single #1 > combine #2/t/m/T/M [Repeated 1 time(s)] > select add #4 13133 atoms, 13245 bonds, 47 pseudobonds, 2069 residues, 2 models selected > select subtract #4 Nothing selected > select add #4 13133 atoms, 13245 bonds, 47 pseudobonds, 2069 residues, 2 models selected > view matrix models > #4,-0.89406,-0.082339,-0.4403,820.93,0.3529,0.47591,-0.80559,333.18,0.27587,-0.87563,-0.39643,631.59 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.60373,-0.4835,-0.63383,888.54,-0.037508,0.81143,-0.58325,307.77,0.79631,-0.32835,-0.50802,345.99 > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.60373,-0.4835,-0.63383,884.21,-0.037508,0.81143,-0.58325,311.25,0.79631,-0.32835,-0.50802,352.8 > view matrix models > #4,-0.60373,-0.4835,-0.63383,882.62,-0.037508,0.81143,-0.58325,312.58,0.79631,-0.32835,-0.50802,354.93 > select subtract #4 Nothing selected > select add #5 13133 atoms, 13245 bonds, 47 pseudobonds, 2069 residues, 2 models selected > view matrix models > #5,-0.89406,-0.082339,-0.4403,830.97,0.3529,0.47591,-0.80559,414.26,0.27587,-0.87563,-0.39643,480.81 > ui mousemode right ""rotate selected models"" > view matrix models > #5,-0.57119,0.54664,-0.61232,611.55,0.70494,-0.055449,-0.70709,399.99,-0.42048,-0.83553,-0.35368,695.89 > view matrix models > #5,-0.63048,0.64873,-0.42619,544.96,0.574,0.020048,-0.81861,461.45,-0.52252,-0.76075,-0.38501,721.61 > ui mousemode right ""translate selected models"" > view matrix models > #5,-0.63048,0.64873,-0.42619,558.18,0.574,0.020048,-0.81861,450.4,-0.52252,-0.76075,-0.38501,722.31 > ui tool show ""Fit in Map"" Opened copy of GCP23_CM1.pdb map 10 as #6, grid size 55,51,68, pixel 3.33, shown at level 0.0554, step 1, values float32 > fitmap #5 inMap #1 resolution 10 metric correlation Fit map copy of GCP23_CM1.pdb map 10 in map run_class001 (1).mrc using 10613 points correlation = 0.8738, correlation about mean = 0.1674, overlap = 1213 steps = 68, shift = 12.1, angle = 13.1 degrees Position of copy of GCP23_CM1.pdb map 10 (#6) relative to run_class001 (1).mrc (#1) coordinates: Matrix rotation and translation -0.58971490 0.77127803 -0.23951313 446.34672743 0.50299180 0.11873189 -0.85609695 462.58732082 -0.63185092 -0.62532626 -0.45796450 759.99027481 Axis 0.43677004 0.74256135 -0.50777414 Axis point 162.95905479 0.00000000 503.77347107 Rotation angle (degrees) 164.68184296 Shift along axis 152.54693665 Average map value = 0.5447 for 13133 atoms, 886 outside contour > select subtract #5 Nothing selected > select add #4 13133 atoms, 13245 bonds, 47 pseudobonds, 2069 residues, 2 models selected > view matrix models > #4,-0.60373,-0.4835,-0.63383,878.03,-0.037508,0.81143,-0.58325,305.05,0.79631,-0.32835,-0.50802,354.35 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.52211,-0.68669,-0.50582,861.52,-0.026432,0.60582,-0.79516,423.59,0.85247,-0.40179,-0.33446,297.96 > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.52211,-0.68669,-0.50582,852.7,-0.026432,0.60582,-0.79516,428.95,0.85247,-0.40179,-0.33446,289.45 > fitmap #4 inMap #1 resolution 10 metric correlation Fit map copy of GCP23_CM1.pdb map 10 in map run_class001 (1).mrc using 10613 points correlation = 0.8943, correlation about mean = 0.2828, overlap = 1664 steps = 84, shift = 8.79, angle = 12.1 degrees Position of copy of GCP23_CM1.pdb map 10 (#6) relative to run_class001 (1).mrc (#1) coordinates: Matrix rotation and translation -0.38207317 -0.77227608 -0.50755271 824.72621024 0.07112021 0.52301992 -0.84934803 443.96161173 0.92139134 -0.36061035 -0.14490745 191.84274001 Axis 0.28254685 -0.82609475 0.48758049 Axis point 414.59508322 0.00000000 518.33342204 Rotation angle (degrees) 120.13110550 Shift along axis -40.19179094 Average map value = 0.7478 for 13133 atoms, 703 outside contour > select clear > hide #!2 models > select clear > hide #!1 models Drag select of 53 residues > select up 935 atoms, 925 bonds, 187 residues, 1 model selected > select up 980 atoms, 970 bonds, 196 residues, 1 model selected > select up 1085 atoms, 1074 bonds, 217 residues, 1 model selected > select up 13133 atoms, 13245 bonds, 2069 residues, 1 model selected > select down 1085 atoms, 1074 bonds, 217 residues, 1 model selected > delete sel Drag select of 68 residues > select up 875 atoms, 866 bonds, 175 residues, 1 model selected > select up 920 atoms, 911 bonds, 184 residues, 1 model selected > select up 1085 atoms, 1074 bonds, 217 residues, 1 model selected > select up 13133 atoms, 13245 bonds, 2069 residues, 1 model selected > select down 1085 atoms, 1074 bonds, 217 residues, 1 model selected > delete sel Drag select of 3700 residues > color sel #A9A9A9 > color #1 #A9A9A9 > show #!2 models > select clear Drag select of 595 residues > select up 4738 atoms, 4765 bonds, 775 residues, 1 model selected > select up 6904 atoms, 6981 bonds, 1059 residues, 1 model selected > select up 7074 atoms, 7146 bonds, 1082 residues, 1 model selected > select up 9894 atoms, 10013 bonds, 1471 residues, 1 model selected > select up 9959 atoms, 10077 bonds, 1481 residues, 1 model selected > select up 10587 atoms, 10713 bonds, 1576 residues, 1 model selected > select up 10609 atoms, 10733 bonds, 1580 residues, 1 model selected > select up 11175 atoms, 11302 bonds, 1685 residues, 1 model selected > select up 11185 atoms, 11311 bonds, 1687 residues, 1 model selected > select up 11502 atoms, 11628 bonds, 1751 residues, 1 model selected > select up 11571 atoms, 11694 bonds, 1765 residues, 1 model selected > select up 11641 atoms, 11764 bonds, 1779 residues, 1 model selected > select up 12048 atoms, 12171 bonds, 1852 residues, 1 model selected > select up 13133 atoms, 13245 bonds, 2069 residues, 1 model selected > select down 12048 atoms, 12171 bonds, 1852 residues, 1 model selected > color sel #A9A9A9 > select clear > ui tool show ""Color Zone"" > combine #2#4#5 Remapping chain ID 'M' in copy of GCP23_CM1.pdb #4 to 'N' Remapping chain ID 'T' in copy of GCP23_CM1.pdb #4 to 'U' Remapping chain ID 'm' in copy of GCP23_CM1.pdb #4 to 'n' Remapping chain ID 't' in copy of GCP23_CM1.pdb #4 to 'u' Remapping chain ID 'M' in copy of GCP23_CM1.pdb #5 to 'O' Remapping chain ID 'T' in copy of GCP23_CM1.pdb #5 to 'X' Remapping chain ID 'm' in copy of GCP23_CM1.pdb #5 to 'o' Remapping chain ID 't' in copy of GCP23_CM1.pdb #5 to 'v' > color zone #1 near #7 distance 50 > color zone #1 near #7 distance 51 > color zone #1 near #7 distance 51.42 > color zone #1 near #7 distance 222.41 > color zone #1 near #7 distance 60.53 > color zone #1 near #7 distance 71.2 > color zone #1 near #7 distance 10 > color zone #1 near #7 distance 100 [Repeated 2 time(s)] > volume splitbyzone #1 Opened run_class001 (1).mrc 0 as #8.1, grid size 128,128,128, pixel 5.08, shown at level 0.235, step 1, values float32 Opened run_class001 (1).mrc 1 as #8.2, grid size 128,128,128, pixel 5.08, shown at level 0.235, step 1, values float32 Opened run_class001 (1).mrc 2 as #8.3, grid size 128,128,128, pixel 5.08, shown at level 0.235, step 1, values float32 Opened run_class001 (1).mrc 3 as #8.4, grid size 128,128,128, pixel 5.08, shown at level 0.235, step 1, values float32 Opened run_class001 (1).mrc 4 as #8.5, grid size 128,128,128, pixel 5.08, shown at level 0.235, step 1, values float32 Opened run_class001 (1).mrc 5 as #8.6, grid size 128,128,128, pixel 5.08, shown at level 0.235, step 1, values float32 > hide #!2 models > hide #!7 models > show #!7 models > hide #!7 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8.1 models > hide #!8.2 models > hide #!4 models > hide #!5 models > show #!8.1 models > hide #!8.6 models > show #!8.2 models > hide #!8.2 models > hide #!8.1 models > volume #8.3 level 0.1009 > volume #8.4 level 0.1504 > volume #8.5 level 0.16 > volume #8.5 level 0.202 > show #!1 models > transparency #8.3-5 60 > hide #!1 models > show #!2 models > show #!8.1 models > ui tool show ""Volume Viewer"" > hide #!8.1 models > show #!8.2 models > volume #8.2 level 0.4736 > save /Users/pfefferlab/Desktop/CM1_revision_1.cxs includeMaps true ——— End of log from Wed Aug 28 17:14:39 2024 ——— opened ChimeraX session > close #8.2 > select clear > show #!4 models > show #!5 models Drag select of 746 residues > select #4 12048 atoms, 12171 bonds, 38 pseudobonds, 1852 residues, 2 models selected > color #4 #a9a9a9 > color #5 #a9a9a9 > select clear [Repeated 1 time(s)] > close #8 > open > /Users/pfefferlab/Desktop/fold_2024_08_28_16_54/fold_2024_08_28_16_54_model_0.cif Chain information for fold_2024_08_28_16_54_model_0.cif #8 --- Chain | Description A B | . C | . D | . E | . F G | . > matchmaker #8/C to #2/M 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 GCP23_CM1.pdb, chain M (#2) with fold_2024_08_28_16_54_model_0.cif, chain C (#8), sequence alignment score = 3649.4 RMSD between 501 pruned atom pairs is 1.146 angstroms; (across all 538 pairs: 1.326) > select clear > select add #8 25151 atoms, 25629 bonds, 3151 residues, 1 model selected > hide sel atoms > show sel cartoons > select clear > select #8/A/B 2314 atoms, 2332 bonds, 282 residues, 1 model selected > select ~sel & ##selected 22837 atoms, 23297 bonds, 2869 residues, 1 model selected > hide sel cartoons > color #8/A/B > color #8/A/B white > select clear > hide #!4 models > hide #!5 models > show #!7 models Drag select of 1733 residues > select up 14636 atoms, 14687 bonds, 2341 residues, 2 models selected > select up 21204 atoms, 21381 bonds, 3295 residues, 2 models selected > select up 21750 atoms, 21920 bonds, 3371 residues, 2 models selected > select up 25609 atoms, 25846 bonds, 3931 residues, 2 models selected > select down 21750 atoms, 21920 bonds, 3371 residues, 2 models selected > color sel #a9a9a9 > select clear > ui tool show ""Color Zone"" > color zone #1 near #2 distance 5.08 > color zone #1 near #7 distance 5.08 > show #!1 models > color zone #1 near #7 distance 92.06 > color zone #1 near #7 distance 92.25 > color zone #1 near #7 distance 92.44 > color zone #1 near #7 distance 92.63 > color zone #1 near #8 distance 92.63 > color zone #1 near #7 distance 92.63 > color zone #1 near #7 distance 92.06 > color zone #1 near #7 distance 130.94 > color zone #1 near #7 distance 10 > color zone #1 near #7 distance 100 [Repeated 1 time(s)] > volume splitbyzone #1 Opened run_class001 (1).mrc 0 as #9.1, grid size 128,128,128, pixel 5.08, shown at level 0.235, step 1, values float32 Opened run_class001 (1).mrc 1 as #9.2, grid size 128,128,128, pixel 5.08, shown at level 0.235, step 1, values float32 Opened run_class001 (1).mrc 2 as #9.3, grid size 128,128,128, pixel 5.08, shown at level 0.235, step 1, values float32 Opened run_class001 (1).mrc 3 as #9.4, grid size 128,128,128, pixel 5.08, shown at level 0.235, step 1, values float32 Opened run_class001 (1).mrc 4 as #9.5, grid size 128,128,128, pixel 5.08, shown at level 0.235, step 1, values float32 Opened run_class001 (1).mrc 5 as #9.6, grid size 128,128,128, pixel 5.08, shown at level 0.235, step 1, values float32 > volume #9.1 level 0.2505 > transparency 60 > transparency 50 > show #!9.2 models > transparency #9.2 0 > volume #9.2 level 0.309 > volume #9.2 level 0.1332 > volume #9.2 level 0.3062 > graphics silhouettes depthJump 0.005 > view name front > save /Users/pfefferlab/Desktop/image27.png supersample 3 > hide #!9 models > show #!1 models > transparency #1 0 > save /Users/pfefferlab/Desktop/image28.png supersample 3 > ui tool show ""Side View"" > lighting depthCue false > graphics silhouettes depthJump 0.1 > graphics silhouettes depthJump 0.2 > graphics silhouettes depthJump 0.05 > save /Users/pfefferlab/Desktop/image29.png supersample 3 > hide #!1 models > show #!9 models > save /Users/pfefferlab/Desktop/image30.png supersample 3 > save /Users/pfefferlab/Desktop/CM1_revision_1.cxs includeMaps true ——— End of log from Thu Aug 29 11:27:54 2024 ——— opened ChimeraX session > show #!1 models > hide #!9 models > color #8 pink > volume #1 level 0.2835 > volume #1 level 0.2211 > ui tool show ""Hide Dust"" > surface dust #1 size 30.48 > lighting depthCueStart 0.8 > lighting depthCueStart 0.8 depthCueEnd 1 > lighting depthCueStart 0.2 depthCueEnd 1 > lighting depthCueStart 0.2 depthCueEnd 1 depthCue true > lighting depthCueStart 0.1 depthCueEnd 1 depthCue true > lighting depthCueStart 0.3 depthCueEnd 1 depthCue true > ui tool show ""Side View"" > graphics silhouettes width 1 > graphics silhouettes width 2 > graphics silhouettes width 1 > graphics silhouettes width 1 depthJump 0.1 > graphics silhouettes width 1 depthJump 0.05 > graphics silhouettes width 1 depthJump 0.01 > graphics silhouettes width 1 depthJump 0.02 > graphics silhouettes width 1 depthJump 0.03 > graphics silhouettes width 1 depthJump 0.02 > hide #!7 models > hide #!2 models > show #!2 models > select #2/M/T 7211 atoms, 7291 bonds, 17 pseudobonds, 1111 residues, 2 models selected > hide sel cartoons > select clear > volume #1 level 0.241 > volume #1 level 0.2296 > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting full > lighting simple > lighting full > lighting shadows false > save /Users/pfefferlab/Desktop/image60.png supersample 3 > volume #1 level 0.275 > volume #1 level 0.2892 > volume #1 level 0.3232 > save /Users/pfefferlab/Desktop/image61.png supersample 3 > volume #1 level 0.2807 > save /Users/pfefferlab/Desktop/image62.png supersample 3 > volume #1 level 0.2495 > volume #1 level 0.2637 > volume #1 level 0.2778 > save /Users/pfefferlab/Desktop/image63.png supersample 3 > save /Users/pfefferlab/Desktop/CM1_revision_1.cxs includeMaps true ——— End of log from Fri Aug 30 13:47:56 2024 ——— opened ChimeraX session > volume #1 level 0.2353 > volume #1 level 0.1984 > ui tool show ""Side View"" > volume #1 level 0.1332 > volume #1 level 0.2154 ===== Log before crash end ===== Log: > alias af open alphafold:$1 UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 88.1 OpenGL renderer: Apple M1 Pro 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: MacBookPro18,3 Model Number: Z15G0007SD/A Chip: Apple M1 Pro Total Number of Cores: 8 (6 performance and 2 efficiency) Memory: 16 GB System Firmware Version: 10151.121.1 OS Loader Version: 10151.121.1 Software: System Software Overview: System Version: macOS 14.5 (23F79) Kernel Version: Darwin 23.5.0 Time since boot: 5 hours, 13 minutes Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 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 VW246: 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