id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19098 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.2-arm64-arm-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x00000001e0fa5000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, openmm._openmm, openmm.app.internal.compiled, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath (total: 55) {""app_name"":""ChimeraX"",""timestamp"":""2025-10-10 14:32:44.00 +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"":1,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 14.2 (23C64)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""9B75C73D-AD20-4B11-B623-CD70D4673CC9""} { ""uptime"" : 3800000, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""Mac14,3"", ""coalitionID"" : 339939, ""osVersion"" : { ""train"" : ""macOS 14.2"", ""build"" : ""23C64"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2025-10-10 14:32:26.0386 +0200"", ""codeSigningMonitor"" : 1, ""incident"" : ""9B75C73D-AD20-4B11-B623-CD70D4673CC9"", ""pid"" : 52885, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2025-10-09 14:58:59.6659 +0200"", ""procStartAbsTime"" : 90521269610205, ""procExitAbsTime"" : 91210432115734, ""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"":""B37B9A4F-3C95-5B11-BACD-1BDB3DB05CC4"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""0C748E25-7680-0375-14CE-AD2C31BE7E26"", ""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==""}, ""wakeTime"" : 1, ""sleepWakeUUID"" : ""459380F2-54C6-4E40-BB8C-02F6B83063EC"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x5001c5628638 is not in any region. 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""60da5e84ab0ca017dace9abf"", ""factorPackIds"" : { }, ""deploymentId"" : 240000008 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== 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/janpetrovsky/Desktop/RNA_POL_2/backup_maps/cryosparc_P8_J2067_007_volume_map > (7).mrc"" Opened cryosparc_P8_J2067_007_volume_map (7).mrc as #1, grid size 250,250,250, pixel 1.12, shown at level 0.117, step 1, values float32 > open > /Users/janpetrovsky/Desktop/rnapol_p4a_isolda/final_model/isolda_phenix_7.pdb Chain information for isolda_phenix_7.pdb #2 --- Chain | Description B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available Q | No description available T | No description available > select add #2 64621 atoms, 65383 bonds, 31 pseudobonds, 3978 residues, 3 models selected > hide sel atoms > show sel cartoons > select ::name=""B4P"" 77 atoms, 82 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select /T:31 32 atoms, 33 bonds, 1 residue, 1 model selected > select up 1204 atoms, 1297 bonds, 38 residues, 1 model selected > color sel blue > select clear > select /Q:2 34 atoms, 36 bonds, 1 residue, 1 model selected > select up 260 atoms, 279 bonds, 8 residues, 1 model selected > select up 64621 atoms, 65383 bonds, 3978 residues, 1 model selected > select down 260 atoms, 279 bonds, 8 residues, 1 model selected > color sel red > select clear > surface dust #1 size 11.2 > open ""/Users/janpetrovsky/Downloads/cryosparc_P8_J2925_004_volume_map > (1).mrc"" Opened cryosparc_P8_J2925_004_volume_map (1).mrc as #3, grid size 256,256,256, pixel 1.52, shown at level 0.0714, step 1, values float32 > surface dust #1 size 11.2 > surface dust #3 size 15.2 > select #3 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.38511,-0.30274,-0.87181,522.15,0.92278,-0.13966,-0.35912,95.325,-0.013038,-0.94279,0.33314,315.48 > view matrix models > #3,-0.99303,-0.071487,-0.093717,461.07,-0.11205,0.8192,0.56246,-45.461,0.036565,0.56904,-0.8215,220.79 > volume #3 level 0.1504 > volume #1 level 0.1134 > volume #3 level 0.1472 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.99303,-0.071487,-0.093717,383.48,-0.11205,0.8192,0.56246,-94.454,0.036565,0.56904,-0.8215,174.91 > view matrix models > #3,-0.99303,-0.071487,-0.093717,366.38,-0.11205,0.8192,0.56246,-103.91,0.036565,0.56904,-0.8215,180.9 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.99526,-0.090571,-0.035479,359.69,-0.093868,0.79861,0.59448,-109.63,-0.025508,0.59499,-0.80333,185.29 > view matrix models > #3,-0.95436,-0.29277,-0.058994,395.69,-0.2778,0.79775,0.53519,-59.957,-0.10962,0.52715,-0.84267,223.68 > fitmap #3 inMap #1 Fit map cryosparc_P8_J2925_004_volume_map (1).mrc in map cryosparc_P8_J2067_007_volume_map (7).mrc using 72040 points correlation = 0.5677, correlation about mean = 0.05338, overlap = 1387 steps = 156, shift = 2.11, angle = 5.74 degrees Position of cryosparc_P8_J2925_004_volume_map (1).mrc (#3) relative to cryosparc_P8_J2067_007_volume_map (7).mrc (#1) coordinates: Matrix rotation and translation -0.95369779 -0.30000030 0.02145559 379.30130107 -0.23140097 0.77744760 0.58483230 -73.94385412 -0.19213046 0.55278843 -0.81087042 228.42984382 Axis -0.14140594 0.94253082 0.30272101 Axis point 191.48557165 0.00000000 114.88444722 Rotation angle (degrees) 173.49415683 Shift along axis -54.17930559 > view matrix models > #3,-0.99757,0.06955,0.0043675,318.34,0.069507,0.98855,0.13391,-93.862,0.0049958,0.13389,-0.99098,304.27 > fitmap #3 inMap #1 Fit map cryosparc_P8_J2925_004_volume_map (1).mrc in map cryosparc_P8_J2067_007_volume_map (7).mrc using 72040 points correlation = 0.9165, correlation about mean = 0.6178, overlap = 3640 steps = 104, shift = 2.6, angle = 8.19 degrees Position of cryosparc_P8_J2925_004_volume_map (1).mrc (#3) relative to cryosparc_P8_J2067_007_volume_map (7).mrc (#1) coordinates: Matrix rotation and translation -0.99745435 -0.07128823 0.00167430 347.71737025 -0.07066014 0.99127878 0.11123632 -60.86070385 -0.00958954 0.11083485 -0.99379257 312.67720271 Axis -0.03556501 0.99781730 0.05563965 Axis point 173.22061941 0.00000000 157.54651332 Rotation angle (degrees) 179.67660716 Shift along axis -55.69718209 > select clear > volume #3 level 0.1082 > volume #1 level 0.1497 > volume #3 level 0.124 > volume #3 level 0.1366 > volume #3 level 0.1524 > show #!1 models > select /T:28 32 atoms, 34 bonds, 1 residue, 1 model selected > select /T:29 33 atoms, 35 bonds, 1 residue, 1 model selected > select add /T:28 65 atoms, 69 bonds, 2 residues, 1 model selected > select add /T:30 98 atoms, 104 bonds, 3 residues, 1 model selected > select add /T:31 130 atoms, 137 bonds, 4 residues, 1 model selected > select add /T:33 163 atoms, 172 bonds, 5 residues, 1 model selected > select add /T:32 193 atoms, 203 bonds, 6 residues, 1 model selected > select add /T:34 225 atoms, 236 bonds, 7 residues, 1 model selected > select add /T:35 257 atoms, 269 bonds, 8 residues, 1 model selected > select add /T:36 289 atoms, 303 bonds, 9 residues, 3 models selected > select clear > select #1/T:26-39 Nothing selected > select #2/T:26-39 444 atoms, 477 bonds, 14 residues, 1 model selected > delete sel > select /N:13 30 atoms, 31 bonds, 1 residue, 1 model selected > select #2/N:1-13 408 atoms, 440 bonds, 13 residues, 1 model selected > delete sel > select /N:37 32 atoms, 33 bonds, 1 residue, 1 model selected > select add /N:38 65 atoms, 67 bonds, 2 residues, 1 model selected > select add /T:6 97 atoms, 100 bonds, 3 residues, 1 model selected > select add /T:5 127 atoms, 131 bonds, 4 residues, 1 model selected > select add /T:2 159 atoms, 165 bonds, 5 residues, 1 model selected > select add /T:4 192 atoms, 200 bonds, 6 residues, 1 model selected > select add /T:3 224 atoms, 234 bonds, 7 residues, 1 model selected > delete sel > select /T:9 32 atoms, 34 bonds, 1 residue, 1 model selected > select up 601 atoms, 647 bonds, 19 residues, 1 model selected > select up 63545 atoms, 64224 bonds, 3944 residues, 1 model selected > select down 601 atoms, 647 bonds, 19 residues, 1 model selected > select add /N:34 633 atoms, 681 bonds, 20 residues, 1 model selected > select up 952 atoms, 1025 bonds, 30 residues, 1 model selected > select add /Q:3 983 atoms, 1057 bonds, 31 residues, 1 model selected > select up 1212 atoms, 1304 bonds, 38 residues, 1 model selected > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 77 atoms, 82 bonds, 1 residue, 1 model selected > select up 63545 atoms, 64224 bonds, 3944 residues, 1 model selected > select down 77 atoms, 82 bonds, 1 residue, 1 model selected > select add /Q:2 111 atoms, 118 bonds, 2 residues, 1 model selected > select up 337 atoms, 361 bonds, 9 residues, 1 model selected > select add /N:34 369 atoms, 395 bonds, 10 residues, 1 model selected > select up 688 atoms, 739 bonds, 20 residues, 1 model selected > select add /T:9 720 atoms, 773 bonds, 21 residues, 1 model selected > select up 1289 atoms, 1386 bonds, 39 residues, 1 model selected > select up 63545 atoms, 64224 bonds, 3944 residues, 1 model selected > select down 1289 atoms, 1386 bonds, 39 residues, 1 model selected > color zone #1 near sel distance 2.5 > volume #1 level 0.09521 > volume #1 level 0.1101 > undo > close #2 > open > /Users/janpetrovsky/Desktop/rnapol_p4a_isolda/final_model/isolda_phenix_7.pdb Chain information for isolda_phenix_7.pdb #2 --- Chain | Description B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available Q | No description available T | No description available > select add #2 64621 atoms, 65383 bonds, 31 pseudobonds, 3978 residues, 3 models selected > hide sel atoms > show sel cartoons > select ::name=""B4P"" 77 atoms, 82 bonds, 1 residue, 1 model selected > show sel atoms > select /Q:4 34 atoms, 36 bonds, 1 residue, 1 model selected > select up 260 atoms, 279 bonds, 8 residues, 1 model selected > color sel red > select /T:7 30 atoms, 31 bonds, 1 residue, 1 model selected > select up 1204 atoms, 1297 bonds, 38 residues, 1 model selected > hide #!1 models > color sel blue > select /N:34 32 atoms, 34 bonds, 1 residue, 1 model selected > select up 824 atoms, 887 bonds, 26 residues, 1 model selected > color sel cyan > select clear > show #!1 models > volume #1 level 0.09687 > select #2/N:1-13 408 atoms, 440 bonds, 13 residues, 1 model selected > lsel Unknown command: devel lsel > delete sel > select #2/T:28-39 384 atoms, 413 bonds, 12 residues, 1 model selected > delete sel > hide #!2 models > show #!2 models > hide #!1 models > select /T:12 32 atoms, 34 bonds, 1 residue, 1 model selected > select up 820 atoms, 883 bonds, 26 residues, 1 model selected > select add /N:27 853 atoms, 918 bonds, 27 residues, 1 model selected > select up 1236 atoms, 1330 bonds, 39 residues, 1 model selected > select add /Q:8 1267 atoms, 1362 bonds, 40 residues, 1 model selected > select up 1496 atoms, 1609 bonds, 47 residues, 1 model selected > show #!1 models > color zone #1 near sel distance 2.5 > color zone #1 near sel distance 3 > color zone #1 near sel distance 3.2 > color zone #1 near sel distance 3.5 > color zone #1 near sel distance 3.2 > volume #1 level 0.1051 > volume #1 level 0.1084 > color zone #1 near sel distance 3 > volume zone #1 nearAtoms sel range 3 newMap true Opened cryosparc_P8_J2067_007_volume_map (7).mrc zone as #4, grid size 250,250,250, pixel 1.12, shown at step 1, values float32 > hide #!2 models > volume #4 level 0.1194 > surface dust #4 size 11.2 > show #!2 models > color zone #4 near sel distance 3 > hide #!2 models > show #!1 models > volume #1 level 0.1866 > color #1 #b2b2b23d models > set bgColor white > lighting simple > lighting soft > lighting shadows true intensity 0.5 > lighting full > lighting soft > color #1 white models > lighting soft > lighting full > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > lighting simple > graphics silhouettes false > graphics silhouettes true > lighting soft > lighting simple > lighting full > color #1 #ebebebff models > color #1 #ebebebce models > color #1 white models > color #1 #ffffff52 models > show #!2 models > graphics silhouettes false > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!4 models > show #!3 models > hide #!1 models > lighting simple > color #3 #ffffb270 models > select #2/C 4076 atoms, 4118 bonds, 5 pseudobonds, 258 residues, 3 models selected > select #2/Q 260 atoms, 279 bonds, 8 residues, 1 model selected > view sel > ui tool show ""Side View"" > volume #3 level 0.1589 > volume #3 level 0.1557 > volume #3 level 0.1654 > volume #3 level 0.1492 > select /T:26 30 atoms, 31 bonds, 1 residue, 1 model selected > view sel > close #3 > lighting soft > hide #!2 models > show #!1 models > show #!4 models > lighting full > lighting flat > hide #!4 models > show #!4 models > lighting simple > lighting soft > lighting simple > lighting soft > volume #1 level 0.1833 > volume #1 level 0.1569 > volume #4 level 0.117 > color #4 #b2ffffff models > color zone #4 near sel distance 3 > show #!2 models > select up 820 atoms, 883 bonds, 26 residues, 1 model selected > select add /Q:2 854 atoms, 919 bonds, 27 residues, 1 model selected > select up 1080 atoms, 1162 bonds, 34 residues, 1 model selected > select add /N:36 1110 atoms, 1193 bonds, 35 residues, 1 model selected > select up 1496 atoms, 1609 bonds, 47 residues, 1 model selected > color zone #4 near sel distance 3 > hide #!2 models > view name p1 > volume #1 level 0.1767 > select up 63829 atoms, 64529 bonds, 3953 residues, 1 model selected > select down 1496 atoms, 1609 bonds, 47 residues, 1 model selected > view name p1 > roll x 1 800 > roll y 1 360 > view name p2 > view name p3 > view name p4 > view name p5 > fly p1 p2 p3 p4 p5 > ui tool show ""Side View"" > fly p1 p2 p3 p4 p5 > view name p4 > fly p1 p2 p3 p4 p5 > view name p2 > fly p1 p2 p3 p4 p5 > view name p4 > fly p1 p2 p3 p4 p5 > ui mousemode right pivot > ui mousemode right ""translate selected models"" > view name p1 > view name p2 > view name p3 > view name p4 > view name p5 > view name p6 > volume #4 level 0.1046 > fly p1 p2 p3 p4 p5 p6 > show #!2 models > select ~sel & ##selected 62333 atoms, 62920 bonds, 30 pseudobonds, 3906 residues, 3 models selected > hide sel cartoons > volume #4 level 0.1013 > volume #4 level 0.1038 > hide #!4 models > volume #1 level 0.1338 > volume #1 level 0.1024 > volume #1 level 0.18 > hide sel atoms > select /Q:2 34 atoms, 36 bonds, 1 residue, 1 model selected > select up 260 atoms, 279 bonds, 8 residues, 1 model selected > select add /T:3 292 atoms, 313 bonds, 9 residues, 1 model selected > select up 1080 atoms, 1162 bonds, 34 residues, 1 model selected > hide sel cartoons > roll y 1 360 > ui mousemode right pivot > ui mousemode right ""translate selected models"" > movie record > roll y 1 360 > stop > movie encode Movie saved to /Users/janpetrovsky/Desktop/movie.mp4 > ui mousemode right pivot > ui mousemode right ""translate selected models"" > movie record > roll y 1 360 > fly p1 p2 p3 p4 p5 p6 > stop > encodew Unknown command: movie encodew > movie encode Movie saved to /Users/janpetrovsky/Desktop/movie.mp4 > roll y 1 360 > movie record > roll y 1 380 > roll x 1 90 > fly p1 p2 p3 p4 p5 p6 > stop > movie encode Movie saved to /Users/janpetrovsky/Desktop/movie.mp4 > view name p1 > fly p1 p2 p3 p4 p5 p6 > stop > fly p1 p2 p3 p4 p5 p6 > stop > movie record > roll y 1 370 > select add #2 63829 atoms, 64529 bonds, 30 pseudobonds, 3953 residues, 3 models selected > select subtract #2 Nothing selected > select add #2 63829 atoms, 64529 bonds, 30 pseudobonds, 3953 residues, 3 models selected > hide sel cartoons > fly p20 p1 p2 p3 p4 p5 p6 fly: Unknown position name ""p20"" > view name p20 > fly p20 p1 p2 p3 p4 p5 p6 > movie encode Movie saved to /Users/janpetrovsky/Desktop/movie.mp4 > movie record > roll y 1 370 > view name p20 > fly p20 p1 p2 p3 p4 p5 p6 > stop > movie encode Movie saved to /Users/janpetrovsky/Desktop/movie.mp4 > movie record > roll y 1 370 > view name p20 > fly p20 p1 p2 p3 200 p4 p5 p6 > select up 63829 atoms, 64529 bonds, 30 pseudobonds, 3953 residues, 3 models selected > select down 292 atoms, 313 bonds, 30 pseudobonds, 9 residues, 3 models selected > movie encode Movie saved to /Users/janpetrovsky/Desktop/movie.mp4 > view name p30 > lighting simple > graphics silhouettes false > hide #!4 models > volume #1 color #ffffffb9 > volume #1 color #d6d6d6 > volume #1 level 0.1239 > volume #1 level 0.1074 > select ::name=""B4P"" 77 atoms, 82 bonds, 1 residue, 1 model selected > show sel atoms > select clear > volume #1 level 0.09911 > volume #4 level 0.08895 > hide #!2 models > show #!2 models > select add #2 63829 atoms, 64529 bonds, 30 pseudobonds, 3953 residues, 3 models selected > show sel cartoons > select clear > select /Q:2 34 atoms, 36 bonds, 1 residue, 1 model selected > select up 260 atoms, 279 bonds, 8 residues, 1 model selected > select add /A:1@O3A 261 atoms, 279 bonds, 9 residues, 1 model selected > select up 337 atoms, 361 bonds, 9 residues, 1 model selected > select add /T:26 367 atoms, 392 bonds, 10 residues, 1 model selected > select up 1157 atoms, 1244 bonds, 35 residues, 1 model selected > select add /N:37 1189 atoms, 1277 bonds, 36 residues, 1 model selected > select up 1573 atoms, 1691 bonds, 48 residues, 1 model selected > color zone #4 near sel distance 3 > color zone #1 near sel distance 3 > select clear > select /A:1@O2G 1 atom, 1 residue, 1 model selected > select up 77 atoms, 82 bonds, 1 residue, 1 model selected > color sel yellow > color zone #1 near sel distance 3 > undo > color sel byhetero > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 77 atoms, 82 bonds, 1 residue, 1 model selected > color sel red > select add /T:2 109 atoms, 116 bonds, 2 residues, 1 model selected > select up 897 atoms, 965 bonds, 27 residues, 1 model selected > select add /N:38 930 atoms, 999 bonds, 28 residues, 1 model selected > select up 1313 atoms, 1412 bonds, 40 residues, 1 model selected > color zone #1 near sel distance 3 > select add /Q:4 1347 atoms, 1448 bonds, 41 residues, 1 model selected > select up 1573 atoms, 1691 bonds, 48 residues, 1 model selected > color zone #1 near sel distance 3 > volume zone #1 nearAtoms sel range 3 newMap true Opened cryosparc_P8_J2067_007_volume_map (7).mrc zone as #3, grid size 250,250,250, pixel 1.12, shown at step 1, values float32 > color zone #3 near sel distance 3 > surface dust #3 size 11.2 > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!3 models > show #!3 models > hide #!4 models > hide #!3 models > show #!4 models > hide #!4 models > hide #!2 models > show #!4 models > show #!1 models > volume #1 level 0.1348 > volume #1 level 0.1314 > hide #!4 models > show #!3 models > p30 Unknown command: p30 > fly p30 > lighting flat > volume #1 color #ffffff1d > lighting full > volume #1 color #ffffff1c > lighting soft > movie record > roll y 1 370 > fly p20 p1 p2 p3 200 p4 p5 p6 > stop > fly p30 > movie encode Movie saved to /Users/janpetrovsky/Desktop/movie.mp4 > fly p30 > movie record > roll y 1 370 > view name p20 > fly p20 p1 p2 p3 200 p4 p5 p6 > movie encode Movie saved to /Users/janpetrovsky/Desktop/movie.mp4 > volume #1 color silver > lighting simple > transparency #3 80 > color #1 white models > color #1 #ffffff3c models > color #1 #ffffff3b models > show #!2 models > select ~sel & ##selected 62256 atoms, 62838 bonds, 30 pseudobonds, 3905 residues, 3 models selected > hide sel cartoons > select /T:27 30 atoms, 31 bonds, 1 residue, 1 model selected > select up 820 atoms, 883 bonds, 26 residues, 1 model selected > select /Q:2 34 atoms, 36 bonds, 1 residue, 1 model selected > select up 260 atoms, 279 bonds, 8 residues, 1 model selected > select /T:27 30 atoms, 31 bonds, 1 residue, 1 model selected > select up 820 atoms, 883 bonds, 26 residues, 1 model selected > select clear > select #3 3 models selected > select clear > hide #!1 models > select #3 3 models selected > select clear > hide #!3 models > select /T:11 32 atoms, 33 bonds, 1 residue, 1 model selected > select up 820 atoms, 883 bonds, 26 residues, 1 model selected > select add /N:32 852 atoms, 916 bonds, 27 residues, 1 model selected > select up 1236 atoms, 1330 bonds, 39 residues, 1 model selected > select add /Q:2 1270 atoms, 1366 bonds, 40 residues, 1 model selected > select up 1496 atoms, 1609 bonds, 47 residues, 1 model selected > select add /A:1@N3B 1497 atoms, 1609 bonds, 48 residues, 1 model selected > select up 1573 atoms, 1691 bonds, 48 residues, 1 model selected > show #!3 models > show #!1 models > show sel atoms > nucleotides sel atoms > style nucleic & sel stick Changed 1496 atom styles > color sel byhetero > hide @h > hide @H > select @H 3705 atoms, 3705 residues, 1 model selected > delete h Missing or invalid ""atoms"" argument: invalid atoms specifier > delete @h > hide h Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide H > transparency #3 90 > transparency #3 50 > transparency #3 40 > transparency #3 70 > view name 11 > cview sel > select clear > select #3 4 models selected > hide #!3 models > hide #!1 models > select /A:1@N3A 1 atom, 1 residue, 1 model selected > select up 77 atoms, 82 bonds, 1 residue, 1 model selected > show #!3 models > show #!1 models > cview sel > select /Q:2 34 atoms, 36 bonds, 1 residue, 1 model selected > select up 260 atoms, 279 bonds, 8 residues, 1 model selected > hide sel cartoons > select /T:27 30 atoms, 31 bonds, 1 residue, 1 model selected > select up 820 atoms, 883 bonds, 26 residues, 1 model selected > hide sel cartoons ===== Log before crash end ===== Log: 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 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: Mac mini Model Identifier: Mac14,3 Model Number: Z16L000FTCZ/A Chip: Apple M2 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 10151.61.4 OS Loader Version: 10151.61.4 Software: System Software Overview: System Version: macOS 14.2 (23C64) Kernel Version: Darwin 23.2.0 Time since boot: 101 days, 23 hours, 47 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: U27P2G6B: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported U2790B: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.23.1 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 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