id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17258 Crash running open/save dialog chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-15.3-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 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 0x00000001ef630840 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py"", line 50 in display File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py"", line 138 in show_save_file_dialog File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py"", line 127 in File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 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, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, 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, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, psutil._psutil_osx, psutil._psutil_posix, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 55) {""app_name"":""ChimeraX"",""timestamp"":""2025-04-01 14:56:58.00 +0800"",""app_version"":""1.9.0"",""slice_uuid"":""17982d98-65bc-3327-8526-577ec996453c"",""build_version"":""1.9.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 15.3 (24D60)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""1D871B8A-1DE7-4D43-9C4B-D4BCE1895CB6""} { ""uptime"" : 1100000, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""MacBookAir10,1"", ""coalitionID"" : 105829, ""osVersion"" : { ""train"" : ""macOS 15.3"", ""build"" : ""24D60"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2025-04-01 14:56:53.9643 +0800"", ""codeSigningMonitor"" : 1, ""incident"" : ""1D871B8A-1DE7-4D43-9C4B-D4BCE1895CB6"", ""pid"" : 86195, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2025-04-01 14:31:22.6640 +0800"", ""procStartAbsTime"" : 26589341273712, ""procExitAbsTime"" : 26626092642704, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.9.0"",""CFBundleVersion"":""1.9.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""E5AA5BE9-FE5E-5395-9EDD-C4B65938E3BF"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""D01310E2-EFFE-3418-970D-8CBCF139FECF"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""instructionByteStream"" : {""beforePC"":""fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A=="",""atPC"":""AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g==""}, ""bootSessionUUID"" : ""44ADBD3A-8618-49C3-9BDD-311E234DA9C7"", ""wakeTime"" : 1789, ""sleepWakeUUID"" : ""49429E98-9771-4CBF-8F34-E04822A00189"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x2b5bf4a14e2e is not in any region. 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\nshared memory 4464K 35 \n=========== ======= ======= \nTOTAL 5.3G 6114 \nTOTAL, minus reserved VM space 5.2G 6114 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""1c2a4878735a82b17438af5428eb4a25f9b1d1f2"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""644114de41e7236e6177f9bd"", ""factorPackIds"" : { }, ""deploymentId"" : 240000013 }, { ""rolloutId"" : ""639124e81d92412bfb4880b3"", ""factorPackIds"" : { }, ""deploymentId"" : 240000012 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Volumes/data-4T/Projects/校外合作/SunLitao/5-BCZ-complex/C550BZ complex > 结构预测/AlphaFold3/fold_2025_02_06_16_38_model_0.cif"" Chain information for fold_2025_02_06_16_38_model_0.cif #1 --- Chain | Description A | . B | . C | . Computing secondary structure > color bychain > open ""/Volumes/data-4T/Projects/校外合作/SunLitao/5-BCZ-complex/C550BZ complex > 结构预测/cryosparc_P19_J325_005_volume_map-3.23A.mrc"" Opened cryosparc_P19_J325_005_volume_map-3.23A.mrc as #2, grid size 320,320,320, pixel 0.86, shown at level 0.0315, step 2, values float32 > ui mousemode right zoom > volume #2 step 1 > volume #2 level 0.1296 > open /Volumes/data-4T/Projects/校外合作/SunLitao/4-BrxC/PDB- > models/RealSpaceRefine_8/N550-dimer-inimod- > coot-8_real_space_refined_008-coot_pro-addAGS-addto564.pdb Chain information for N550-dimer-inimod- coot-8_real_space_refined_008-coot_pro-addAGS-addto564.pdb #3 --- Chain | Description A | No description available B | No description available > ui mousemode right ""translate selected models"" > select add #3 9157 atoms, 9331 bonds, 1125 residues, 1 model selected > view matrix models #3,1,0,0,-5.7909,0,1,0,-39.132,0,0,1,-10.593 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.37223,0.2285,-0.89958,308.7,0.29219,0.94879,0.12009,-94.233,0.88095,-0.21815,-0.41993,119.16 > view matrix models > #3,-0.69676,0.67663,-0.23809,178.45,-0.47376,-0.68333,-0.55553,397.55,-0.53859,-0.27427,0.79668,148.52 > view matrix models > #3,0.26591,-0.94816,0.17404,232.95,-0.88546,-0.16885,0.43296,217.25,-0.38113,-0.26923,-0.88445,393.11 > view matrix models > #3,0.70404,-0.69021,0.16712,125.41,-0.71007,-0.6804,0.1813,314.84,-0.011425,-0.24631,-0.96912,346.91 > view matrix models > #3,0.68216,-0.54078,0.49215,52.17,-0.66615,-0.73716,0.11335,328.38,0.30149,-0.40517,-0.8631,308.57 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.68216,-0.54078,0.49215,54.747,-0.66615,-0.73716,0.11335,334.85,0.30149,-0.40517,-0.8631,305.14 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.8152,-0.57431,-0.075013,130.94,-0.54279,-0.80272,0.24702,305.5,-0.20208,-0.16065,-0.9661,357.83 > fitmap #3 inMap #2 Fit molecule N550-dimer-inimod-coot-8_real_space_refined_008-coot_pro-addAGS- addto564.pdb (#3) to map cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2) using 9157 atoms average map value = 0.05333, steps = 280 shifted from previous position = 13.4 rotated from previous position = 20 degrees atoms outside contour = 7710, contour level = 0.12961 Position of N550-dimer-inimod-coot-8_real_space_refined_008-coot_pro-addAGS- addto564.pdb (#3) relative to cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2) coordinates: Matrix rotation and translation 0.95267151 -0.26822987 -0.14307249 59.01134143 -0.24610664 -0.95676971 0.15499437 304.33632268 -0.17846154 -0.11244763 -0.97750039 345.25794382 Axis -0.98804169 0.13074185 0.08173239 Axis point 0.00000000 167.92297449 164.64340021 Rotation angle (degrees) 172.22175202 Shift along axis 9.70258351 > fitmap #3 inMap #2 Fit molecule N550-dimer-inimod-coot-8_real_space_refined_008-coot_pro-addAGS- addto564.pdb (#3) to map cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2) using 9157 atoms average map value = 0.05333, steps = 64 shifted from previous position = 0.0138 rotated from previous position = 0.0186 degrees atoms outside contour = 7705, contour level = 0.12961 Position of N550-dimer-inimod-coot-8_real_space_refined_008-coot_pro-addAGS- addto564.pdb (#3) relative to cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2) coordinates: Matrix rotation and translation 0.95270424 -0.26800051 -0.14328418 59.01005925 -0.24587294 -0.95684849 0.15487886 304.32077469 -0.17860886 -0.11232404 -0.97748769 345.25507278 Axis -0.98805011 0.13062193 0.08182227 Axis point 0.00000000 167.90049672 164.65462415 Rotation angle (degrees) 172.22881560 Shift along axis 9.69562337 > volume #2 level 0.03023 > volume #2 level 0.122 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.9527,-0.268,-0.14328,85.71,-0.24587,-0.95685,0.15488,336.7,-0.17861,-0.11232,-0.97749,274.93 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.52241,-0.82135,-0.22909,255.34,-0.71934,-0.56877,0.39881,305.73,-0.45786,-0.043543,-0.88796,291.62 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.52241,-0.82135,-0.22909,227.62,-0.71934,-0.56877,0.39881,271.38,-0.45786,-0.043543,-0.88796,355.98 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.77538,-0.29852,0.55648,212.67,0.10871,-0.93116,-0.34803,324.98,0.62207,-0.20936,0.75446,-43.495 > view matrix models > #3,-0.99016,0.0070287,-0.13976,306.64,-0.026244,-0.99034,0.13613,277.57,-0.13745,0.13846,0.98078,-21.713 > fitmap #3 inMap #2 Fit molecule N550-dimer-inimod-coot-8_real_space_refined_008-coot_pro-addAGS- addto564.pdb (#3) to map cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2) using 9157 atoms average map value = 0.1503, steps = 272 shifted from previous position = 9.25 rotated from previous position = 44.5 degrees atoms outside contour = 3491, contour level = 0.12197 Position of N550-dimer-inimod-coot-8_real_space_refined_008-coot_pro-addAGS- addto564.pdb (#3) relative to cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2) coordinates: Matrix rotation and translation -0.72711438 0.68159229 0.08207695 125.62170437 -0.67472361 -0.73156312 0.09779287 348.46591547 0.12669934 0.01572735 0.99181648 -42.95845621 Axis -0.06036321 -0.03282195 -0.99763671 Axis point 132.75151949 149.96721374 0.00000000 Rotation angle (degrees) 137.17476244 Shift along axis 23.83667299 > fitmap #3 inMap #2 Fit molecule N550-dimer-inimod-coot-8_real_space_refined_008-coot_pro-addAGS- addto564.pdb (#3) to map cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2) using 9157 atoms average map value = 0.1503, steps = 40 shifted from previous position = 0.0197 rotated from previous position = 0.0112 degrees atoms outside contour = 3493, contour level = 0.12197 Position of N550-dimer-inimod-coot-8_real_space_refined_008-coot_pro-addAGS- addto564.pdb (#3) relative to cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2) coordinates: Matrix rotation and translation -0.72708409 0.68161930 0.08212096 125.60753256 -0.67472618 -0.73153573 0.09797989 348.41603670 0.12685940 0.01583045 0.99179438 -42.98471289 Axis -0.06042322 -0.03290638 -0.99763029 Axis point 132.74015013 149.94601340 0.00000000 Rotation angle (degrees) 137.17326283 Shift along axis 23.82812955 > fitmap #3 inMap #2 Fit molecule N550-dimer-inimod-coot-8_real_space_refined_008-coot_pro-addAGS- addto564.pdb (#3) to map cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2) using 9157 atoms average map value = 0.1503, steps = 36 shifted from previous position = 0.00746 rotated from previous position = 0.00342 degrees atoms outside contour = 3488, contour level = 0.12197 Position of N550-dimer-inimod-coot-8_real_space_refined_008-coot_pro-addAGS- addto564.pdb (#3) relative to cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2) coordinates: Matrix rotation and translation -0.72707260 0.68163570 0.08208661 125.61463200 -0.67474863 -0.73152068 0.09793766 348.42808464 0.12680585 0.01581996 0.99180139 -42.97611343 Axis -0.06039827 -0.03289139 -0.99763230 Axis point 132.74754586 149.94944732 0.00000000 Rotation angle (degrees) 137.17184823 Shift along axis 23.82716884 > fitmap #3 inMap #2 Fit molecule N550-dimer-inimod-coot-8_real_space_refined_008-coot_pro-addAGS- addto564.pdb (#3) to map cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2) using 9157 atoms average map value = 0.1503, steps = 36 shifted from previous position = 0.0155 rotated from previous position = 0.018 degrees atoms outside contour = 3492, contour level = 0.12197 Position of N550-dimer-inimod-coot-8_real_space_refined_008-coot_pro-addAGS- addto564.pdb (#3) relative to cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2) coordinates: Matrix rotation and translation -0.72716677 0.68151934 0.08221848 125.61787410 -0.67466186 -0.73163460 0.09768416 348.48555827 0.12672753 0.01556300 0.99181547 -42.92958410 Axis -0.06041012 -0.03274183 -0.99763650 Axis point 132.74391807 149.97882401 0.00000000 Rotation angle (degrees) 137.18002525 Shift along axis 23.82947626 > fitmap #3 inMap #2 Fit molecule N550-dimer-inimod-coot-8_real_space_refined_008-coot_pro-addAGS- addto564.pdb (#3) to map cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2) using 9157 atoms average map value = 0.1503, steps = 40 shifted from previous position = 0.012 rotated from previous position = 0.0126 degrees atoms outside contour = 3491, contour level = 0.12197 Position of N550-dimer-inimod-coot-8_real_space_refined_008-coot_pro-addAGS- addto564.pdb (#3) relative to cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2) coordinates: Matrix rotation and translation -0.72710741 0.68159166 0.08214399 125.61400717 -0.67471142 -0.73156339 0.09787495 348.44120658 0.12680428 0.01574211 0.99180283 -42.96369464 Axis -0.06041305 -0.03285001 -0.99763277 Axis point 132.74387602 149.95703592 0.00000000 Rotation angle (degrees) 137.17505489 Shift along axis 23.82696649 > select subtract #3 Nothing selected > volume #2 color #b2b2b289 > ui tool show Matchmaker > ui mousemode right zoom > matchmaker #1/A to #3/B pairing ss Computing secondary structure Parameters --- Chain pairing | ss 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 N550-dimer-inimod-coot-8_real_space_refined_008-coot_pro-addAGS- addto564.pdb, chain B (#3) with fold_2025_02_06_16_38_model_0.cif, chain A (#1), sequence alignment score = 2634.1 RMSD between 274 pruned atom pairs is 1.035 angstroms; (across all 559 pairs: 7.850) > hide #!2 models > show #!2 models > open ""/Volumes/data-4T/Projects/校外合作/SunLitao/5-BCZ-complex/C550BZ complex > 结构预测/AF-brxB.pdb"" Summary of feedback from opening /Volumes/data-4T/Projects/校外合作/SunLitao/5-BCZ-complex/C550BZ complex 结构预测/AF- brxB.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 ILE A 17 ILE A 20 1 4 Start residue of secondary structure not found: HELIX 2 2 ASP A 40 GLU A 49 1 10 Start residue of secondary structure not found: HELIX 3 3 ARG A 54 THR A 71 1 18 Start residue of secondary structure not found: HELIX 4 4 ARG A 75 MET A 78 1 4 Start residue of secondary structure not found: HELIX 5 5 LYS A 94 LEU A 105 1 12 99 messages similar to the above omitted Chain information for AF-brxB.pdb #4 --- Chain | Description B | No description available Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 3 atomic models, 1 maps. > hide #3 models > show #3 models > hide #1 models > hide #4 models > show #4 models Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 2 atomic models, 1 maps. > ui mousemode right ""rotate selected models"" > hide #4 models > show #4 models > ui mousemode right ""translate selected models"" > select #4/B:50 10 atoms, 10 bonds, 1 residue, 1 model selected > select up 183 atoms, 185 bonds, 21 residues, 1 model selected > select up 1669 atoms, 1711 bonds, 206 residues, 1 model selected > view matrix models #4,1,0,0,0.84142,0,1,0,0.9042,0,0,1,-2.3685 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.87437,0.45992,-0.15476,-4.6382,-0.47243,0.87965,-0.054976,83.52,0.11085,0.12118,0.98642,-26.939 > view matrix models > #4,0.99046,0.12409,-0.059896,-1.2675,-0.12351,0.99225,0.013368,16.2,0.061091,-0.0058429,0.99812,-9.679 > view matrix models > #4,0.97777,0.15678,-0.13926,8.7132,-0.15747,0.9875,0.0061251,22.236,0.13848,0.015941,0.99024,-20.976 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.97777,0.15678,-0.13926,9.6312,-0.15747,0.9875,0.0061251,24.555,0.13848,0.015941,0.99024,-23.486 > fitmap #4 inMap #2 Fit molecule AF-brxB.pdb (#4) to map cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2) using 1669 atoms average map value = 0.1168, steps = 88 shifted from previous position = 5.29 rotated from previous position = 10.1 degrees atoms outside contour = 870, contour level = 0.12197 Position of AF-brxB.pdb (#4) relative to cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2) coordinates: Matrix rotation and translation 0.99428376 0.09169075 -0.05470478 -2.93318254 -0.09851074 0.98540277 -0.13884166 37.65032173 0.04117574 0.14343701 0.98880250 -22.87973986 Axis 0.79824205 -0.27113584 -0.53786149 Axis point 0.00000000 180.07848216 251.76610812 Rotation angle (degrees) 10.18416361 Shift along axis -0.24361031 > fitmap #4 inMap #2 Fit molecule AF-brxB.pdb (#4) to map cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2) using 1669 atoms average map value = 0.1168, steps = 28 shifted from previous position = 0.0238 rotated from previous position = 0.0135 degrees atoms outside contour = 865, contour level = 0.12197 Position of AF-brxB.pdb (#4) relative to cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2) coordinates: Matrix rotation and translation 0.99425898 0.09188852 -0.05482315 -2.94335710 -0.09872141 0.98538960 -0.13878553 37.68675605 0.04126937 0.14340098 0.98880382 -22.90478918 Axis 0.79752170 -0.27157878 -0.53870596 Axis point 0.00000000 180.32170649 252.08745033 Rotation angle (degrees) 10.19009676 Shift along axis -0.24336796 > fitmap #4 inMap #2 Fit molecule AF-brxB.pdb (#4) to map cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2) using 1669 atoms average map value = 0.1168, steps = 28 shifted from previous position = 0.0193 rotated from previous position = 0.00917 degrees atoms outside contour = 868, contour level = 0.12197 Position of AF-brxB.pdb (#4) relative to cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2) coordinates: Matrix rotation and translation 0.99427095 0.09184760 -0.05467439 -2.95232204 -0.09865794 0.98540116 -0.13874859 37.66272739 0.04113249 0.14334776 0.98881724 -22.86844927 Axis 0.79773048 -0.27092896 -0.53872403 Axis point 0.00000000 180.09177056 252.02967958 Rotation angle (degrees) 10.18411182 Shift along axis -0.23929770 > fitmap #4 inMap #2 Fit molecule AF-brxB.pdb (#4) to map cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2) using 1669 atoms average map value = 0.1168, steps = 40 shifted from previous position = 0.00407 rotated from previous position = 0.0123 degrees atoms outside contour = 868, contour level = 0.12197 Position of AF-brxB.pdb (#4) relative to cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2) coordinates: Matrix rotation and translation 0.99426586 0.09178151 -0.05487762 -2.91335159 -0.09862102 0.98540695 -0.13873367 37.65380769 0.04134361 0.14335024 0.98880808 -22.89851145 Axis 0.79758908 -0.27206444 -0.53836102 Axis point 0.00000000 180.31302577 251.97290682 Rotation angle (degrees) 10.18548275 Shift along axis -0.24025353 > show #1 models > hide #1 models > select subtract #4 Nothing selected > ui mousemode right zoom > show #1 models > ui tool show Matchmaker > matchmaker #4/B to #1/B pairing ss Computing secondary structure Parameters --- Chain pairing | ss 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_2025_02_06_16_38_model_0.cif, chain B (#1) with AF-brxB.pdb, chain B (#4), sequence alignment score = 1092.9 RMSD between 206 pruned atom pairs is 0.000 angstroms; (across all 206 pairs: 0.000) > undo > show #1 models > open ""/Volumes/data-4T/Projects/校外合作/SunLitao/5-BCZ-complex/C550BZ complex > 结构预测/AF-BrxZ.pdb"" Summary of feedback from opening /Volumes/data-4T/Projects/校外合作/SunLitao/5-BCZ-complex/C550BZ complex 结构预测/AF- BrxZ.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 ILE A 17 ILE A 20 1 4 Start residue of secondary structure not found: HELIX 2 2 ASP A 40 GLU A 49 1 10 Start residue of secondary structure not found: HELIX 3 3 ARG A 54 THR A 71 1 18 Start residue of secondary structure not found: HELIX 4 4 ARG A 75 MET A 78 1 4 Start residue of secondary structure not found: HELIX 5 5 LYS A 94 LEU A 105 1 12 51 messages similar to the above omitted Chain information for AF-BrxZ.pdb #5 --- Chain | Description C | No description available > hide #4 models > hide #3 models > hide #!2 models > hide #1 models > show #!2 models > show #3 models > show #4 models > hide #5 models > show #5 models > select #5/C:8 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 118 atoms, 119 bonds, 15 residues, 1 model selected > select up 7133 atoms, 7292 bonds, 871 residues, 1 model selected > volume #2 level 0.06315 > volume #2 level 0.07593 > fitmap #5 inMap #2 Fit molecule AF-BrxZ.pdb (#5) to map cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2) using 7133 atoms average map value = 0.04619, steps = 484 shifted from previous position = 37.8 rotated from previous position = 19 degrees atoms outside contour = 5410, contour level = 0.075935 Position of AF-BrxZ.pdb (#5) relative to cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2) coordinates: Matrix rotation and translation 0.98166123 -0.05374970 -0.18289943 69.15628069 0.10063652 0.96096034 0.25773534 -49.75606256 0.16190591 -0.27141516 0.94874669 35.23366351 Axis -0.81385997 -0.53032788 0.23745374 Axis point 0.00000000 100.94248704 252.64231618 Rotation angle (degrees) 18.97084245 Shift along axis -21.53013615 > hide #5 models > hide #4 models > show #4 models Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 2 atomic models, 1 maps. ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/Li/Downloads/cryosparc_P22_J202_008_volume_map.mrc Opened cryosparc_P22_J202_008_volume_map.mrc as #1, grid size 360,360,360, pixel 0.86, shown at level 0.00785, step 2, values float32 OpenGL version: 4.1 Metal - 89.3 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: MacBookAir10,1 Model Number: Z1250003LCH/A Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 11881.81.2 OS Loader Version: 11881.81.2 Software: System Software Overview: System Version: macOS 15.3 (24D60) Kernel Version: Darwin 24.3.0 Time since boot: 31 days, 5 hours, 18 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 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: 2.3 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: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 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: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 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: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 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-MutationScores: 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: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 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: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 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: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 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: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 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: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 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: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Window Toolkit can't reproduce Tom Goddard all ChimeraX