id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16339 Crash on Mac waking from sleep ccaffalett@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-12.7.6-x86_64-i386-64bit 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 0x000000011ce8e600 (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, 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, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lxml._elementpath, lxml.etree (total: 61) {""app_name"":""ChimeraX"",""timestamp"":""2024-11-19 16:54:00.00 -0500"",""app_version"":""1.8.0"",""slice_uuid"":""194a3167-3db5-3029-8d22-1d742b826bb9"",""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 12.7.6 (21H1320)"",""incident_id"":""20D711A4-60D8-4A22-AD1E-C85CA9A29F9D"",""name"":""ChimeraX""} { ""uptime"" : 640000, ""procLaunch"" : ""2024-11-19 16:00:41.4534 -0500"", ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro16,1"", ""procStartAbsTime"" : 637899576058883, ""coalitionID"" : 67514, ""osVersion"" : { ""train"" : ""macOS 12.7.6"", ""build"" : ""21H1320"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2024-11-19 16:53:55.5275 -0500"", ""incident"" : ""20D711A4-60D8-4A22-AD1E-C85CA9A29F9D"", ""bug_type"" : ""309"", ""pid"" : 5553, ""procExitAbsTime"" : 641093558561858, ""cpuType"" : ""X86-64"", ""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"":""50CBB6BD-7B68-58C9-8508-A9CF1854A0EE"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""61E580C7-5D45-4263-2295-2F14C708A704"", ""wakeTime"" : 93865, ""bridgeVersion"" : {""build"":""21P6074"",""train"":""8.6""}, ""sleepWakeUUID"" : ""A4CAA0E8-79F7-4115-9E5A-08C37BAA8813"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x119b6f569138 is not in any region. 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""\/usr\/lib\/system\/libsystem_malloc.dylib"", ""name"" : ""libsystem_malloc.dylib"" } ], ""sharedCache"" : { ""base"" : 140703392215040, ""size"" : 19331678208, ""uuid"" : ""246818c3-4b9f-3462-bcaf-fdf71975e5fe"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=34.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=34.3G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 1280K 10 \nActivity Tracing 256K 1 \nCG backing stores 2688K 4 \nCG image 684K 55 \nColorSync 232K 28 \nCoreAnimation 3036K 127 \nCoreGraphics 12K 2 \nCoreServices 220K 1 \nCoreUI image data 5184K 37 \nFoundation 36K 2 \nIOKit 15.5M 2 \nKernel Alloc Once 8K 1 \nMALLOC 32.0G 799 \nMALLOC guard page 48K 11 \nMALLOC_LARGE (reserved) 128.0M 1 reserved VM address space (unallocated)\nMALLOC_MEDIUM (reserved) 1.4G 15 reserved VM address space 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""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open pdb:7N9F Summary of feedback from opening 7N9F fetched from pdb --- note | Fetching compressed mmCIF 7n9f from http://files.rcsb.org/download/7n9f.cif 7n9f title: Structure of the in situ yeast NPC [more info...] Chain information for 7n9f #1 --- Chain | Description | UniProt 0 Y | Nucleoporin NUP170 | NU170_YEAST 1-1502 1 Z | Nucleoporin NUP157 | NU157_YEAST 1-1391 5 6 | orphans bound to Nup192 NTD | A D G J y z | Nucleoporin NSP1 | NSP1_YEAST 1-823 B E H K | Nucleoporin NUP57 | NUP57_YEAST 1-541 C F I L | Nucleoporin NUP49/NSP49 | NUP49_YEAST 1-472 M O | Nucleoporin NUP192 | NU192_YEAST 1-1683 N P | Nucleoporin NUP188 | NU188_YEAST 1-1655 Q R S T | Nucleoporin NIC96 | NIC96_YEAST 1-839 U W | Nucleoporin NUP53 | NUP53_YEAST 1-475 V X | Nucleoporin ASM4 | NUP59_YEAST 1-528 a h | Nucleoporin NUP120 | NU120_YEAST 1-1037 b i | Nucleoporin NUP85 | NUP85_YEAST 1-744 c j | Nucleoporin 145c | NU145_YEAST 0-797 d k | Protein transport protein SEC13 | SEC13_YEAST 1-297 e l | Nucleoporin SEH1 | SEH1_YEAST 1-349 f m | Nucleoporin NUP84 | NUP84_YEAST 1-726 g n | Nucleoporin NUP133 | NU133_YEAST 1-1157 o p q r s t | Dynein light chain 1, cytoplasmic | DYL1_YEAST 1-92 u v | Nucleoporin NUP82 | NUP82_YEAST 1-713 w x | Nucleoporin NUP159 | NU159_YEAST 1-1460 7n9f mmCIF Assemblies --- 1| complete point assembly 2| point asymmetric unit 3| point asymmetric unit, std point frame > open /Users/chris/Library/CloudStorage/OneDrive- > rockefeller.edu/Brickner_JH/2024_0318_Crm1-ppx- > GFP_Heat_Map/Crm1_Heat_Map_Figure/Version_3/EMDB/emd_44377.map Opened emd_44377.map as #2, grid size 224,224,224, pixel 10, shown at level 602, step 1, values float32 > ui tool show ""Side View"" > volume #2 level 554.8 > volume #2 level 534 > open /Users/chris/Library/CloudStorage/OneDrive- > rockefeller.edu/Brickner_JH/2024_0318_Crm1-ppx- > GFP_Heat_Map/Crm1_Heat_Map_Figure/Version_3/2024_1115_ChimeraX_Session_to_determine_a_plan.cxs > surface cap true Opened emd_24258.map as #2, grid size 320,320,320, pixel 6.74, shown at level 2.25e+03, step 1, values float32 Opened emd_44377.map as #3, grid size 224,224,224, pixel 10, shown at level 556, step 1, values float32 > surface cap false opened ChimeraX session > select add #4 1703696 atoms, 1734208 bonds, 2080 pseudobonds, 216568 residues, 2 models selected > select subtract #4 Nothing selected > select add #4 1703696 atoms, 1734208 bonds, 2080 pseudobonds, 216568 residues, 2 models selected > open pdb:8tie 8tie title: Double nuclear outer ring of Nup84-complexes from the yeast NPC [more info...] Chain information for 8tie #1 --- Chain | Description | UniProt a l | Nucleoporin NUP120 | NU120_YEAST 1-1037 b m | Nucleoporin NUP85 | NUP85_YEAST 1-744 c n | NUP145 isoform 1 | A0A8H4C085_YEASX -605-711 d o | Protein transport protein SEC13 | SEC13_YEAST 1-297 e p | Nucleoporin Seh1 | f q | Nucleoporin NUP84 | NUP84_YEAST 1-726 g r | NUP133 isoform 1 | A0A6V8RYD2_YEASX 1-1157 > select add #1 1780317 atoms, 1812453 bonds, 2084 pseudobonds, 226047 residues, 4 models selected > select subtract #4 76621 atoms, 78245 bonds, 4 pseudobonds, 9479 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #1,1,0,0,-1064.2,0,1,0,-708.55,0,0,1,-83.832 > view matrix models > #1,0.97542,0.0049896,0.2203,-1221.2,-0.080623,-0.92234,0.37787,418.73,0.20508,-0.38634,-0.89927,1517.8 > view matrix models > #1,0.75624,-0.50525,0.41572,-783.85,-0.62498,-0.74585,0.23044,1010,0.19364,-0.43408,-0.87982,1547.8 > view matrix models > #1,0.74417,-0.51523,0.42514,-771.38,-0.60474,-0.78997,0.10118,1124.6,0.28372,-0.33239,-0.89945,1394.2 > view matrix models > #1,0.74417,-0.51523,0.42514,-604.67,-0.60474,-0.78997,0.10118,1034.4,0.28372,-0.33239,-0.89945,451.85 > view matrix models > #1,0.74417,-0.51523,0.42514,-630.3,-0.60474,-0.78997,0.10118,1058,0.28372,-0.33239,-0.89945,456.09 > view matrix models > #1,0.74417,-0.51523,0.42514,-612.4,-0.60474,-0.78997,0.10118,1062.6,0.28372,-0.33239,-0.89945,455.92 > view matrix models > #1,0.74417,-0.51523,0.42514,-475.63,-0.60474,-0.78997,0.10118,753.88,0.28372,-0.33239,-0.89945,456.16 > view matrix models > #1,0.80292,-0.57464,0.15844,-279.81,-0.58923,-0.80534,0.065148,777.21,0.090162,-0.14567,-0.98522,606.72 > view matrix models > #1,0.62119,-0.76659,0.16265,49.835,-0.78094,-0.62282,0.0471,873.29,0.065195,-0.15628,-0.98556,641.7 > view matrix models > #1,0.62119,-0.76659,0.16265,42.361,-0.78094,-0.62282,0.0471,870.61,0.065195,-0.15628,-0.98556,640.89 > view matrix models > #1,0.61546,-0.77233,0.15722,57.084,-0.77997,-0.62552,-0.019516,925.96,0.11342,-0.11062,-0.98737,557.68 > view matrix models > #1,0.61617,-0.7794,0.11348,97.069,-0.77246,-0.62613,-0.10609,989.06,0.15375,-0.022291,-0.98786,452.09 > view matrix models > #1,0.68045,-0.72185,0.12616,-23.866,-0.71462,-0.69177,-0.10375,970.04,0.16217,-0.019557,-0.98657,439.92 > view matrix models > #1,0.70218,-0.70758,0.079176,-19.156,-0.71198,-0.69715,0.084006,817.25,-0.0042435,-0.11536,-0.99331,694.35 > view matrix models > #1,0.70218,-0.70758,0.079176,-12.898,-0.71198,-0.69715,0.084006,821.71,-0.0042435,-0.11536,-0.99331,695.13 > ui tool show ""Fit in Map"" > fitmap #1 inMap #3 Fit molecule 8tie (#1) to map emd_44377.map (#3) using 76621 atoms average map value = 561.1, steps = 76 shifted from previous position = 17.5 rotated from previous position = 9.23 degrees atoms outside contour = 31152, contour level = 556.13 Position of 8tie (#1) relative to emd_44377.map (#3) coordinates: Matrix rotation and translation 0.73322863 -0.67628301 -0.07083110 1175.40549284 -0.66782038 -0.73580988 0.11224856 1879.70676416 -0.12803001 -0.03500141 -0.99115246 1909.31002321 Axis -0.93080882 0.36157055 0.05349465 Axis point 0.00000000 1209.12640343 946.03248590 Rotation angle (degrees) 175.46328733 Shift along axis -312.29331154 > hide #!1 models > show #!2 models > hide #!3 models > volume #2 level 1988 > volume #2 level 1981 > show #!1 models > hide #!2 models > show #!3 models > color zone #3 near sel & #1 distance 60 > surface cap true > surface cap true color black Expected a keyword > surface cap color black Expected true or false or a keyword > ui tool show ""Surface Color"" > color radial #3.1.1 palette #ff0000:#ffffff:#0000ff > select add #3.1.1 76621 atoms, 78245 bonds, 4 pseudobonds, 9479 residues, 3 models selected > select subtract #3.1.1 76621 atoms, 78245 bonds, 4 pseudobonds, 9479 residues, 2 models selected > select add #3.1 76621 atoms, 78245 bonds, 4 pseudobonds, 9479 residues, 4 models selected > select subtract #3.1 76621 atoms, 78245 bonds, 4 pseudobonds, 9479 residues, 2 models selected > color #3.1.1 black > view matrix models > #1,0.73685,-0.67227,-0.071412,66.927,-0.66383,-0.73948,0.11178,854.87,-0.12796,-0.034962,-0.99116,560.47 > view matrix models > #1,0.73685,-0.67227,-0.071412,70.299,-0.66383,-0.73948,0.11178,864.49,-0.12796,-0.034962,-0.99116,475.83 > view matrix models > #1,0.73685,-0.67227,-0.071412,70.055,-0.66383,-0.73948,0.11178,860.1,-0.12796,-0.034962,-0.99116,490.09 > hide #!3 models > hide #3.1 models > hide #!4 models > show #!3 models > hide #!1 models > select subtract #1 Nothing selected > show #3.1 models > hide #!3 models > show #!3 models > color #3.1.1 black > hide #!3 models > show #!3 models > hide #!3.1 models > show #3.1 models > close session > open /Users/chris/Library/CloudStorage/OneDrive- > rockefeller.edu/Brickner_JH/2024_0318_Crm1-ppx- > GFP_Heat_Map/Crm1_Heat_Map_Figure/Version_3/EMDB/emd_44377.map format ccp4 Opened emd_44377.map as #1, grid size 224,224,224, pixel 10, shown at level 602, step 1, values float32 > ui mousemode right ""map eraser"" > volume erase #1 center 1514.4,1228.8,362.34 radius 226.97 Opened emd_44377.map copy as #3, grid size 224,224,224, pixel 10, shown at step 1, values float32 > volume erase #3 center 1534.5,1291.9,545.55 radius 226.24 > volume copy #3 subregion 130,106,31,177,153,78 Opened emd_44377.map copy as #4, grid size 48,48,48, pixel 10, shown at step 1, values float32 > close session > open /Users/chris/Library/CloudStorage/OneDrive- > rockefeller.edu/Brickner_JH/2024_0318_Crm1-ppx- > GFP_Heat_Map/Crm1_Heat_Map_Figure/Version_3/EMDB/emd_44377.map format ccp4 Opened emd_44377.map as #1, grid size 224,224,224, pixel 10, shown at level 602, step 1, values float32 > volume #1 level 540.4 > ui mousemode right ""map eraser"" > volume erase #1 center 1589.9,468.34,1013.5 radius 549.55 Opened emd_44377.map copy as #3, grid size 224,224,224, pixel 10, shown at step 1, values float32 > volume erase #3 center 989.98,550.2,933.02 radius 548.8 > volume erase #3 center 680.19,716.28,1018.8 radius 548.8 > volume erase #3 center 710.86,642.99,1406.6 radius 548.8 > volume erase #3 center 1143,492.49,1462.9 radius 548.8 > volume erase #3 center 1036.5,681.56,389.54 radius 548.8 > volume erase #3 center 799.64,670.44,449.72 radius 548.8 > volume erase #3 center 1165.8,955.81,170.69 radius 599.2 > color #3.1.1 black > surface cap true > color #3.1.1 black > color #3.1.1 white > volume erase #3 center 1801,765.51,1081.1 radius 599.2 > hide #!3 models > show #!1 models > hide #3.1 models > open /Users/chris/Library/CloudStorage/OneDrive- > rockefeller.edu/Brickner_JH/2024_0318_Crm1-ppx- > GFP_Heat_Map/Crm1_Heat_Map_Figure/Version_3/EMDB/8tie-assembly1.cif 8tie-assembly1.cif title: Double nuclear outer ring of Nup84-complexes from the yeast NPC [more info...] Chain information for 8tie-assembly1.cif #4 --- Chain | Description a l | Nucleoporin NUP120 b m | Nucleoporin NUP85 c n | NUP145 isoform 1 d o | Protein transport protein SEC13 e p | Nucleoporin Seh1 f q | Nucleoporin NUP84 g r | NUP133 isoform 1 > open pdb:7n9f 7n9f title: Structure of the in situ yeast NPC [more info...] Chain information for 7n9f #5 --- Chain | Description | UniProt 0 Y | Nucleoporin NUP170 | NU170_YEAST 1-1502 1 Z | Nucleoporin NUP157 | NU157_YEAST 1-1391 5 6 | orphans bound to Nup192 NTD | A D G J y z | Nucleoporin NSP1 | NSP1_YEAST 1-823 B E H K | Nucleoporin NUP57 | NUP57_YEAST 1-541 C F I L | Nucleoporin NUP49/NSP49 | NUP49_YEAST 1-472 M O | Nucleoporin NUP192 | NU192_YEAST 1-1683 N P | Nucleoporin NUP188 | NU188_YEAST 1-1655 Q R S T | Nucleoporin NIC96 | NIC96_YEAST 1-839 U W | Nucleoporin NUP53 | NUP53_YEAST 1-475 V X | Nucleoporin ASM4 | NUP59_YEAST 1-528 a h | Nucleoporin NUP120 | NU120_YEAST 1-1037 b i | Nucleoporin NUP85 | NUP85_YEAST 1-744 c j | Nucleoporin 145c | NU145_YEAST 0-797 d k | Protein transport protein SEC13 | SEC13_YEAST 1-297 e l | Nucleoporin SEH1 | SEH1_YEAST 1-349 f m | Nucleoporin NUP84 | NUP84_YEAST 1-726 g n | Nucleoporin NUP133 | NU133_YEAST 1-1157 o p q r s t | Dynein light chain 1, cytoplasmic | DYL1_YEAST 1-92 u v | Nucleoporin NUP82 | NUP82_YEAST 1-713 w x | Nucleoporin NUP159 | NU159_YEAST 1-1460 7n9f mmCIF Assemblies --- 1| complete point assembly 2| point asymmetric unit 3| point asymmetric unit, std point frame > select #5:0 Nothing selected > select #5/0 8762 atoms, 8935 bonds, 16 pseudobonds, 1085 residues, 2 models selected > select #5/0,l 11200 atoms, 11434 bonds, 17 pseudobonds, 1392 residues, 2 models selected > hide #!1 models > select ~sel & ##selected 201762 atoms, 205342 bonds, 243 pseudobonds, 25679 residues, 2 models selected > select #5:0,Y Nothing selected > select #5:0,Y Nothing selected > select #5:0 Nothing selected > select #5/0 8762 atoms, 8935 bonds, 16 pseudobonds, 1085 residues, 2 models selected > select #5/0,Y 17532 atoms, 17878 bonds, 32 pseudobonds, 2171 residues, 2 models selected > select #5/0, Expected an objects specifier or a keyword > select #5/0 8762 atoms, 8935 bonds, 16 pseudobonds, 1085 residues, 2 models selected > open /Users/chris/Library/CloudStorage/OneDrive- > rockefeller.edu/Brickner_JH/2024_0318_Crm1-ppx- > GFP_Heat_Map/Crm1_Heat_Map_Figure/Version_3/EMDB/7n9f-assembly1.cif 7n9f-assembly1.cif title: Structure of the in situ yeast NPC [more info...] Chain information for 7n9f-assembly1.cif #6 --- Chain | Description 0 0-2 0-3 0-4 0-5 0-6 0-7 0-8 Y Y-2 Y-3 Y-4 Y-5 Y-6 Y-7 Y-8 | Nucleoporin NUP170 1 1-2 1-3 1-4 1-5 1-6 1-7 1-8 Z Z-2 Z-3 Z-4 Z-5 Z-6 Z-7 Z-8 | Nucleoporin NUP157 5 5-2 5-3 5-4 5-5 5-6 5-7 5-8 6 6-2 6-3 6-4 6-5 6-6 6-7 6-8 | orphans bound to Nup192 NTD A A-2 A-3 A-4 A-5 A-6 A-7 A-8 D D-2 D-3 D-4 D-5 D-6 D-7 D-8 G G-2 G-3 G-4 G-5 G-6 G-7 G-8 J J-2 J-3 J-4 J-5 J-6 J-7 J-8 y y-2 y-3 y-4 y-5 y-6 y-7 y-8 z z-2 z-3 z-4 z-5 z-6 z-7 z-8 | Nucleoporin NSP1 B B-2 B-3 B-4 B-5 B-6 B-7 B-8 E E-2 E-3 E-4 E-5 E-6 E-7 E-8 H H-2 H-3 H-4 H-5 H-6 H-7 H-8 K K-2 K-3 K-4 K-5 K-6 K-7 K-8 | Nucleoporin NUP57 C C-2 C-3 C-4 C-5 C-6 C-7 C-8 F F-2 F-3 F-4 F-5 F-6 F-7 F-8 I I-2 I-3 I-4 I-5 I-6 I-7 I-8 L L-2 L-3 L-4 L-5 L-6 L-7 L-8 | Nucleoporin NUP49/NSP49 M M-2 M-3 M-4 M-5 M-6 M-7 M-8 O O-2 O-3 O-4 O-5 O-6 O-7 O-8 | Nucleoporin NUP192 N N-2 N-3 N-4 N-5 N-6 N-7 N-8 P P-2 P-3 P-4 P-5 P-6 P-7 P-8 | Nucleoporin NUP188 Q Q-2 Q-3 Q-4 Q-5 Q-6 Q-7 Q-8 R R-2 R-3 R-4 R-5 R-6 R-7 R-8 S S-2 S-3 S-4 S-5 S-6 S-7 S-8 T T-2 T-3 T-4 T-5 T-6 T-7 T-8 | Nucleoporin NIC96 U U-2 U-3 U-4 U-5 U-6 U-7 U-8 W W-2 W-3 W-4 W-5 W-6 W-7 W-8 | Nucleoporin NUP53 V V-2 V-3 V-4 V-5 V-6 V-7 V-8 X X-2 X-3 X-4 X-5 X-6 X-7 X-8 | Nucleoporin ASM4 a a-2 a-3 a-4 a-5 a-6 a-7 a-8 h h-2 h-3 h-4 h-5 h-6 h-7 h-8 | Nucleoporin NUP120 b b-2 b-3 b-4 b-5 b-6 b-7 b-8 i i-2 i-3 i-4 i-5 i-6 i-7 i-8 | Nucleoporin NUP85 c c-2 c-3 c-4 c-5 c-6 c-7 c-8 j j-2 j-3 j-4 j-5 j-6 j-7 j-8 | Nucleoporin 145c d d-2 d-3 d-4 d-5 d-6 d-7 d-8 k k-2 k-3 k-4 k-5 k-6 k-7 k-8 | Protein transport protein SEC13 e e-2 e-3 e-4 e-5 e-6 e-7 e-8 l l-2 l-3 l-4 l-5 l-6 l-7 l-8 | Nucleoporin SEH1 f f-2 f-3 f-4 f-5 f-6 f-7 f-8 m m-2 m-3 m-4 m-5 m-6 m-7 m-8 | Nucleoporin NUP84 g g-2 g-3 g-4 g-5 g-6 g-7 g-8 n n-2 n-3 n-4 n-5 n-6 n-7 n-8 | Nucleoporin NUP133 o o-2 o-3 o-4 o-5 o-6 o-7 o-8 p p-2 p-3 p-4 p-5 p-6 p-7 p-8 q q-2 q-3 q-4 q-5 q-6 q-7 q-8 r r-2 r-3 r-4 r-5 r-6 r-7 r-8 s s-2 s-3 s-4 s-5 s-6 s-7 s-8 t t-2 t-3 t-4 t-5 t-6 t-7 t-8 | Dynein light chain 1, cytoplasmic u u-2 u-3 u-4 u-5 u-6 u-7 u-8 v v-2 v-3 v-4 v-5 v-6 v-7 v-8 | Nucleoporin NUP82 w w-2 w-3 w-4 w-5 w-6 w-7 w-8 x x-2 x-3 x-4 x-5 x-6 x-7 x-8 | Nucleoporin NUP159 > log metadata #6 Metadata for 7n9f-assembly1.cif #6 --- Title | Structure of the in situ yeast NPC Citation | Akey, C.W., Singh, D., Ouch, C., Echeverria, I., Nudelman, I., Varberg, J.M., Yu, Z., Fang, F., Shi, Y., Wang, J., Salzberg, D., Song, K., Xu, C., Gumbart, J.C., Suslov, S., Unruh, J., Jaspersen, S.L., Chait, B.T., Sali, A., Fernandez-Martinez, J., Ludtke, S.J., Villa, E., Rout, M.P. (2022). Comprehensive structure and functional adaptations of the yeast nuclear pore complex. Cell, 185, 361-378.e25. PMID: 34982960. DOI: 10.1016/j.cell.2021.12.015 Experimental method | Electron microscopy > select clear ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 ATI-4.8.101 OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine OpenGL vendor: ATI Technologies Inc. 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: MacBookPro16,1 Processor Name: 8-Core Intel Core i9 Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 32 GB System Firmware Version: 2022.140.5.0.0 (iBridge: 21.16.6074.0.0,0) OS Loader Version: 540.120.3~37 Software: System Software Overview: System Version: macOS 12.7.6 (21H1320) Kernel Version: Darwin 21.6.0 Time since boot: 25 days 18:52 Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0002 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Family: Supported, Metal GPUFamily macOS 2 AMD Radeon Pro 5500M: Chipset Model: AMD Radeon Pro 5500M Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 8 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0040 ROM Revision: 113-D3220E-190 VBIOS Version: 113-D32206U1-019 Option ROM Version: 113-D32206U1-019 EFI Driver Version: 01.A1.190 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 3072 x 1920 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal 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