id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15853 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-13.6-x86_64-i386-64bit ChimeraX Version: 1.8rc202405312319 (2024-05-31 23:19:45 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 0x00007ff855d9c700 (most recent call first): File ""/Applications/ChimeraX-1.8-rc2024.05.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 307 in event_loop File ""/Applications/ChimeraX-1.8-rc2024.05.31.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-rc2024.05.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, psutil._psutil_osx, psutil._psutil_posix, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, PIL._webp (total: 62) {""app_name"":""ChimeraX"",""timestamp"":""2024-08-30 16:32:36.00 +0200"",""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 13.6 (22G120)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""50D1148B-45E9-4FEA-BCB3-C98E4FEB163D""} { ""uptime"" : 820000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 503, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro15,1"", ""coalitionID"" : 239253, ""osVersion"" : { ""train"" : ""macOS 13.6"", ""build"" : ""22G120"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2024-08-30 16:32:33.8544 +0200"", ""incident"" : ""50D1148B-45E9-4FEA-BCB3-C98E4FEB163D"", ""pid"" : 91541, ""cpuType"" : ""X86-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2024-08-30 11:51:34.8715 +0200"", ""procStartAbsTime"" : 818366004935414, ""procExitAbsTime"" : 825751541130904, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.8-rc2024.05.31.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.8.0"",""CFBundleVersion"":""1.8.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""3DB4FC6A-27E9-56B8-95F0-FC21B148075B"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""407E303B-BF04-4FEE-B7F6-8A8451CA77F1"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 0, ""wakeTime"" : 1821, ""bridgeVersion"" : {""build"":""21P365"",""train"":""8.0""}, ""sleepWakeUUID"" : ""D551DAD9-A913-4929-B4DB-EE7884068F42"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0 is not in any region. 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UCSF ChimeraX version: 1.8rc202405312319 (2024-05-31) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/rosspopoff/Dropbox/Trono_Lab/37-FindingDUF3669/9-PTPSP_data/cryosparc/2024.05.29_Modelpaper.cxs > format session Opened cryosparc_P110_J215_002_volume_mask_refine.mrc as #1, grid size 440,440,440, pixel 0.926, shown at level 5e-05, step 1, values float32 Opened Cryo_Rod_volume_map as #4, grid size 440,440,440, pixel 0.926, shown at level 0.0395, step 2, values float32 Opened Cryo_Coiled_coil as #5, grid size 256,256,256, pixel 1.59, shown at level 0.263, step 1, values float32 Opened Cryo_Coiled_coil x flip as #6, grid size 256,256,256, pixel 1.59, shown at level 0.259, step 1, values float32 Opened Cryo_Rod_Aligned_AF3#8_Volume as #7, grid size 440,440,440, pixel 0.926, shown at level 0.041, step 1, values float32 Opened Cryo_Rod_Aligned_Xflip_AF3#10_Volume as #9, grid size 440,440,440, pixel 0.926, shown at level 0.0388, step 1, values float32 opened ChimeraX session > combine #3 > select add #11 9444 atoms, 9660 bonds, 1194 residues, 2 models selected > select subtract #10 4722 atoms, 4830 bonds, 597 residues, 1 model selected > show sel cartoons > ui mousemode right ""translate selected models"" > view matrix models > #11,-0.71372,-0.60391,0.3548,187.12,-0.68351,0.71118,-0.16445,331.03,-0.15302,-0.35988,-0.92037,145.56 > view matrix models > #11,-0.71372,-0.60391,0.3548,208.37,-0.68351,0.71118,-0.16445,337.08,-0.15302,-0.35988,-0.92037,36.383 > ui mousemode right select > select subtract #11 Nothing selected Drag select of 22 residues > delete atoms sel > delete bonds sel Drag select of 2 residues Drag select of 24 residues > delete atoms sel > delete bonds sel Drag select of 22 residues > delete atoms sel > delete bonds sel > select add #11 4240 atoms, 4332 bonds, 529 residues, 1 model selected > ui mousemode right select > ui mousemode right ""translate selected models"" > view matrix models > #11,-0.71372,-0.60391,0.3548,408.05,-0.68351,0.71118,-0.16445,367.04,-0.15302,-0.35988,-0.92037,206.32 > ui mousemode right select > select clear Drag select of 5 residues > select add #11 4240 atoms, 4332 bonds, 529 residues, 1 model selected > select subtract #11 Nothing selected > close #3 > close session > open > /Users/rosspopoff/Dropbox/Trono_Lab/37-FindingDUF3669/9-PTPSP_data/cryosparc/2024.05.29_Modelpaper.cxs > format session Opened cryosparc_P110_J215_002_volume_mask_refine.mrc as #1, grid size 440,440,440, pixel 0.926, shown at level 5e-05, step 1, values float32 Opened Cryo_Rod_volume_map as #4, grid size 440,440,440, pixel 0.926, shown at level 0.0395, step 2, values float32 Opened Cryo_Coiled_coil as #5, grid size 256,256,256, pixel 1.59, shown at level 0.263, step 1, values float32 Opened Cryo_Coiled_coil x flip as #6, grid size 256,256,256, pixel 1.59, shown at level 0.259, step 1, values float32 Opened Cryo_Rod_Aligned_AF3#8_Volume as #7, grid size 440,440,440, pixel 0.926, shown at level 0.041, step 1, values float32 Opened Cryo_Rod_Aligned_Xflip_AF3#10_Volume as #9, grid size 440,440,440, pixel 0.926, shown at level 0.0388, step 1, values float32 opened ChimeraX session > combine #8 > select add #11 9444 atoms, 9660 bonds, 1194 residues, 2 models selected > select subtract #10 4722 atoms, 4830 bonds, 597 residues, 1 model selected > select up 23610 atoms, 24150 bonds, 2985 residues, 17 models selected > select up 23610 atoms, 24150 bonds, 2985 residues, 24 models selected > close #11 > open > /Users/rosspopoff/Dropbox/Trono_Lab/37-FindingDUF3669/9-PTPSP_data/OR1_a26ff_Alphafold/OR1_a26ff_scores_rank_004_alphafold2_multimer_v3_model_1_seed_000.json Traceback (most recent call last): File ""/Applications/ChimeraX-1.8-rc2024.05.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/open_command/dialog.py"", line 334, in _qt_safe run(session, ""open "" + "" "".join([FileNameArg.unparse(p) for p in paths]) + ("""" File ""/Applications/ChimeraX-1.8-rc2024.05.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8-rc2024.05.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8-rc2024.05.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 131, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8-rc2024.05.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8-rc2024.05.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 213, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8-rc2024.05.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 513, in collated_open return remember_data_format() ^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8-rc2024.05.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 484, in remember_data_format models, status = func(*func_args, **func_kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8-rc2024.05.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/alphafold/__init__.py"", line 129, in open structs = [m for m in session.models.list(type = AtomicStructure) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8-rc2024.05.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/alphafold/__init__.py"", line 130, in if hasattr(m, 'filename') and dirname(m.filename) == dirname(path)] ^^^^^^^^^^^^^^^^^^^ File """", line 152, in dirname TypeError: expected str, bytes or os.PathLike object, not NoneType TypeError: expected str, bytes or os.PathLike object, not NoneType File """", line 152, in dirname See log for complete Python traceback. > open > /Users/rosspopoff/Dropbox/Trono_Lab/37-FindingDUF3669/9-PTPSP_data/OR1_a26ff_Alphafold/OR1_a26ff_unrelaxed_rank_004_alphafold2_multimer_v3_model_1_seed_000.pdb Chain information for OR1_a26ff_unrelaxed_rank_004_alphafold2_multimer_v3_model_1_seed_000.pdb #11 --- Chain | Description A B C | No description available > open > /Users/rosspopoff/Dropbox/Trono_Lab/37-FindingDUF3669/9-PTPSP_data/OR1_a26ff_Alphafold/OR1_a26ff_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb Chain information for OR1_a26ff_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #12 --- Chain | Description A B C | No description available > select subtract #1 18888 atoms, 19320 bonds, 2388 residues, 20 models selected > select subtract #2 14166 atoms, 14490 bonds, 1791 residues, 19 models selected > select subtract #3 9444 atoms, 9660 bonds, 1194 residues, 15 models selected > select subtract #4 9444 atoms, 9660 bonds, 1194 residues, 10 models selected > select subtract #5 9444 atoms, 9660 bonds, 1194 residues, 8 models selected > select subtract #6 9444 atoms, 9660 bonds, 1194 residues, 6 models selected > select subtract #7 9444 atoms, 9660 bonds, 1194 residues, 4 models selected > select subtract #8 4722 atoms, 4830 bonds, 597 residues, 3 models selected > select subtract #9 4722 atoms, 4830 bonds, 597 residues, 1 model selected > select subtract #10 Nothing selected > select add #11 4722 atoms, 4830 bonds, 597 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #11,1,0,0,-116.57,0,1,0,-44.183,0,0,1,-11.013 > select subtract #11 Nothing selected > select add #11 4722 atoms, 4830 bonds, 597 residues, 1 model selected > view matrix models #11,1,0,0,-107.99,0,1,0,-28.469,0,0,1,1.6822 > view matrix models > #11,0.73417,0.097041,-0.672,-104.44,0.51687,-0.72166,0.46048,-9.5469,-0.44027,-0.68541,-0.57998,21.823 > view matrix models > #11,0.6985,0.18244,-0.69196,-105.35,0.4822,-0.83447,0.26675,-6.763,-0.52876,-0.51998,-0.67085,20.429 > close #11 #12 > select add #9 2 models selected > select subtract #9 Nothing selected > select add #10 4722 atoms, 4830 bonds, 597 residues, 1 model selected > view matrix models > #10,0.020416,-0.03601,-0.99914,238.41,0.79209,0.61038,-0.0058134,222.74,0.61007,-0.79129,0.040985,-102.28 > show sel cartoons > ui mousemode right select Drag select of 20 residues > select clear Drag select of 21 residues > delete atoms sel > delete bonds sel Drag select of 12 residues > select clear Drag select of 34 residues > select clear Drag select of 21 residues > delete atoms sel > delete bonds sel > select clear Drag select of 18 residues > delete atoms sel > delete bonds sel Drag select of 4 residues > delete atoms sel > delete bonds sel > select add #10 4269 atoms, 4362 bonds, 533 residues, 1 model selected > show sel surfaces > hide sel surfaces > show sel surfaces > transparency (#!10 & sel) 80 > hide sel cartoons > color (#!10 & sel) light gray > show sel cartoons > hide sel surfaces > undo > show sel surfaces > rename #10 Model > select clear > ui mousemode right ""translate selected models"" > select add #10 4269 atoms, 4362 bonds, 533 residues, 1 model selected > view matrix models > #10,0.020416,-0.03601,-0.99914,268.51,0.79209,0.61038,-0.0058134,291.87,0.61007,-0.79129,0.040985,-71.204 > view matrix models > #10,0.020416,-0.03601,-0.99914,265.05,0.79209,0.61038,-0.0058134,284.55,0.61007,-0.79129,0.040985,-74.86 > view matrix models > #10,0.60627,-0.15861,-0.77928,265.75,0.77022,0.36108,0.52573,285.86,0.198,-0.91895,0.34107,-74.224 > view matrix models > #10,0.76801,-0.094854,-0.63338,268.08,0.63622,0.2264,0.73754,286.02,0.073436,-0.96941,0.23422,-75.984 > select subtract #10 3 models selected > select add #10 4269 atoms, 4362 bonds, 533 residues, 1 model selected > select subtract #10 3 models selected > select add #9 2 models selected > select subtract #9 Nothing selected > select add #3 4722 atoms, 4830 bonds, 597 residues, 1 model selected > select subtract #3 3 models selected > select add #3 4722 atoms, 4830 bonds, 597 residues, 1 model selected > select subtract #3 3 models selected > select add #2 4722 atoms, 4830 bonds, 597 residues, 1 model selected > view matrix models > #2,-0.09195,0.31094,-0.94597,151.18,0.7664,0.62862,0.13213,476.46,0.63575,-0.71285,-0.29611,13.95 > select add #10 8991 atoms, 9192 bonds, 1130 residues, 5 models selected > select subtract #2 4269 atoms, 4362 bonds, 533 residues, 7 models selected > view matrix models > #10,0.76801,-0.094854,-0.63338,371.52,0.63622,0.2264,0.73754,314.87,0.073436,-0.96941,0.23422,269.65 > view matrix models > #10,0.76801,-0.094854,-0.63338,368.7,0.63622,0.2264,0.73754,313.96,0.073436,-0.96941,0.23422,260.33 > select subtract #10 3 models selected > select add #3 4722 atoms, 4830 bonds, 597 residues, 1 model selected > select add #2 9444 atoms, 9660 bonds, 1194 residues, 5 models selected > select subtract #3 4722 atoms, 4830 bonds, 597 residues, 7 models selected > view matrix models > #2,-0.09195,0.31094,-0.94597,174.09,0.7664,0.62862,0.13213,331.4,0.63575,-0.71285,-0.29611,-100.79 > select add #10 8991 atoms, 9192 bonds, 1130 residues, 5 models selected > select subtract #2 4269 atoms, 4362 bonds, 533 residues, 7 models selected > view matrix models > #10,0.76801,-0.094854,-0.63338,210.55,0.63622,0.2264,0.73754,350.97,0.073436,-0.96941,0.23422,338.6 > view matrix models > #10,0.78403,-0.070115,-0.61675,211.02,0.60046,0.33748,0.72495,352.17,0.15731,-0.93872,0.30669,339.74 > view matrix models > #10,0.78403,-0.070115,-0.61675,208.97,0.60046,0.33748,0.72495,359.37,0.15731,-0.93872,0.30669,329.86 > view matrix models > #10,0.78299,-0.071937,-0.61787,208.93,0.60293,0.33206,0.7254,359.31,0.15298,-0.94051,0.30337,329.8 > view matrix models > #10,0.79137,-0.05649,-0.60872,209.21,0.5815,0.3768,0.72103,359.79,0.18863,-0.92457,0.33104,330.29 > view matrix models > #10,0.79137,-0.05649,-0.60872,210.54,0.5815,0.3768,0.72103,361.29,0.18863,-0.92457,0.33104,333.04 > hide #8 models > hide #!9 models > hide #7.1 models > hide #!7 models > hide #6.1 models > hide #!6 models > hide #!4 models > show #!4 models > hide #!2 models > view matrix models > #10,0.79137,-0.05649,-0.60872,210.68,0.5815,0.3768,0.72103,356.1,0.18863,-0.92457,0.33104,328.4 > view matrix models > #10,0.53504,0.047901,-0.84347,205.71,0.71625,0.50373,0.48295,355,0.44801,-0.86253,0.23521,330.01 > view matrix models > #10,0.49775,0.11104,-0.86018,206.32,0.78904,0.35378,0.50225,353.39,0.36009,-0.92871,0.088484,327.83 > view matrix models > #10,-0.17025,0.23652,-0.95659,206.85,0.73205,0.6802,0.037899,353.32,0.65964,-0.69382,-0.28895,327.49 > view matrix models > #10,-0.070496,0.2364,-0.96909,206.97,0.76628,0.63482,0.099116,353.35,0.63863,-0.73561,-0.2259,327.45 > select subtract #10 3 models selected > hide #!10 models > combine #3 > close session > open > /Users/rosspopoff/Dropbox/Trono_Lab/37-FindingDUF3669/9-PTPSP_data/cryosparc/2024.05.28_Model_Yoan.cxs Opened cryosparc_P110_J215_002_volume_map.mrc as #2, grid size 440,440,440, pixel 0.926, shown at level 0.0687, step 2, values float32 Opened map_core.mrc as #10, grid size 256,256,256, pixel 1.59, shown at level 0.263, step 1, values float32 Opened cryosparc_P110_J215_002_volume_mask_refine.mrc as #1, grid size 440,440,440, pixel 0.926, shown at level 5e-05, step 1, values float32 opened ChimeraX session > show #!1 models > select add #2 2 models selected > select subtract #2 Nothing selected > rename #1 CryoEM_rod_mask > rename #2 CryoEM_rod_volume > hide #4 models > show #4 models > rename #4 A > rename #4 CryoEM_rod_AF3 > select add #9 4722 atoms, 4830 bonds, 597 residues, 1 model selected > select subtract #9 Nothing selected > rename #10 CryoEM_CC_volume > rename #10 id #5 > rename #9 CryoEM_CC_AF3 > rename #9 id #6 > combine CryoEM_rod_AF3 Expected a keyword > rename #4 id #3 > rename #5 id #4 > rename #6 id #5 > combine #3 > select add #6 4722 atoms, 4830 bonds, 597 residues, 1 model selected > view matrix models > #6,-0.44116,-0.57715,0.68722,107,-0.84317,0.52879,-0.097174,367.64,-0.30731,-0.62232,-0.71992,116.34 > view matrix models > #6,-0.44116,-0.57715,0.68722,107.75,-0.84317,0.52879,-0.097174,431.7,-0.30731,-0.62232,-0.71992,74.632 > ui mousemode right select > select clear Drag select of 24 residues > delete atoms sel > delete bonds sel Drag select of 17 residues > select clear Drag select of 16 residues > select clear Drag select of 21 residues > delete atoms sel > delete bonds sel Drag select of 24 residues > delete atoms sel > delete bonds sel > rename #6 AF3_surface > name DUF3669 #6:10-93 > name KRAB #6:109-184 > color #4 light gray > color DUF3669 medium purple > color KRAB steel blue > color #6 light gray > color DUF3669 medium purple > color KRAB steel blue > color DUF3669 #D8CEE6 > color DUF3669 #9167AC > color DUF3669 #D8CEE6 > color DUF3669 #74459B > color DUF3669 #9F82BC > color KRAB #A2ADBA > color KRAB #8898A9 > combine #6 > select add #7 4238 atoms, 4329 bonds, 528 residues, 1 model selected Drag select of 30 residues > undo > ui mousemode right ""translate selected models"" > view matrix models > #7,-0.44116,-0.57715,0.68722,163.03,-0.84317,0.52879,-0.097174,409.22,-0.30731,-0.62232,-0.71992,51.993 > select subtract #7 Nothing selected > color #7.1 #BFA1C3 > color #7.2 #9167AC > color #7.3 #64417F > split #7 Split copy of AF3_surface (#7) into 3 models Chain information for copy of AF3_surface A #7.1 --- Chain | Description A | No description available Chain information for copy of AF3_surface B #7.2 --- Chain | Description B | No description available Chain information for copy of AF3_surface C #7.3 --- Chain | Description C | No description available > split #6 Split AF3_surface (#6) into 3 models Chain information for AF3_surface A #6.1 --- Chain | Description A | No description available Chain information for AF3_surface B #6.2 --- Chain | Description B | No description available Chain information for AF3_surface C #6.3 --- Chain | Description C | No description available > select add #5 4722 atoms, 4830 bonds, 597 residues, 1 model selected > select subtract #5 Nothing selected > split #5 Split CryoEM_CC_AF3 (#5) into 3 models Chain information for CryoEM_CC_AF3 A #5.1 --- Chain | Description A | No description available Chain information for CryoEM_CC_AF3 B #5.2 --- Chain | Description B | No description available Chain information for CryoEM_CC_AF3 C #5.3 --- Chain | Description C | No description available > split #3 Split CryoEM_rod_AF3 (#3) into 3 models Chain information for CryoEM_rod_AF3 A #3.1 --- Chain | Description A | No description available Chain information for CryoEM_rod_AF3 B #3.2 --- Chain | Description B | No description available Chain information for CryoEM_rod_AF3 C #3.3 --- Chain | Description C | No description available > split #2 > rename #6 AF3_DK_surface > rename #7 AF3_TRIMER_surface > color #7.1 #BFA1C3 > color #7.2 #9167AC > color #7.3 #64417F > select add #7 4238 atoms, 4329 bonds, 528 residues, 4 models selected > view matrix models #7,1,0,0,-74.09,0,1,0,82.431,0,0,1,64.257 > show sel surfaces > hide sel surfaces > show sel surfaces > select subtract #7 3 models selected > select add #7.1 1406 atoms, 1436 bonds, 175 residues, 1 model selected > select add #7 4238 atoms, 4329 bonds, 528 residues, 5 models selected > select subtract #7 3 models selected > select add #6 4238 atoms, 4329 bonds, 528 residues, 4 models selected > show sel surfaces > transparency (#!6.1-3 & sel) 90 > ui mousemode right select > select clear > select add #7 4238 atoms, 4329 bonds, 528 residues, 4 models selected > ui mousemode right ""translate selected models"" > view matrix models #7,1,0,0,-75.07,0,1,0,83.671,0,0,1,61.184 > volume flip #2 axis x Opened CryoEM_rod_volume x flip as #8, grid size 440,440,440, pixel 0.926, shown at step 1, values float32 > volume flip #8 axis x Opened CryoEM_rod_volume x flip x flip as #9, grid size 440,440,440, pixel 0.926, shown at step 1, values float32 > show #!8 models > hide #!1 models > show #!2 models > hide #!2 models > color #8 #ffb24b75 models > color #8 #1d62eaff models > select subtract #7 3 models selected > select add #8 2 models selected > view matrix models > #8,0.087553,-0.0054174,0.99615,-130.66,-0.87083,0.48516,0.079178,236.14,-0.48372,-0.87441,0.03776,235.18 > select subtract #8 Nothing selected > select add #9 2 models selected > view matrix models > #9,0.087553,-0.0054174,0.99615,-167.69,-0.87083,0.48516,0.079178,314.03,-0.48372,-0.87441,0.03776,280.38 > rename #9 CryoEM_rod_volume > rename #8 CryoEM_rod_volume_Xflip > rename #9 CryoEM_rod_volume_2 > rename #8 id #10 > rename #9 id #8 > rename #10 id #9 > ui mousemode right select > select clear > select add #8 2 models selected > select add #9 4 models selected > ui mousemode right ""translate selected models"" > view matrix models > #8,0.087553,-0.0054174,0.99615,-164.77,-0.87083,0.48516,0.079178,399.52,-0.48372,-0.87441,0.03776,301.28,#9,0.087553,-0.0054174,0.99615,-127.74,-0.87083,0.48516,0.079178,321.64,-0.48372,-0.87441,0.03776,256.08 > select subtract #8 2 models selected > select subtract #9 Nothing selected > hide #!3 models > hide #!4 models > hide #!5 models > hide #!6 models > hide #!7 models > hide #!8 models > hide #!9 models > show #!1 models > show #!2 models > show #!3 models > show #!4 models > show #!5 models > select add #1 3 models selected > select add #2 5 models selected > select add #3 4722 atoms, 4830 bonds, 597 residues, 9 models selected > select add #4 4722 atoms, 4830 bonds, 597 residues, 11 models selected > select add #5 9444 atoms, 9660 bonds, 1194 residues, 15 models selected > view matrix models > #2,0.087553,-0.0054174,0.99615,-126.95,-0.87083,0.48516,0.079178,669.46,-0.48372,-0.87441,0.03776,739.35,#1,0.13568,0.017664,0.9906,-141.79,-0.87217,0.47646,0.11096,662.72,-0.47002,-0.87902,0.080052,729.58,#4,1,0,0,18.98,0,1,0,328.98,0,0,1,203.48,#5,1,0,0,18.98,0,1,0,328.98,0,0,1,203.48,#3,1,0,0,18.98,0,1,0,328.98,0,0,1,203.48 > view matrix models > #2,0.087553,-0.0054174,0.99615,-304.16,-0.87083,0.48516,0.079178,895.58,-0.48372,-0.87441,0.03776,904.19,#1,0.13568,0.017664,0.9906,-319,-0.87217,0.47646,0.11096,888.85,-0.47002,-0.87902,0.080052,894.42,#4,1,0,0,-158.23,0,1,0,555.1,0,0,1,368.32,#5,1,0,0,-158.23,0,1,0,555.1,0,0,1,368.32,#3,1,0,0,-158.23,0,1,0,555.1,0,0,1,368.32 > hide #!1 models > hide #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > select subtract #1 9444 atoms, 9660 bonds, 1194 residues, 12 models selected > select subtract #2 9444 atoms, 9660 bonds, 1194 residues, 10 models selected > select subtract #3 4722 atoms, 4830 bonds, 597 residues, 6 models selected > select subtract #4 4722 atoms, 4830 bonds, 597 residues, 4 models selected > select subtract #5 Nothing selected > show #!6 models > show #!7 models > show #!8 models > show #!9 models > select add #8 2 models selected > view matrix models > #8,0.087553,-0.0054174,0.99615,-118.06,-0.87083,0.48516,0.079178,412.77,-0.48372,-0.87441,0.03776,310.17 > select add #9 4 models selected > select subtract #8 2 models selected > view matrix models > #9,0.087553,-0.0054174,0.99615,-93.297,-0.87083,0.48516,0.079178,335.93,-0.48372,-0.87441,0.03776,265.89 > volume #9 level 0.05334 > volume #8 level 0.0533 > select add #8 4 models selected > select subtract #9 2 models selected > view matrix models > #8,0.087553,-0.0054174,0.99615,-407.88,-0.87083,0.48516,0.079178,445.46,-0.48372,-0.87441,0.03776,312.07 > select subtract #8 Nothing selected > select add #9 2 models selected > hide #!8 models > view matrix models > #9,0.087553,-0.0054174,0.99615,-131.66,-0.87083,0.48516,0.079178,421.98,-0.48372,-0.87441,0.03776,294.72 > view matrix models > #9,0.087553,-0.0054174,0.99615,-132.54,-0.87083,0.48516,0.079178,431.18,-0.48372,-0.87441,0.03776,300.33 > view matrix models > #9,0.087553,-0.0054174,0.99615,-130,-0.87083,0.48516,0.079178,417.09,-0.48372,-0.87441,0.03776,310.95 > show #!8 models > select add #8 4 models selected > select subtract #9 2 models selected > view matrix models > #8,0.087553,-0.0054174,0.99615,-158.65,-0.87083,0.48516,0.079178,396.29,-0.48372,-0.87441,0.03776,172.41 > view matrix models > #8,0.087553,-0.0054174,0.99615,-122.22,-0.87083,0.48516,0.079178,340.88,-0.48372,-0.87441,0.03776,272.5 > select subtract #8 Nothing selected > select add #9 2 models selected > view matrix models > #9,0.087553,-0.0054174,0.99615,-205.05,-0.87083,0.48516,0.079178,390.81,-0.48372,-0.87441,0.03776,314.95 > select add #8 4 models selected > select subtract #9 2 models selected > view matrix models > #8,0.087553,-0.0054174,0.99615,-127.11,-0.87083,0.48516,0.079178,409.09,-0.48372,-0.87441,0.03776,326.22 > hide #!9 models > volume #8 level 0.03045 > surface dust #8 size 9.26 > show #!9 models > select subtract #8 Nothing selected > select add #9 2 models selected > view matrix models > #9,0.087553,-0.0054174,0.99615,-275.85,-0.87083,0.48516,0.079178,384.65,-0.48372,-0.87441,0.03776,324.26 > select subtract #9 Nothing selected > select add #8 2 models selected > view matrix models > #8,0.087553,-0.0054174,0.99615,-128.68,-0.87083,0.48516,0.079178,415,-0.48372,-0.87441,0.03776,314.07 > select subtract #8 Nothing selected > select add #9 2 models selected > view matrix models > #9,0.087553,-0.0054174,0.99615,-221.68,-0.87083,0.48516,0.079178,251.45,-0.48372,-0.87441,0.03776,227.98 > view matrix models > #9,0.087553,-0.0054174,0.99615,-223.3,-0.87083,0.48516,0.079178,251.24,-0.48372,-0.87441,0.03776,218.02 > view matrix models > #9,0.087553,-0.0054174,0.99615,-219.1,-0.87083,0.48516,0.079178,201.87,-0.48372,-0.87441,0.03776,204.77 > hide #!6 models > show #!6 models > select add #8 4 models selected > select subtract #8 2 models selected > select add #8 4 models selected > select subtract #9 2 models selected > color #8 #ebebebff models > color #8 white models > color #8 #ebebebff models > color #8 #d6d6d6ff models > color #8 silver models > color #8 #d783ffff models > color #8 #ff85ffff models > color #8 #bfa1c3ff models > transparency #8.1 70 > lighting flat > lighting full > lighting soft > graphics silhouettes false > graphics silhouettes true > lighting flat > lighting full > lighting soft > lighting simple > ui tool show ""Side View"" > select add #8 3 models selected > select subtract #8 Nothing selected > save > /Users/rosspopoff/Dropbox/Trono_Lab/37-FindingDUF3669/9-PTPSP_data/cryosparc/2024.05.29_Modelpaper_2.cxs No map chosen to save > save > /Users/rosspopoff/Dropbox/Trono_Lab/37-FindingDUF3669/9-PTPSP_data/cryosparc/blo.tif > width 2000 height 1443 supersample 3 transparentBackground true ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8rc202405312319 (2024-05-31) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 ATI-4.14.1 OpenGL renderer: AMD Radeon Pro 560X 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: MacBookPro15,1 Processor Name: 6-Core Intel Core i9 Processor Speed: 2.9 GHz Number of Processors: 1 Total Number of Cores: 6 L2 Cache (per Core): 256 KB L3 Cache: 12 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 2020.0.1.0.0 (iBridge: 21.16.365.0.0,0) OS Loader Version: 577.140.2~15 Software: System Software Overview: System Version: macOS 13.6 (22G120) Kernel Version: Darwin 22.6.0 Time since boot: 20 days, 14 hours, 47 minutes 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: 0x0000 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 Radeon Pro 560X: Chipset Model: Radeon Pro 560X Type: GPU Bus: PCIe PCIe Lane Width: x8 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x67ef Revision ID: 0x00c2 ROM Revision: 113-C980AL-075 VBIOS Version: 113-C97501U-005 EFI Driver Version: 01.A1.075 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 2 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2880 x 1800 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes 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: 1.6.3 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 ChimeraX-AtomicLibrary: 14.0.5 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: 1.8rc202405312319 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: 1.5.16 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: 1.13.4 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: 3.0.45 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 traitlets: 5.14.2 typing-extensions: 4.12.1 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