id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16005 Graphics crash, macOS 14.6.1, Iris Plus Graphics 655 chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.6.1-x86_64-i386-64bit ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Aborted Current thread 0x00007ff853526dc0 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/GL/VERSION/GL_1_5.py"", line 125 in glBufferSubData File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 1689 in set_multishadow_view File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 250 in _draw_scene File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 188 in draw File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 84 in 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: ""\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit"", ""name"" : ""AppKit"", ""CFBundleVersion"" : ""2487.70.105"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 140703393189888, ""size"" : 591904, ""uuid"" : ""18f658dd-20f3-324d-b7ac-8a9c60b574b3"", ""path"" : ""\/usr\/lib\/dyld"", ""name"" : ""dyld"" } ], ""sharedCache"" : { ""base"" : 140703392493568, ""size"" : 25769803776, ""uuid"" : ""b8509d0f-c366-3716-9a03-efa00b40318a"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.3G resident=0K(0%) swapped_out_or_unallocated=1.3G(100%)\nWritable regions: Total=1.9G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.9G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG image 384K 37 \nColorSync 248K 30 \nCoreAnimation 1764K 190 \nCoreGraphics 20K 4 \nCoreGraphics (reserved) 8K 1 reserved VM address space (unallocated)\nCoreUI image data 5364K 43 \nFoundation 32K 2 \nKernel Alloc Once 8K 1 \nMALLOC 1.4G 648 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 256K 1 reserved VM address space (unallocated)\nMach message 16K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 100K 25 \nStack 155.7M 26 \nStack Guard 56.0M 1 \nVM_ALLOCATE 331.3M 283 \nVM_ALLOCATE (reserved) 32.0M 1 reserved VM address space (unallocated)\n__CTF 824 1 \n__DATA 58.1M 865 \n__DATA_CONST 51.2M 466 \n__DATA_DIRTY 1851K 236 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 219.0M 178 \n__OBJC_RO 71.9M 1 \n__OBJC_RW 2201K 2 \n__TEXT 1.1G 872 \ndyld private memory 256K 2 \nmapped file 229.8M 62 \nshared memory 3552K 39 \n=========== ======= ======= \nTOTAL 3.7G 4038 \nTOTAL, minus reserved VM space 3.7G 4038 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""b30cb884865bfce9bc2eb2be2b1d100a6968d085"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""645eb1d0417dab722a215927"", ""factorPackIds"" : { }, ""deploymentId"" : 240000005 }, { ""rolloutId"" : ""62745b8e85854550ad70b6e4"", ""factorPackIds"" : { }, ""deploymentId"" : 240000073 } ], ""experiments"" : [ { ""treatmentId"" : ""c47ab4cc-c9c3-4b5d-a87c-e2433ce02597"", ""experimentId"" : ""6639bc6ba73d460582162323"", ""deploymentId"" : 400000006 }, { ""treatmentId"" : ""45f4e2a5-551b-4bc2-a2dc-19c244dda8f8"", ""experimentId"" : ""6643969b3099cf28e049862f"", ""deploymentId"" : 400000007 } ] } } ===== Log before crash start ===== Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/gabrielumajioka/Desktop/project T7SS /refinament modelling > T7SS/Validation Table 24-09-23/pdb_extract_coord_16040.cif"" Summary of feedback from opening /Users/gabrielumajioka/Desktop/project T7SS /refinament modelling T7SS/Validation Table 24-09-23/pdb_extract_coord_16040.cif --- warnings | Unknown polymer entity '1' near line 80 Unknown polymer entity '2' near line 718 Unknown polymer entity '3' near line 2530 Unknown polymer entity '4' near line 4345 Unknown polymer entity '5' near line 7365 Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for pdb_extract_coord_16040.cif #1 --- Chain | Description A | No description available C | No description available D | No description available G | No description available H | No description available > show cartoons > hide atoms > open ""/Users/gabrielumajioka/Desktop/project T7SS /refinament modelling > T7SS/Validation Table 24-09-23/pdb_extract_coord_16040.cif"" Summary of feedback from opening /Users/gabrielumajioka/Desktop/project T7SS /refinament modelling T7SS/Validation Table 24-09-23/pdb_extract_coord_16040.cif --- warnings | Unknown polymer entity '1' near line 80 Unknown polymer entity '2' near line 718 Unknown polymer entity '3' near line 2530 Unknown polymer entity '4' near line 4345 Unknown polymer entity '5' near line 7365 Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for pdb_extract_coord_16040.cif #2 --- Chain | Description A | No description available C | No description available D | No description available G | No description available H | No description available > open ""/Users/gabrielumajioka/Desktop/project T7SS /refinament modelling > T7SS/Validation Table 24-09-23/isolde pre Real > Space/isolde/model_paper_sept2024(start_model).pdb"" Summary of feedback from opening /Users/gabrielumajioka/Desktop/project T7SS /refinament modelling T7SS/Validation Table 24-09-23/isolde pre Real Space/isolde/model_paper_sept2024(start_model).pdb --- warnings | PDB SEQRES record for chain C is incomplete. Ignoring input sequence records as basis for sequence. PDB SEQRES record for chain D is incomplete. Ignoring input sequence records as basis for sequence. Chain information for model_paper_sept2024(start_model).pdb #3 --- Chain | Description A | No description available C | No description available D | No description available G | No description available H | No description available > hide atoms > show cartoons > select add #1 11945 atoms, 12209 bonds, 4 pseudobonds, 1441 residues, 2 models selected > color (#!1 & sel) red > select add #3 35556 atoms, 36085 bonds, 8 pseudobonds, 2882 residues, 4 models selected > color (#!1,3 & sel) light gray > select add #2 47501 atoms, 48294 bonds, 12 pseudobonds, 4323 residues, 6 models selected > select subtract #2 35556 atoms, 36085 bonds, 8 pseudobonds, 2882 residues, 4 models selected > select add #2 47501 atoms, 48294 bonds, 12 pseudobonds, 4323 residues, 6 models selected > close #2 > hide #!3 models > hide #!1 models > show #!1 models > color (#!1 & sel) red > show #!3 models > select clear > ui tool show Matchmaker > matchmaker #!3 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker pdb_extract_coord_16040.cif, chain H (#1) with model_paper_sept2024(start_model).pdb, chain H (#3), sequence alignment score = 2320.4 RMSD between 550 pruned atom pairs is 0.618 angstroms; (across all 564 pairs: 0.969) > hide #!1 models > select add #3 23611 atoms, 23876 bonds, 4 pseudobonds, 1441 residues, 2 models selected > close #1 > open ""/Users/gabrielumajioka/Desktop/project T7SS /1-PAPER > T7SS/MAPS/J2727-refined dimer/cryosparc_P14_J2627_004_volume_map_sharp.mrc"" Opened cryosparc_P14_J2627_004_volume_map_sharp.mrc as #1, grid size 300,300,300, pixel 1.2, shown at level 0.0587, step 2, values float32 > volume #1 level 0.269 > volume #1 level 0.03586 > volume #1 level 0.4439 > select add #1 23611 atoms, 23876 bonds, 4 pseudobonds, 1441 residues, 4 models selected > select subtract #3 2 models selected > select add #3 23611 atoms, 23876 bonds, 4 pseudobonds, 1441 residues, 4 models selected > select subtract #1 23611 atoms, 23876 bonds, 4 pseudobonds, 1441 residues, 2 models selected > hide #!1 models > close #3 > open ""/Users/gabrielumajioka/Desktop/project T7SS /1-PAPER T7SS/Validation > Table 24-09-23/Monomer_final_24-09-24.pdb"" Chain information for Monomer_final_24-09-24.pdb #2 --- Chain | Description A | No description available C | No description available D | No description available G | No description available H | No description available > show #!1 models > hide atoms > show cartoons > volume #1 level 0.1525 > volume #1 level 0.07895 > volume #1 level 0.02066 > volume #1 level 0.05614 > hide #!1 models > open /Users/gabrielumajioka/Desktop/dimer/Sub2.pdb Chain information for Sub2.pdb #3 --- Chain | Description A | No description available C | No description available D | No description available G | No description available H | No description available > open /Users/gabrielumajioka/Desktop/dimer/Sub1.pdb Chain information for Sub1.pdb #4 --- Chain | Description A | No description available C | No description available D | No description available G | No description available H | No description available > select add #2 11945 atoms, 12210 bonds, 4 pseudobonds, 1441 residues, 2 models selected > close #2 > hide atoms > show cartoons > select add #3 11945 atoms, 12210 bonds, 4 pseudobonds, 1441 residues, 2 models selected > select subtract #3 Nothing selected > ui tool show Matchmaker > matchmaker #3/H to #4/G pairing ss 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 Sub1.pdb, chain G (#4) with Sub2.pdb, chain H (#3), sequence alignment score = 1665.4 RMSD between 308 pruned atom pairs is 0.601 angstroms; (across all 356 pairs: 3.201) > show #!1 models > hide #!1 models > select #4/G 3020 atoms, 3086 bonds, 1 pseudobond, 356 residues, 2 models selected > delete atoms (#!4 & sel) Traceback (most recent call last): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/triggerset.py"", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 392, in _items_change item_names = self._item_names() ^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 47, in _item_names values = [v for v in self.list_func() if self.filter_func(v)] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 47, in values = [v for v in self.list_func() if self.filter_func(v)] ^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/match_maker/tool.py"", line 518, in filter_func=lambda c, ref=chain: c.structure != ref.structure) ^^^^^^^^^^^^^ AttributeError: 'Sequence' object has no attribute 'structure' Error processing trigger ""changes"": AttributeError: 'Sequence' object has no attribute 'structure' File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/match_maker/tool.py"", line 518, in filter_func=lambda c, ref=chain: c.structure != ref.structure) ^^^^^^^^^^^^^ See log for complete Python traceback. > delete bonds (#!4 & sel) > select #3/H 4660 atoms, 4760 bonds, 3 pseudobonds, 564 residues, 2 models selected > select #3/H 4660 atoms, 4760 bonds, 3 pseudobonds, 564 residues, 2 models selected > select #3/G 3020 atoms, 3086 bonds, 1 pseudobond, 356 residues, 2 models selected > show #!1 models > hide #!1 models > delete atoms (#!3 & sel) > delete bonds (#!3 & sel) > show #!1 models > hide #!1 models > show #!1 models > volume #1 level 0.07132 > volume #1 level 0.07891 > volume #1 level 0.1143 > volume #1 level 0.08397 > open ""/Users/gabrielumajioka/Desktop/project T7SS /1-PAPER T7SS/Other > files/hypothesis/heterotetrameric diverse species > YukB_2xYukC_YukD/BSU/BSU168_YukBCD.pdb"" Chain information for BSU168_YukBCD.pdb #2 --- Chain | Description A B | No description available C | No description available D | No description available > ui tool show Matchmaker > matchmaker #2 to #4 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker Sub1.pdb, chain H (#4) with BSU168_YukBCD.pdb, chain C (#2), sequence alignment score = 2611.1 RMSD between 227 pruned atom pairs is 1.042 angstroms; (across all 561 pairs: 4.905) > hide #!1 models > hide #2 models > show #2 models > hide #2 models > show #2 models > select add #2 12518 atoms, 12797 bonds, 1543 residues, 1 model selected > close #2 > open ""/Users/gabrielumajioka/Desktop/project T7SS /1-PAPER T7SS/Other > files/hypothesis/heterotetrameric diverse species > YukB_2xYukC_YukD/BSU/YukBCD_BSU168_unrelaxed_rank_003_alphafold2_multimer_v3_model_5_seed_000.pdb"" Chain information for YukBCD_BSU168_unrelaxed_rank_003_alphafold2_multimer_v3_model_5_seed_000.pdb #2 --- Chain | Description A B | No description available C | No description available D | No description available > select add #2 12518 atoms, 12797 bonds, 1543 residues, 1 model selected > close #2 > open ""/Users/gabrielumajioka/Desktop/project T7SS /1-PAPER T7SS/Other > files/DIMER of heterotetramermeric diverse species > /dimer_BSU168ls/BSU168_2.pdb"" Chain information for BSU168_2.pdb #2 --- Chain | Description A B | No description available C D E F | No description available G H | No description available > ui tool show Matchmaker > matchmaker #2 to #4 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker Sub1.pdb, chain H (#4) with BSU168_2.pdb, chain G (#2), sequence alignment score = 2596.1 RMSD between 358 pruned atom pairs is 1.329 angstroms; (across all 561 pairs: 4.528) > hide atoms > show cartoons > hide #!3 models > show #!3 models > close #3 > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > select add #2 31756 atoms, 32398 bonds, 3908 residues, 1 model selected > select add #4 40681 atoms, 41522 bonds, 3 pseudobonds, 4993 residues, 3 models selected > close #4 > select subtract #2 Nothing selected > select add #2 31756 atoms, 32398 bonds, 3908 residues, 1 model selected > open /Users/gabrielumajioka/Desktop/dimer/Sub1.pdb Chain information for Sub1.pdb #3 --- Chain | Description A | No description available C | No description available D | No description available G | No description available H | No description available > hide #2 models > show #!3 cartoons > show #!3 atoms > hide #!3 atoms > show #!3 cartoons > show #2 models > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A #2/B #3/A Alignment identifier is 1 > sequence chain #2/C #2/D #2/E #2/F Alignment identifier is 2 > sequence chain #2/G #2/H Alignment identifier is 3 > sequence chain #3/C Alignment identifier is 3/C > sequence chain #3/D Alignment identifier is 3/D > sequence chain #3/G Alignment identifier is 3/G > sequence chain #3/H Alignment identifier is 3/H > select #2/G-H:1 16 atoms, 14 bonds, 2 residues, 1 model selected > select #2/G-H 15742 atoms, 16084 bonds, 1946 residues, 1 model selected > select #2/G-H:947-973 434 atoms, 444 bonds, 54 residues, 1 model selected > select #2/G-H:541-973 6880 atoms, 7018 bonds, 866 residues, 1 model selected ===== Log before crash end ===== Log: Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-22.5.11 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655 OpenGL vendor: Intel Inc. Python: 3.11.2 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro15,2 Processor Name: Quad-Core Intel Core i5 Processor Speed: 2,3 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 2022.140.5.0.0 (iBridge: 21.16.6074.0.0,0) OS Loader Version: 580.140.1~8 Software: System Software Overview: System Version: macOS 14.6.1 (23G93) Kernel Version: Darwin 23.6.0 Time since boot: 6 days, 5 hours, 59 minutes Graphics/Displays: Intel Iris Plus Graphics 655: Chipset Model: Intel Iris Plus Graphics 655 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3ea5 Revision ID: 0x0001 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL UP3216Q: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 3840 x 2160 @ 30.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: 4NCD077E073P Mirror: Off Online: Yes Rotation: Supported Connection Type: DVI or HDMI Adapter Firmware Version: 7,55 LG UltraFine: Resolution: 6016 x 3384 UI Looks like: 3008 x 1692 Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: 806NTKF1F589 Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: Yes Connection Type: Thunderbolt/DisplayPort Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.5 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.22.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.7.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 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: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6.1 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.14 ChimeraX-ModelPanel: 1.4 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: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 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 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 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-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.4 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 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: 1.33.3 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 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: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.1 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.2 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.7.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.4 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.6.0 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.2.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 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: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.4 urllib3: 2.1.0 wcwidth: 0.2.13 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Graphics nonchimerax all ChimeraX