id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9103 Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-13.2.1-arm64-arm-64bit ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 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 0x00000001dec60140 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 892 in init File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 1043 in File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 197 in _run_module_as_main {""app_name"":""ChimeraX"",""timestamp"":""2023-05-31 12:07:26.00 -0400"",""app_version"":""1.6.1"",""slice_uuid"":""a5992708-d5b4-36ec-ac0a-e525f6105b56"",""build_version"":""1.6.1.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":1,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 13.2.1 (22D68)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""D9229C22-55A7-4041-82E5-4A16F1589CE1""} { ""uptime"" : 260000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""Mac14,6"", ""coalitionID"" : 12132, ""osVersion"" : { ""train"" : ""macOS 13.2.1"", ""build"" : ""22D68"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2023-05-31 12:07:13.1370 -0400"", ""incident"" : ""D9229C22-55A7-4041-82E5-4A16F1589CE1"", ""pid"" : 19908, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2023-05-23 15:06:27.7941 -0400"", ""procStartAbsTime"" : 3296891248065, ""procExitAbsTime"" : 6306475595686, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.6.1"",""CFBundleVersion"":""1.6.1.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""05A50C29-5E72-59FB-BE53-960212ACD08B"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""072F8185-3B57-AAC5-2693-67E3F0E895CF"", ""throttleTimeout"" : 2147483647, ""sleepWakeUUID"" : ""74002A5C-F34F-4EF4-B1E3-1E830B13D103"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x18 is not in any region. 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: 154959872, ""uuid"" : ""1b766dc4-2490-3425-8726-45387675bc14"", ""path"" : ""\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore"", ""name"" : ""QtWebEngineCore"" }, { ""size"" : 0, ""source"" : ""A"", ""base"" : 0, ""uuid"" : ""00000000-0000-0000-0000-000000000000"" } ], ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=21.1G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=21.1G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG backing stores 1216K 8 \nCG image 1536K 75 \nColorSync 592K 29 \nCoreAnimation 1312K 61 \nCoreGraphics 48K 3 \nCoreUI image data 5120K 40 \nFoundation 32K 2 \nKernel Alloc Once 32K 1 \nMALLOC 19.2G 1080 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""rolloutId"" : ""6347054113acce15305b7b82"", ""factorPackIds"" : { ""SIRI_MEMORY_SYNC_CONFIG"" : ""634705e78e8be655c1316a6e"" }, ""deploymentId"" : 240000005 }, { ""rolloutId"" : ""62cdf63ddb3b7109d6d765cc"", ""factorPackIds"" : { ""SIRI_UNDERSTANDING_TMDC"" : ""62cdf6dddb3b7109d6d765cd"" }, ""deploymentId"" : 240000007 } ], ""experiments"" : [ { ""treatmentId"" : ""79516245-b830-464e-bb6c-a2998d9e2191"", ""experimentId"" : ""63b8ec83fd1d345f491884ba"", ""deploymentId"" : 400000024 }, { ""treatmentId"" : ""6dd670af-0633-45e4-ae5f-122ae4df02be"", ""experimentId"" : ""64406ba83deb637ac8a04419"", ""deploymentId"" : 900000005 } ] }, ""reportNotes"" : [ ""dyld_process_snapshot_create_for_process failed with 5"" ] } ===== Log before crash start ===== UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/brendansheehan/python/7XZX.cif Summary of feedback from opening /Users/brendansheehan/python/7XZX.cif --- warnings | Missing entity information. Treating each chain as a separate entity. Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. Chain information for 7XZX.cif #1 --- Chain | Description N | No description available > open /Users/brendansheehan/python/7XZX.pdb 7XZX.pdb title: Cryo-em structure of the nucleosome In complex with P53 DNA-binding domain [more info...] Chain information for 7XZX.pdb #2 --- Chain | Description | UniProt A E | histone H3.1 | H31_HUMAN 1-135 B F | histone H4 | H4_HUMAN 0-102 C G | histone H2A type 1-B/E | H2A1B_HUMAN 0-129 D H | histone H2B type 1-J | H2B1J_HUMAN -3-122 I | DNA (193-mer) | J | DNA (193-mer) | K L M N | cellular tumor antigen P53 | P53_HUMAN 94-293 > sequence chain #2/K#2/L#2/M#2/N Alignment identifier is 1 > hide #2 models > hide #1 models > show #2 models > color #2 bychain No model chosen to save relative to > open /Users/brendansheehan/python/7XZX.cif Summary of feedback from opening /Users/brendansheehan/python/7XZX.cif --- warnings | Missing entity information. Treating each chain as a separate entity. Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. Chain information for 7XZX.cif #3 --- Chain | Description N | No description available > hide #3 models > hide #2 models > show #3 models > show #1 models > hide #3 models > close #3 > close #2 > close > open /Users/brendansheehan/python/7XZX.cif Summary of feedback from opening /Users/brendansheehan/python/7XZX.cif --- warnings | Missing entity information. Treating each chain as a separate entity. Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. Chain information for 7XZX.cif #1 --- Chain | Description N | No description available > close > open /Users/brendansheehan/python/7XZX.pdb format pdb 7XZX.pdb title: Cryo-em structure of the nucleosome In complex with P53 DNA-binding domain [more info...] Chain information for 7XZX.pdb #1 --- Chain | Description | UniProt A E | histone H3.1 | H31_HUMAN 1-135 B F | histone H4 | H4_HUMAN 0-102 C G | histone H2A type 1-B/E | H2A1B_HUMAN 0-129 D H | histone H2B type 1-J | H2B1J_HUMAN -3-122 I | DNA (193-mer) | J | DNA (193-mer) | K L M N | cellular tumor antigen P53 | P53_HUMAN 94-293 > select 1.A Expected an objects specifier or a keyword > select /A 801 atoms, 813 bonds, 97 residues, 1 model selected > select /K 1555 atoms, 1590 bonds, 198 residues, 1 model selected > select /K /L 3110 atoms, 3180 bonds, 396 residues, 1 model selected > select not (/K /L) Expected an objects specifier or a keyword > select ~/K 17715 atoms, 18753 bonds, 1698 residues, 1 model selected > select ~/K/L/M/N 13050 atoms, 13983 bonds, 1104 residues, 1 model selected > delete ~/K/L/M/N > save TP53_tetramer.mmCIF format mmcif > open /Users/brendansheehan/Desktop/TP53_tetramer.mmCIF Chain information for TP53_tetramer.mmCIF #2 --- Chain | Description K L M N | cellular tumor antigen P53 > hide #1 models > close #1 > cd /Users/brendansheehan/python/chimeraX Current working directory is: /Users/brendansheehan/python/chimeraX > open /Users/brendansheehan/Desktop/TP53_tetramer.mmCIF Chain information for TP53_tetramer.mmCIF #1 --- Chain | Description K L M N | cellular tumor antigen P53 > close > open /Users/brendansheehan/python/7XZX.pdb format pdb 7XZX.pdb title: Cryo-em structure of the nucleosome In complex with P53 DNA-binding domain [more info...] Chain information for 7XZX.pdb #1 --- Chain | Description | UniProt A E | histone H3.1 | H31_HUMAN 1-135 B F | histone H4 | H4_HUMAN 0-102 C G | histone H2A type 1-B/E | H2A1B_HUMAN 0-129 D H | histone H2B type 1-J | H2B1J_HUMAN -3-122 I | DNA (193-mer) | J | DNA (193-mer) | K L M N | cellular tumor antigen P53 | P53_HUMAN 94-293 > select /K:94-291 1555 atoms, 1590 bonds, 198 residues, 1 model selected > select /K:94-291 1555 atoms, 1590 bonds, 198 residues, 1 model selected > show target m > log metadata #1 Metadata for 7XZX.pdb #1 --- Title | Cryo-em structure of the nucleosome In complex with P53 DNA-binding domain Citation | Structural basis for P53 binding to its nucleosomal targetDNA sequence. PMID: 36714865 Gene sources | Synthetic construct Synthetic construct Experimental method | Electron microscopy Resolution | 4.53Å > select /K:94-291 1555 atoms, 1590 bonds, 198 residues, 1 model selected > sequence chain #1/A#1/E Alignment identifier is 1 > ui tool show ""Show Sequence Viewer"" > sequence chain /K /L /M /N Alignment identifier is 2 > select /K-N:94-150 1736 atoms, 1780 bonds, 228 residues, 1 model selected > select /K-N:94-150 1736 atoms, 1780 bonds, 228 residues, 1 model selected > select /K-N:94-150 1736 atoms, 1780 bonds, 228 residues, 1 model selected > select /K:92 Nothing selected > select /K:94 6 atoms, 5 bonds, 1 residue, 1 model selected > color sel red > /K-N:94-96 Unknown command: /K-N:94-96 > select /K-N:94-96 72 atoms, 68 bonds, 12 residues, 1 model selected > color sel red > select /BFCGDH Nothing selected > select /B/F/C/G/D/H 4445 atoms, 4501 bonds, 567 residues, 1 model selected > color sel dim gray > color sel light gray > color sel dim gray > select /A/E 1611 atoms, 1635 bonds, 195 residues, 1 model selected > color sel gray > color sel light gray > sequence chain /A/E Alignment identifier is 1 > select /A:38-59/E:37-59 391 atoms, 399 bonds, 45 residues, 1 model selected > select /A:38-59/E:37-56 369 atoms, 377 bonds, 42 residues, 1 model selected > select /A:38-59/E:37-53 339 atoms, 346 bonds, 39 residues, 1 model selected > open pdb 7w9v 'pdb' has no suffix > open 7w9v Summary of feedback from opening 7w9v fetched from pdb --- warnings | Atom HO5' is not in the residue template for DA /I:-72 Atom HO5' is not in the residue template for DA /J:-72 note | Fetching compressed mmCIF 7w9v from http://files.rcsb.org/download/7w9v.cif 7w9v title: Cryo-EM structure of nucleosome in complex with p300 acetyltransferase catalytic core (complex I) [more info...] Chain information for 7w9v #2 --- Chain | Description | UniProt A E | Histone H3.1 | H31_HUMAN 1-135 B F | Histone H4 | H4_HUMAN 0-102 C G | Histone H2A type 1-B/E | H2A1B_HUMAN 0-129 D H | Histone H2B type 1-J | H2B1J_HUMAN 0-125 I | DNA (145-MER) | J | DNA (145-MER) | K | Histone acetyltransferase p300 | EP300_HUMAN 1035-1519 1581-1720 > align #1 toAtoms #2 Unequal number of atoms to pair, 19270 and 18546 > sequence chain #1/I Alignment identifier is 1/I > fitmap #1 toAtoms #2 Expected a keyword Must specify one map, got 0 > sequence chain #2/I Alignment identifier is 2/I > select add #2 18885 atoms, 19816 bonds, 374 pseudobonds, 1631 residues, 4 models selected > select add #1 37816 atoms, 39813 bonds, 374 pseudobonds, 3488 residues, 4 models selected > select subtract #1 18546 atoms, 19470 bonds, 374 pseudobonds, 1592 residues, 3 models selected > select #2 18546 atoms, 19470 bonds, 374 pseudobonds, 1592 residues, 3 models selected > ui tool show ""Fit to Segments"" > mmaker #1 to #2 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 7w9v, chain I (#2) with 7XZX.pdb, chain I (#1), sequence alignment score = 753.9 RMSD between 109 pruned atom pairs is 1.101 angstroms; (across all 144 pairs: 9.852) > view sel > hide #1 models > show #1 models > select add #1 37816 atoms, 39813 bonds, 374 pseudobonds, 3488 residues, 4 models selected > open 6GYR Summary of feedback from opening 6GYR fetched from pdb --- notes | Fetching compressed mmCIF 6gyr from http://files.rcsb.org/download/6gyr.cif Fetching CCD ZN from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ZN/ZN.cif Fetching CCD 01K from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/K/01K/01K.cif 6gyr title: Transcription factor dimerization activates the p300 acetyltransferase [more info...] Chain information for 6gyr #3 --- Chain | Description | UniProt A B C D | Histone acetyltransferase p300 | EP300_HUMAN 1046-1664 Non-standard residues in 6gyr #3 --- 01K — [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl (3R,20R)-20-carbamoyl-3-hydroxy-2,2-dimethyl-4,8,14,22-tetraoxo-12-thia-5,9,15,21-tetraazatricos-1-yl dihydrogen diphosphate (Lysine-COENZYME A derivative) ZN — zinc ion 6gyr mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > hide #1 models > hide #!2 models > view sel > Incomplete command: sequence > Unknown command: sequence #3/A > Unknown command: sequence #3 > /A Unknown command: sequence /A > ui tool show ""Show Sequence Viewer"" > sequence chain #3/A #3/B #3/C #3/D Alignment identifier is 1 > select /A:1520-1580 463 atoms, 464 bonds, 29 residues, 1 model selected > select /A/B/C/D:1520-1580 34168 atoms, 34598 bonds, 34 pseudobonds, 2356 residues, 5 models selected > select /A:1520-1580 463 atoms, 464 bonds, 29 residues, 1 model selected > select /A:1520-1580/B:1520-1580 840 atoms, 841 bonds, 1 pseudobond, 53 residues, 2 models selected > select /A:1520-1580/B:1520-1580/C:1520-1580 1123 atoms, 1122 bonds, 2 pseudobonds, 70 residues, 2 models selected > select /A:1520-1580/B:1520-1580/C:1520-1580/D:1520-1580 1521 atoms, 1520 bonds, 3 pseudobonds, 95 residues, 2 models selected > open 6GYT Summary of feedback from opening 6GYT fetched from pdb --- notes | Fetching compressed mmCIF 6gyt from http://files.rcsb.org/download/6gyt.cif Fetching CCD ALY from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Y/ALY/ALY.cif 6gyt title: Transcription factor dimerization activates the p300 acetyltransferase [more info...] Chain information for 6gyt #4 --- Chain | Description | UniProt A | Histone acetyltransferase p300 | EP300_HUMAN 1047-1168 B | Histone acetyltransferase p300 | EP300_HUMAN 1047-1168 C | Histone H4 | Non-standard residues in 6gyt #4 --- ZN — zinc ion > ui tool show ""Show Sequence Viewer"" > sequence chain #4/A Alignment identifier is 4/A > sequence chain #4/B Alignment identifier is 4/B > sequence chain #4/C Alignment identifier is 4/C > select #4/C:9-10 25 atoms, 24 bonds, 2 residues, 1 model selected > select #4/C 116 atoms, 115 bonds, 9 residues, 1 model selected > zoom 2 moved plane near 284.7246646041093 [0.4113376 0.64802213 0.6409904 ] moved plane far 284.7246646041093 [0.4113376 0.64802213 0.6409904 ] > select #4/A:1098-1099 31 atoms, 30 bonds, 2 residues, 1 model selected > select #4/A:1098-1157 1021 atoms, 1035 bonds, 60 residues, 1 model selected > select #4/B:1103-1104 46 atoms, 45 bonds, 2 residues, 1 model selected > select #4/B:1069-1103 558 atoms, 566 bonds, 35 residues, 1 model selected > select > #4/B:1050-1067,1072-1076,1080-1085,1088-1093,1098-1109,1113-1132,1136-1160,1256-1260,1272-1282 1765 atoms, 1778 bonds, 108 residues, 1 model selected > select #4/A 2655 atoms, 2670 bonds, 8 pseudobonds, 182 residues, 2 models selected > color (#!4 & sel) orange > select #4/B 2741 atoms, 2758 bonds, 8 pseudobonds, 187 residues, 2 models selected > zoom 1 moved plane near -0.0 [ 0.97322543 -0.11669096 0.19802899] moved plane far -0.0 [ 0.97322543 -0.11669096 0.19802899] > zoom .5 moved plane near -284.72465920292035 [ 0.97322543 -0.11669096 0.19802899] moved plane far -284.72465920292035 [ 0.97322543 -0.11669096 0.19802899] > select /A:1532-1567/B:1532-1567/C:1532-1567/D:1532-1567 132 atoms, 128 bonds, 10 residues, 1 model selected > hide #!3 models > hide #!4 models > show #1 models > show #!2 models > zoom 1.5 moved plane near 284.2313501240269 [ 0.89736995 -0.14949485 0.41518483] moved plane far 284.2313501240269 [ 0.89736995 -0.14949485 0.41518483] > open > /Users/brendansheehan/python/alphafold/output/output/TP53_tetramer_relaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb > /Users/brendansheehan/python/alphafold/output/output/TP53_tetramer_relaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb > /Users/brendansheehan/python/alphafold/output/output/TP53_tetramer_relaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb > /Users/brendansheehan/python/alphafold/output/output/TP53_tetramer_relaxed_rank_004_alphafold2_multimer_v3_model_1_seed_000.pdb > /Users/brendansheehan/python/alphafold/output/output/TP53_tetramer_relaxed_rank_005_alphafold2_multimer_v3_model_3_seed_000.pdb Chain information for TP53_tetramer_relaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb #5 --- Chain | Description A B C D | No description available Chain information for TP53_tetramer_relaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb #6 --- Chain | Description A B C D | No description available Chain information for TP53_tetramer_relaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb #7 --- Chain | Description A B C D | No description available Chain information for TP53_tetramer_relaxed_rank_004_alphafold2_multimer_v3_model_1_seed_000.pdb #8 --- Chain | Description A B C D | No description available Chain information for TP53_tetramer_relaxed_rank_005_alphafold2_multimer_v3_model_3_seed_000.pdb #9 --- Chain | Description A B C D | No description available > hide #1 models > show #1 models > hide #!2 models > show #!2 models > mmaker #1 #5-9 > matchmaker #1 #5-9 Missing required ""to"" argument > mmaker #5-9 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 7XZX.pdb, chain M (#1) with TP53_tetramer_relaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb, chain A (#5), sequence alignment score = 1029.7 RMSD between 195 pruned atom pairs is 0.283 angstroms; (across all 198 pairs: 0.438) Matchmaker 7XZX.pdb, chain M (#1) with TP53_tetramer_relaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb, chain B (#6), sequence alignment score = 1029.7 RMSD between 195 pruned atom pairs is 0.258 angstroms; (across all 198 pairs: 0.405) Matchmaker 7XZX.pdb, chain M (#1) with TP53_tetramer_relaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb, chain B (#7), sequence alignment score = 1026.7 RMSD between 194 pruned atom pairs is 0.263 angstroms; (across all 198 pairs: 0.461) Matchmaker 7XZX.pdb, chain M (#1) with TP53_tetramer_relaxed_rank_004_alphafold2_multimer_v3_model_1_seed_000.pdb, chain C (#8), sequence alignment score = 1029.7 RMSD between 194 pruned atom pairs is 0.320 angstroms; (across all 198 pairs: 0.517) Matchmaker 7XZX.pdb, chain M (#1) with TP53_tetramer_relaxed_rank_005_alphafold2_multimer_v3_model_3_seed_000.pdb, chain B (#9), sequence alignment score = 1029.7 RMSD between 195 pruned atom pairs is 0.311 angstroms; (across all 198 pairs: 0.461) > hide #1 models > select #1/M 1555 atoms, 1590 bonds, 198 residues, 1 model selected > show #1 models > zoom 1.5 moved plane near 189.487126266606 [0.35405918 0.90229304 0.24598646] moved plane far 189.487126266606 [0.35405918 0.90229304 0.24598646] > cofr sel > hide #1 models > show #1 models > mmaker #5-9 to #1/K-N 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 7XZX.pdb, chain M (#1) with TP53_tetramer_relaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb, chain A (#5), sequence alignment score = 1029.7 RMSD between 195 pruned atom pairs is 0.283 angstroms; (across all 198 pairs: 0.438) Matchmaker 7XZX.pdb, chain M (#1) with TP53_tetramer_relaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb, chain B (#6), sequence alignment score = 1029.7 RMSD between 195 pruned atom pairs is 0.258 angstroms; (across all 198 pairs: 0.405) Matchmaker 7XZX.pdb, chain M (#1) with TP53_tetramer_relaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb, chain B (#7), sequence alignment score = 1026.7 RMSD between 194 pruned atom pairs is 0.263 angstroms; (across all 198 pairs: 0.461) Matchmaker 7XZX.pdb, chain M (#1) with TP53_tetramer_relaxed_rank_004_alphafold2_multimer_v3_model_1_seed_000.pdb, chain C (#8), sequence alignment score = 1029.7 RMSD between 194 pruned atom pairs is 0.320 angstroms; (across all 198 pairs: 0.517) Matchmaker 7XZX.pdb, chain M (#1) with TP53_tetramer_relaxed_rank_005_alphafold2_multimer_v3_model_3_seed_000.pdb, chain B (#9), sequence alignment score = 1029.7 RMSD between 195 pruned atom pairs is 0.311 angstroms; (across all 198 pairs: 0.461) > hide #9 models > hide #8 models > hide #7 models > hide #6 models > hide #1 models > show #1 models > hide #1/K-N > show #1/K-N > show #6 models > hide #5 models > hide #6 models > show #7 models > show #8 models > hide #7 models > hide #8 models > show #9 models > hide #9 models > show #5 models > mmaker #5/A to #1/K 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 7XZX.pdb, chain K (#1) with TP53_tetramer_relaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb, chain A (#5), sequence alignment score = 1026.7 RMSD between 198 pruned atom pairs is 0.268 angstroms; (across all 198 pairs: 0.268) > mmaker #5/B to #1/K 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 7XZX.pdb, chain K (#1) with TP53_tetramer_relaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb, chain B (#5), sequence alignment score = 1012.3 RMSD between 198 pruned atom pairs is 0.250 angstroms; (across all 198 pairs: 0.250) > view sel > zoom .9 moved plane near -29.30161236175836 [0.79571606 0.23004343 0.56028203] moved plane far -29.30161236175836 [0.79571606 0.23004343 0.56028203] > zoom .9 moved plane near -32.55734700229572 [0.79571606 0.23004343 0.56028203] moved plane far -32.55734700229572 [0.79571606 0.23004343 0.56028203] > zoom .9 moved plane near -36.17482992885669 [0.79571606 0.23004343 0.56028203] moved plane far -36.17482992885669 [0.79571606 0.23004343 0.56028203] > zoom .9 moved plane near -40.19425539462508 [0.79571606 0.23004343 0.56028203] moved plane far -40.19425539462508 [0.79571606 0.23004343 0.56028203] > zoom .9 moved plane near -44.66028368082526 [0.79571606 0.23004343 0.56028203] moved plane far -44.66028368082526 [0.79571606 0.23004343 0.56028203] > hide #1 models > show #1 models > hide #1/K-N > hide #!2 models > show #!2 models > list chains Unknown command: list chains > list chains #2 Unknown command: list chains #2 > list Unknown command: list > log metadata Metadata for 7XZX.pdb #1 --- Title | Cryo-em structure of the nucleosome In complex with P53 DNA-binding domain Citation | Structural basis for P53 binding to its nucleosomal targetDNA sequence. PMID: 36714865 Gene sources | Synthetic construct Synthetic construct Experimental method | Electron microscopy Resolution | 4.53Å Metadata for 7w9v #2 --- Title | Cryo-EM structure of nucleosome in complex with p300 acetyltransferase catalytic core (complex I) Citation | Hatazawa, S., Liu, J., Takizawa, Y., Zandian, M., Negishi, L., Kutateladze, T.G., Kurumizaka, H. (2022). Structural basis for binding diversity of acetyltransferase p300 to the nucleosome. Iscience, 25, 104563-104563. PMID: 35754730. DOI: 10.1016/j.isci.2022.104563 Gene source | Homo sapiens (human) CryoEM Map | EMDB 32373 — open map Experimental method | Electron microscopy Resolution | 3.95Å Metadata for 6gyr #3 --- Title | Transcription factor dimerization activates the p300 acetyltransferase Citation | Ortega, E., Rengachari, S., Ibrahim, Z., Hoghoughi, N., Gaucher, J., Holehouse, A.S., Khochbin, S., Panne, D. (2018). Transcription factor dimerization activates the p300 acetyltransferase. Nature, 562, 538-544. PMID: 30323286. DOI: 10.1038/s41586-018-0621-1 Non-standard residues | 01K — [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl (3R,20R)-20-carbamoyl-3-hydroxy-2,2-dimethyl-4,8,14,22-tetraoxo-12-thia-5,9,15,21-tetraazatricos-1-yl dihydrogen diphosphate (Lysine-COENZYME A derivative) ZN — zinc ion Gene source | Homo sapiens (human) Experimental method | X-ray diffraction Resolution | 3.1Å Metadata for 6gyt #4 --- Title | Transcription factor dimerization activates the p300 acetyltransferase Citation | Ortega, E., Rengachari, S., Ibrahim, Z., Hoghoughi, N., Gaucher, J., Holehouse, A.S., Khochbin, S., Panne, D. (2018). Transcription factor dimerization activates the p300 acetyltransferase. Nature, 562, 538-544. PMID: 30323286. DOI: 10.1038/s41586-018-0621-1 Non-standard residue | ZN — zinc ion Gene sources | Xenopus laevis (african clawed frog) Homo sapiens (human) Experimental method | X-ray diffraction Resolution | 2.5Å > sym Missing or invalid ""structures"" argument: empty atom specifier > sym #2 7w9v mmCIF Assemblies --- 1| author_defined_assembly| 1 copy of chain A-K > sym #2 assembly 1 Made 1 copies for 7w9v assembly 1 > view > log chains Chain information for 7XZX.pdb #1 --- Chain | Description | UniProt A E | histone H3.1 | H31_HUMAN 1-135 B F | histone H4 | H4_HUMAN 0-102 C G | histone H2A type 1-B/E | H2A1B_HUMAN 0-129 D H | histone H2B type 1-J | H2B1J_HUMAN -3-122 I | DNA (193-mer) | J | DNA (193-mer) | K L M N | cellular tumor antigen P53 | P53_HUMAN 94-293 Chain information for 7w9v #2 --- Chain | Description | UniProt A E | Histone H3.1 | H31_HUMAN 1-135 B F | Histone H4 | H4_HUMAN 0-102 C G | Histone H2A type 1-B/E | H2A1B_HUMAN 0-129 D H | Histone H2B type 1-J | H2B1J_HUMAN 0-125 I | DNA (145-MER) | J | DNA (145-MER) | K | Histone acetyltransferase p300 | EP300_HUMAN 1035-1519 1581-1720 Chain information for 6gyr #3 --- Chain | Description | UniProt A B C D | Histone acetyltransferase p300 | EP300_HUMAN 1046-1664 Chain information for 6gyt #4 --- Chain | Description | UniProt A | Histone acetyltransferase p300 | EP300_HUMAN 1047-1168 B | Histone acetyltransferase p300 | EP300_HUMAN 1047-1168 C | Histone H4 | Chain information for TP53_tetramer_relaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb #5 --- Chain | Description A B C D | No description available Chain information for TP53_tetramer_relaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb #6 --- Chain | Description A B C D | No description available Chain information for TP53_tetramer_relaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb #7 --- Chain | Description A B C D | No description available Chain information for TP53_tetramer_relaxed_rank_004_alphafold2_multimer_v3_model_1_seed_000.pdb #8 --- Chain | Description A B C D | No description available Chain information for TP53_tetramer_relaxed_rank_005_alphafold2_multimer_v3_model_3_seed_000.pdb #9 --- Chain | Description A B C D | No description available Chain information for 7w9v #10.1 --- Chain | Description | UniProt A E | Histone H3.1 | H31_HUMAN 1-135 B F | Histone H4 | H4_HUMAN 0-102 C G | Histone H2A type 1-B/E | H2A1B_HUMAN 0-129 D H | Histone H2B type 1-J | H2B1J_HUMAN 0-125 I | DNA (145-MER) | J | DNA (145-MER) | K | Histone acetyltransferase p300 | EP300_HUMAN 1035-1519 1581-1720 > hide #!10 models > hide #!10.1 models > show #!2 models > select add #2 20101 atoms, 21060 bonds, 374 pseudobonds, 1790 residues, 4 models selected > select subtract #2 1555 atoms, 1590 bonds, 198 residues, 1 model selected > select #2~/K Expected an objects specifier or a keyword > select #2 18546 atoms, 19470 bonds, 374 pseudobonds, 1592 residues, 3 models selected > select #2/A-J 14034 atoms, 14836 bonds, 372 pseudobonds, 1041 residues, 2 models selected > hide #2/A-J > select #5/A 6036 atoms, 6120 bonds, 393 residues, 1 model selected > select #5/A:1-95 1380 atoms, 1409 bonds, 95 residues, 1 model selected > select clear > undo > select #5/A-D:1-95 5520 atoms, 5636 bonds, 380 residues, 1 model selected > hide #5 models > show #6 models > show #5 models > hide #6 models > show #6 models > mmaker #6 to #1/K-N 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 7XZX.pdb, chain M (#1) with TP53_tetramer_relaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb, chain B (#6), sequence alignment score = 1029.7 RMSD between 195 pruned atom pairs is 0.258 angstroms; (across all 198 pairs: 0.405) > hide #1 models > show #1 models > select up 6356 atoms, 6488 bonds, 436 residues, 1 model selected > select up 24144 atoms, 24480 bonds, 1572 residues, 1 model selected > select up 202239 atoms, 206444 bonds, 14074 residues, 10 models selected > select up 202239 atoms, 206444 bonds, 14074 residues, 10 models selected > select up 202239 atoms, 206444 bonds, 14074 residues, 10 models selected > select up 202239 atoms, 206444 bonds, 14074 residues, 10 models selected > select up 202239 atoms, 206444 bonds, 14074 residues, 10 models selected > select down 24144 atoms, 24480 bonds, 1572 residues, 1 model selected > select down 6356 atoms, 6488 bonds, 436 residues, 1 model selected > select down 5520 atoms, 5636 bonds, 380 residues, 1 model selected > select down 5520 atoms, 5636 bonds, 380 residues, 1 model selected > select down 5520 atoms, 5636 bonds, 380 residues, 1 model selected > select down 5520 atoms, 5636 bonds, 380 residues, 1 model selected > select down 5520 atoms, 5636 bonds, 380 residues, 1 model selected > select down 5520 atoms, 5636 bonds, 380 residues, 1 model selected > select down 5520 atoms, 5636 bonds, 380 residues, 1 model selected > select down 5520 atoms, 5636 bonds, 380 residues, 1 model selected > select down 5520 atoms, 5636 bonds, 380 residues, 1 model selected > select down 5520 atoms, 5636 bonds, 380 residues, 1 model selected > select down 5520 atoms, 5636 bonds, 380 residues, 1 model selected > select down 5520 atoms, 5636 bonds, 380 residues, 1 model selected > select down 5520 atoms, 5636 bonds, 380 residues, 1 model selected > select down 5520 atoms, 5636 bonds, 380 residues, 1 model selected > show #1/K-N > select up 6356 atoms, 6488 bonds, 436 residues, 1 model selected > mmaker #6/B to #1/K 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 7XZX.pdb, chain K (#1) with TP53_tetramer_relaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb, chain B (#6), sequence alignment score = 1026.7 RMSD between 198 pruned atom pairs is 0.252 angstroms; (across all 198 pairs: 0.252) > mmaker #6/A to #1/K 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 7XZX.pdb, chain K (#1) with TP53_tetramer_relaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb, chain A (#6), sequence alignment score = 1012.3 RMSD between 198 pruned atom pairs is 0.232 angstroms; (across all 198 pairs: 0.232) > hide #5 models > hide #6 models > show #7 models > mmaker #7/A to #1/K 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 7XZX.pdb, chain K (#1) with TP53_tetramer_relaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb, chain A (#7), sequence alignment score = 1012.3 RMSD between 198 pruned atom pairs is 0.269 angstroms; (across all 198 pairs: 0.269) > hide #7 models > show #8 models > mmaker #8/A to #1/K 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 7XZX.pdb, chain K (#1) with TP53_tetramer_relaxed_rank_004_alphafold2_multimer_v3_model_1_seed_000.pdb, chain A (#8), sequence alignment score = 1009.3 RMSD between 198 pruned atom pairs is 0.334 angstroms; (across all 198 pairs: 0.334) > mmaker #8/B to #1/K 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 7XZX.pdb, chain K (#1) with TP53_tetramer_relaxed_rank_004_alphafold2_multimer_v3_model_1_seed_000.pdb, chain B (#8), sequence alignment score = 1021.3 RMSD between 198 pruned atom pairs is 0.329 angstroms; (across all 198 pairs: 0.329) > show #9 models > hide #8 models > mmaker #8/B to #1/K 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 7XZX.pdb, chain K (#1) with TP53_tetramer_relaxed_rank_004_alphafold2_multimer_v3_model_1_seed_000.pdb, chain B (#8), sequence alignment score = 1021.3 RMSD between 198 pruned atom pairs is 0.329 angstroms; (across all 198 pairs: 0.329) > mmaker #8/A to #1/K 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 7XZX.pdb, chain K (#1) with TP53_tetramer_relaxed_rank_004_alphafold2_multimer_v3_model_1_seed_000.pdb, chain A (#8), sequence alignment score = 1009.3 RMSD between 198 pruned atom pairs is 0.334 angstroms; (across all 198 pairs: 0.334) > show #8 models > mmaker #8/B to #1/K 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 7XZX.pdb, chain K (#1) with TP53_tetramer_relaxed_rank_004_alphafold2_multimer_v3_model_1_seed_000.pdb, chain B (#8), sequence alignment score = 1021.3 RMSD between 198 pruned atom pairs is 0.329 angstroms; (across all 198 pairs: 0.329) > hide #8 models > mmaker #9/B to #1/K 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 7XZX.pdb, chain K (#1) with TP53_tetramer_relaxed_rank_005_alphafold2_multimer_v3_model_3_seed_000.pdb, chain B (#9), sequence alignment score = 1026.7 RMSD between 198 pruned atom pairs is 0.279 angstroms; (across all 198 pairs: 0.279) > mmaker #9/A to #1/K 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 7XZX.pdb, chain K (#1) with TP53_tetramer_relaxed_rank_005_alphafold2_multimer_v3_model_3_seed_000.pdb, chain A (#9), sequence alignment score = 1012.3 RMSD between 198 pruned atom pairs is 0.282 angstroms; (across all 198 pairs: 0.282) > hide #1/K-N > hide #9 models > close #10 > show #5 models > select #5/A 6036 atoms, 6120 bonds, 393 residues, 1 model selected > select #5/A-B 12072 atoms, 12240 bonds, 786 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #5/A #5/B #5/C #5/D #6/A #6/B #6/C #6/D #7/A #7/B #7/C #7/D > #8/A #8/B #8/C #8/D #9/A #9/B #9/C #9/D Alignment identifier is 1 > select #5/A-D:16-25,105-107,128-130,166-168,177-180,278-293,335-357 > #6/A-D:16-25,105-107,128-130,166-168,177-180,278-293,335-357 > #7/A-D:16-25,105-107,128-130,166-168,177-180,278-293,335-357 > #8/A-D:16-25,105-107,128-130,166-168,177-180,278-293,335-357 > #9/A-D:16-25,105-107,128-130,166-168,177-180,278-293,335-357 20400 atoms, 20500 bonds, 1240 residues, 5 models selected > interfaces select #5/A contacting #5/B 37 contacting residues > color sel red > select > #5/A-D:110-113,124-127,132-135,141-146,156-163,195-197,204-207,214-219,230-236,251-258,264-274,327-333 > #6/A-D:110-113,124-127,132-135,141-146,156-163,195-197,204-207,214-219,230-236,251-258,264-274,327-333 > #7/A-D:110-113,124-127,132-135,141-146,156-163,195-197,204-207,214-219,230-236,251-258,264-274,327-333 > #8/A-D:110-113,124-127,132-135,141-146,156-163,195-197,204-207,214-219,230-236,251-258,264-274,327-333 > #9/A-D:110-113,124-127,132-135,141-146,156-163,195-197,204-207,214-219,230-236,251-258,264-274,327-333 24640 atoms, 24720 bonds, 1440 residues, 5 models selected > interfaces select #5/A contacting #5/B 37 contacting residues > interfaces select #5/A contacting #5/C 18 contacting residues > hide #5 models > show #1 > show #5 models > open /Users/brendansheehan/screenshots/scripts/get_last_shot.py Traceback (most recent call last): File ""/Users/brendansheehan/screenshots/scripts/get_last_shot.py"", line 7, in files_ = os.listdir(d) FileNotFoundError: [Errno 2] No such file or directory: '/Users/bsheehan/screenshots/' Failed opening file /Users/brendansheehan/screenshots/scripts/get_last_shot.py: Error opening python file /Users/brendansheehan/screenshots/scripts/get_last_shot.py > open /Users/brendansheehan/screenshots/scripts/get_last_shot.py Traceback (most recent call last): File ""/Users/brendansheehan/screenshots/scripts/get_last_shot.py"", line 7, in files_ = os.listdir(d) FileNotFoundError: [Errno 2] No such file or directory: '/Users/bsheehan/screenshots/' Failed opening file /Users/brendansheehan/screenshots/scripts/get_last_shot.py: Error opening python file /Users/brendansheehan/screenshots/scripts/get_last_shot.py > open /Users/brendansheehan/screenshots/scripts/png_to_txt.py Traceback (most recent call last): File ""/Users/brendansheehan/screenshots/scripts/png_to_txt.py"", line 24, in files_ = os.listdir(d) FileNotFoundError: [Errno 2] No such file or directory: '/Users/bsheehan/screenshots/' Failed opening file /Users/brendansheehan/screenshots/scripts/png_to_txt.py: Error opening python file /Users/brendansheehan/screenshots/scripts/png_to_txt.py > ui tool show ""Show Sequence Viewer"" > sequence chain #5/A #5/B #5/C #5/D #6/A #6/B #6/C #6/D #7/A #7/B #7/C #7/D > #8/A #8/B #8/C #8/D #9/A #9/B #9/C #9/D Alignment identifier is 2 > select #5/A-D:16-25,105-107,128-130,166-168,177-180,278-293,335-357 > #6/A-D:16-25,105-107,128-130,166-168,177-180,278-293,335-357 > #7/A-D:16-25,105-107,128-130,166-168,177-180,278-293,335-357 > #8/A-D:16-25,105-107,128-130,166-168,177-180,278-293,335-357 > #9/A-D:16-25,105-107,128-130,166-168,177-180,278-293,335-357 20400 atoms, 20500 bonds, 1240 residues, 5 models selected > select #5/A-D:333 96 atoms, 92 bonds, 4 residues, 1 model selected > color sel red > style sel stick Changed 96 atom styles > style sel sphere Changed 96 atom styles > show (sel-residues & sidechain) target ab > select #5/A-D:335 96 atoms, 92 bonds, 4 residues, 1 model selected > show (sel-residues & sidechain) target ab > select #5/A-D:333 96 atoms, 92 bonds, 4 residues, 1 model selected > surface hidePatches sel > style sel stick Changed 96 atom styles > select #5/A-D:337 96 atoms, 92 bonds, 4 residues, 1 model selected > show (sel-residues & sidechain) target ab > select #5/A-D:333 96 atoms, 92 bonds, 4 residues, 1 model selected > color sel red > select #5/A-D:335 96 atoms, 92 bonds, 4 residues, 1 model selected > color sel yellow > select #5/A-D:337 96 atoms, 92 bonds, 4 residues, 1 model selected > color sel blue > view sel > interfaces select #5/A-C contacting #5/D:337 0 contacting residues > select #5/D:337 : select #5/D:337 : select #5/D:337 : color (#5 & sel) lime > undo > select #5/D:337 : select #5/D:337 : select #5/D:337 : color sel lime > show (sel-residues & sidechain) target ab > select #5/A-D:16-25,105-107,128-130,166-168,177-180,278-293,335-357 > #6/A-D:16-25,105-107,128-130,166-168,177-180,278-293,335-357 > #7/A-D:16-25,105-107,128-130,166-168,177-180,278-293,335-357 > #8/A-D:16-25,105-107,128-130,166-168,177-180,278-293,335-357 > #9/A-D:16-25,105-107,128-130,166-168,177-180,278-293,335-357 20400 atoms, 20500 bonds, 1240 residues, 5 models selected > select #5/A-D:299-318 1152 atoms, 1168 bonds, 80 residues, 1 model selected > select up 2046 atoms, 2078 bonds, 137 residues, 1 model selected > select #5/D:333 : show (sel-residues & sidechain) target ab > color sel lime > select #5/D:335 : color sel lime > select #5/D:335 : select #5/D:333 : select #5/D:333 : select #5/D:335 : select #5/D:337 : select #5/D:337 : select #5/D:337 : select #5/D:337 : select #5/D:333 : select #5/D:333 : select #5/D:333 : select #5/D:333 : select #5/D:333 : select #5/A-C:326 45 atoms, 42 bonds, 3 residues, 1 model selected > select #5/A-D:326 60 atoms, 56 bonds, 4 residues, 1 model selected > color sel magenta > show (sel-residues & sidechain) target ab > select #5/A-D:335 96 atoms, 92 bonds, 4 residues, 1 model selected > select #5/A-D:3345 Nothing selected > select #5/A-D:345 56 atoms, 52 bonds, 4 residues, 1 model selected > show (sel-residues & sidechain) target ab > select #5/A-D:349 60 atoms, 56 bonds, 4 residues, 1 model selected > show (sel-residues & sidechain) target ab > open 2J0Z Summary of feedback from opening 2J0Z fetched from pdb --- note | Fetching compressed mmCIF 2j0z from http://files.rcsb.org/download/2j0z.cif 2j0z title: p53 tetramerization domain wild type [more info...] Chain information for 2j0z --- Chain | Description | UniProt 10.1/A 10.2/A 10.3/A 10.4/A 10.5/A 10.6/A 10.7/A 10.8/A 10.9/A 10.10/A 10.11/A 10.12/A 10.13/A 10.14/A 10.15/A 10.16/A 10.17/A 10.18/A 10.19/A 10.20/A 10.21/A 10.22/A 10.23/A 10.24/A 10.25/A 10.26/A 10.27/A 10.28/A 10.29/A 10.30/A 10.1/B 10.2/B 10.3/B 10.4/B 10.5/B 10.6/B 10.7/B 10.8/B 10.9/B 10.10/B 10.11/B 10.12/B 10.13/B 10.14/B 10.15/B 10.16/B 10.17/B 10.18/B 10.19/B 10.20/B 10.21/B 10.22/B 10.23/B 10.24/B 10.25/B 10.26/B 10.27/B 10.28/B 10.29/B 10.30/B 10.1/C 10.2/C 10.3/C 10.4/C 10.5/C 10.6/C 10.7/C 10.8/C 10.9/C 10.10/C 10.11/C 10.12/C 10.13/C 10.14/C 10.15/C 10.16/C 10.17/C 10.18/C 10.19/C 10.20/C 10.21/C 10.22/C 10.23/C 10.24/C 10.25/C 10.26/C 10.27/C 10.28/C 10.29/C 10.30/C 10.1/D 10.2/D 10.3/D 10.4/D 10.5/D 10.6/D 10.7/D 10.8/D 10.9/D 10.10/D 10.11/D 10.12/D 10.13/D 10.14/D 10.15/D 10.16/D 10.17/D 10.18/D 10.19/D 10.20/D 10.21/D 10.22/D 10.23/D 10.24/D 10.25/D 10.26/D 10.27/D 10.28/D 10.29/D 10.30/D | CELLULAR TUMOR ANTIGEN P53 | P53_HUMAN 326-356 > hide #!2 models > hide #5 models > hide #!10 models > show #!10 models > hide #1 models > view sel > select #10 62640 atoms, 63000 bonds, 3720 residues, 31 models selected > view sel > ui tool show ""Show Sequence Viewer"" > sequence chain #10.1/A #10.1/B #10.1/C #10.1/D #10.2/A #10.2/B #10.2/C > #10.2/D #10.3/A #10.3/B #10.3/C #10.3/D #10.4/A #10.4/B #10.4/C #10.4/D > #10.5/A #10.5/B #10.5/C #10.5/D #10.6/A #10.6/B #10.6/C #10.6/D #10.7/A > #10.7/B #10.7/C #10.7/D #10.8/A #10.8/B #10.8/C #10.8/D #10.9/A #10.9/B > #10.9/C #10.9/D #10.10/A #10.10/B #10.10/C #10.10/D #10.11/A #10.11/B > #10.11/C #10.11/D #10.12/A #10.12/B #10.12/C #10.12/D #10.13/A #10.13/B > #10.13/C #10.13/D #10.14/A #10.14/B #10.14/C #10.14/D #10.15/A #10.15/B > #10.15/C #10.15/D #10.16/A #10.16/B #10.16/C #10.16/D #10.17/A #10.17/B > #10.17/C #10.17/D #10.18/A #10.18/B #10.18/C #10.18/D #10.19/A #10.19/B > #10.19/C #10.19/D #10.20/A #10.20/B #10.20/C #10.20/D #10.21/A #10.21/B > #10.21/C #10.21/D #10.22/A #10.22/B #10.22/C #10.22/D #10.23/A #10.23/B > #10.23/C #10.23/D #10.24/A #10.24/B #10.24/C #10.24/D #10.25/A #10.25/B > #10.25/C #10.25/D #10.26/A #10.26/B #10.26/C #10.26/D #10.27/A #10.27/B > #10.27/C #10.27/D #10.28/A #10.28/B #10.28/C #10.28/D #10.29/A #10.29/B > #10.29/C #10.29/D #10.30/A #10.30/B #10.30/C #10.30/D Alignment identifier is 3 > select #10/A-D/326E 62640 atoms, 63000 bonds, 3720 residues, 30 models selected > select #10/A-D:327 2520 atoms, 2520 bonds, 120 residues, 30 models selected > show (sel-residues & sidechain) target ab > select #10/A-D/326 62640 atoms, 63000 bonds, 3720 residues, 30 models selected > select #10/A-D:326 2040 atoms, 1920 bonds, 120 residues, 30 models selected > show (sel-residues & sidechain) target ab > select #10/A-D:333 2880 atoms, 2760 bonds, 120 residues, 30 models selected > show (sel-residues & sidechain) target ab > select #10/A-D:335 2880 atoms, 2760 bonds, 120 residues, 30 models selected > show sel target ab > select #10/A-D:352 1440 atoms, 1320 bonds, 120 residues, 30 models selected > show sel target ab > select #10/A-D:337 2880 atoms, 2760 bonds, 120 residues, 30 models selected > show (sel-residues & sidechain) target ab > select #10/A-D:349 1800 atoms, 1680 bonds, 120 residues, 30 models selected > show (sel-residues & sidechain) target ab > select #10/A-D:349,352 3240 atoms, 3000 bonds, 240 residues, 30 models selected > select #10/A-D:349,352,333 6120 atoms, 5760 bonds, 360 residues, 30 models selected > select #10/A-D:349,352,335 6120 atoms, 5760 bonds, 360 residues, 30 models selected > select #10/A-D:349,352,337 6120 atoms, 5760 bonds, 360 residues, 30 models selected > select #10/A-D:349,352,335 6120 atoms, 5760 bonds, 360 residues, 30 models selected > select #10/A-D:345 1680 atoms, 1560 bonds, 120 residues, 30 models selected > show (sel-residues & sidechain) target ab > select #10/A-D:345,333 4560 atoms, 4320 bonds, 240 residues, 30 models selected > select #10/A-D:345,337 4560 atoms, 4320 bonds, 240 residues, 30 models selected > select #10/A-D:345,337,333 7440 atoms, 7080 bonds, 360 residues, 30 models selected > select #10/A-D:345,337,33 4560 atoms, 4320 bonds, 240 residues, 30 models selected > select #10/A-D:345,337,349 6360 atoms, 6000 bonds, 360 residues, 30 models selected > sell Unknown command: sell > select 264879 atoms, 269444 bonds, 436 pseudobonds, 17794 residues, 45 models selected > select #1 19270 atoms, 20343 bonds, 1896 residues, 1 model selected > hide #!10 models > show #1 models > show #!2 models > show #!3 models > show #!4 models > hide #!4 models > hide #!3 models > hide #!2 models > select #1 19270 atoms, 20343 bonds, 1896 residues, 1 model selected > view sel > show #!2 models > show #5 models > hide #5 models > open > /Users/brendansheehan/python/alphafold/TERF2_dimer/output/TERF2_dimer_relaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb Chain information for TERF2_dimer_relaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb #11 --- Chain | Description A B | No description available > open > /Users/brendansheehan/python/alphafold/TERF2_dimer/output/TERF2_dimer_relaxed_rank_002_alphafold2_multimer_v3_model_3_seed_000.pdb Chain information for TERF2_dimer_relaxed_rank_002_alphafold2_multimer_v3_model_3_seed_000.pdb #12 --- Chain | Description A B | No description available > open > /Users/brendansheehan/python/alphafold/TERF2_dimer/output/TERF2_dimer_relaxed_rank_002_alphafold2_multimer_v3_model_3_seed_000.pdb Chain information for TERF2_dimer_relaxed_rank_002_alphafold2_multimer_v3_model_3_seed_000.pdb #13 --- Chain | Description A B | No description available > open > /Users/brendansheehan/python/alphafold/TERF2_dimer/output/TERF2_dimer_relaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb Chain information for TERF2_dimer_relaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb #14 --- Chain | Description A B | No description available > hide #11 models > show #11 models > hide #12 models > hide #13 models > hide #14 models > view sel > hide #1 models > hide #!2 models > select subtract #1 Nothing selected > select add #11 16780 atoms, 16930 bonds, 1084 residues, 1 model selected No model chosen to save relative to > hide #11 models > select subtract #11 Nothing selected > show #1 models > show #!2 models > show #5 models > select add #5 24144 atoms, 24480 bonds, 1572 residues, 1 model selected > view sel > hide #!2 models > show #!2 models > select #1/K-N 6220 atoms, 6360 bonds, 792 residues, 1 model selected > hide #1/K-N > show #1/K-N > hide #5 models Unsupported scale factor (0.000000) detected on Display0 QPainter::begin: Paint device returned engine == 0, type: 3 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 83 OpenGL renderer: Apple M2 Max OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,6 Model Number: MNWE3LL/A Chip: Apple M2 Max Total Number of Cores: 12 (8 performance and 4 efficiency) Memory: 32 GB System Firmware Version: 8419.80.7 OS Loader Version: 8419.80.7 Software: System Software Overview: System Version: macOS 13.2.1 (22D68) Kernel Version: Darwin 22.3.0 Time since boot: 20 days, 22 hours, 15 minutes Graphics/Displays: Apple M2 Max: Chipset Model: Apple M2 Max Type: GPU Bus: Built-In Total Number of Cores: 38 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Crestron: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Main Display: Yes Mirror: On Mirror Status: Master Mirror Online: Yes Rotation: Supported Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Mirror: On Mirror Status: Hardware Mirror Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 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: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 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: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 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: 1.1.1 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: 1.2.1 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-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 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: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 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: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 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: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.2.22 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 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: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0 }}} " defect closed normal Window Toolkit can't reproduce Tom Goddard all ChimeraX