id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15089 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-13.5.1-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: Segmentation fault Thread 0x0000700014efe000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00007ff844f9d700 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 463 in new_pseudobond File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/clashes/cmd.py"", line 230 in _cmd File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/clashes/cmd.py"", line 54 in cmd_contacts File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2908 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py"", line 49 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/clashes/tool.py"", line 59 in run_command File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 918 in init File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1069 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, 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: { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""0cecb27891dff50f26acb7edcbafa325cb79cf67"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""60186475825c62000ccf5450"", ""factorPackIds"" : { }, ""deploymentId"" : 240000069 }, { ""rolloutId"" : ""63582c5f8a53461413999550"", ""factorPackIds"" : { }, ""deploymentId"" : 240000002 } ], ""experiments"" : [ ] } } ===== 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/kelvinchung/Downloads/BPHM4142_Lab1_hLcn2_758d7/BPHM4142_Lab1_hLcn2_758d7_unrelaxed_rank_004_alphafold2_ptm_model_1_seed_000.pdb > format pdb Chain information for BPHM4142_Lab1_hLcn2_758d7_unrelaxed_rank_004_alphafold2_ptm_model_1_seed_000.pdb #1 --- Chain | Description A | No description available > hide target m > show #1 models > close > open ""/Users/kelvinchung/Desktop/BPHM Year 4 Sem 2 Files/BPHM4142 Mol. Pharm > Document/Lab 3 document/Heavy_Light_chains_rank_1.pdb"" Chain information for Heavy_Light_chains_rank_1.pdb #1 --- Chain | Description A | No description available B | No description available > open ""/Users/kelvinchung/Desktop/BPHM Year 4 Sem 2 Files/BPHM4142 Mol. Pharm > Document/Lab 2 document/hLcn2.pdb"" Chain information for hLcn2.pdb #2 --- Chain | Description A | No description available > open ""/Users/kelvinchung/Desktop/BPHM Year 4 Sem 2 Files/BPHM4142 Mol. Pharm > Document/Lab 2 document/C87A.pdb"" Chain information for C87A.pdb #3 --- Chain | Description A | No description available > open ""/Users/kelvinchung/Desktop/BPHM Year 4 Sem 2 Files/BPHM4142 Mol. Pharm > Document/Lab 2 document/R81E.pdb"" Chain information for R81E.pdb #4 --- Chain | Description A | No description available > hide #2 models > hide #3 models > hide #4 models > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A Alignment identifier is 1/A > save ""/Users/kelvinchung/Desktop/BPHM Year 4 Sem 2 Files/BPHM4142 Mol. Pharm > Document/Lab 3 document/BPHM4142_Lab 3_Proteins.cxs"" > set bgColor white > open ""/Users/kelvinchung/Desktop/BPHM Year 4 Sem 2 Files/BPHM4142 Mol. Pharm > Document/Lab 3 document/heavy_rank_1.pdb"" Chain information for heavy_rank_1.pdb #5 --- Chain | Description A | No description available > open ""/Users/kelvinchung/Desktop/BPHM Year 4 Sem 2 Files/BPHM4142 Mol. Pharm > Document/Lab 3 document/light_rank_1.pdb"" Chain information for light_rank_1.pdb #6 --- Chain | Description A | No description available > ui tool show ""Show Sequence Viewer"" > select clear > ui tool show Matchmaker > matchmaker #5-6 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 Heavy_Light_chains_rank_1.pdb, chain A (#1) with heavy_rank_1.pdb, chain A (#5), sequence alignment score = 594.4 RMSD between 117 pruned atom pairs is 0.555 angstroms; (across all 123 pairs: 1.086) Matchmaker Heavy_Light_chains_rank_1.pdb, chain B (#1) with light_rank_1.pdb, chain A (#6), sequence alignment score = 536.7 RMSD between 107 pruned atom pairs is 0.233 angstroms; (across all 107 pairs: 0.233) > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A #5/A Alignment identifier is 1 > sequence chain #1/B #6/A Alignment identifier is 2 > hide #5 models > show #5 models > hide #5 models > hide #6 models > show #5 models > hide #5 models > show #5 models > hide #5 models > show #6 models > hide #6 models > surface #1 > surface hidePatches #1 > select #1/A:13-14 #5/A:13-14 32 atoms, 32 bonds, 4 residues, 2 models selected > select #1/A:13-17 #5/A:13-17 60 atoms, 60 bonds, 10 residues, 2 models selected 1 [ID: 1] region 2 chains [13-17] RMSD: 0.169 > select #1/A:26-27 #5/A:26-27 26 atoms, 26 bonds, 4 residues, 2 models selected > select #1/A:26-31 #5/A:26-31 74 atoms, 74 bonds, 12 residues, 2 models selected 1 [ID: 1] region 2 chains [26-31] RMSD: 3.242 > surface (#!1 & sel) > undo > select clear > surface #1 > cartoon hide #1 > select clear > surface hidePatches #1 > cartoon #1 > hide #!1 models > show #2 models > surface #2 > surface hidePatches #2 > sel: 81, 87 Unknown command: sel: 81, 87 > sel: 81 Unknown command: sel: 81 > sel:81, 87 Unknown command: sel:81, 87 > sel:81 Unknown command: sel:81 > sel: 81 Unknown command: sel: 81 > select: 81 Unknown command: select: 81 > select: 81 Unknown command: select: 81 > sel: /81 Unknown command: sel: /81 > select :81 61 atoms, 54 bonds, 7 residues, 6 models selected > select clear > select :81,87 118 atoms, 106 bonds, 14 residues, 6 models selected > select clear > surface #2 > select :81,87 118 atoms, 106 bonds, 14 residues, 6 models selected > hide #!2 models > show #!1 models > select clear > hide #!1 models > show #!1 models > hide #!1 models > show #3 models > show #4 models > hide #4 models > show #4 models > hide #4 models > show #4 models > hide #4 models > show #4 models > hide #4 models > select clear > select :1 61 atoms, 54 bonds, 7 residues, 6 models selected > select clear > ui tool show ""Show Sequence Viewer"" > sequence chain #3/A Alignment identifier is 3/A > select #3/A:81-82 18 atoms, 17 bonds, 2 residues, 1 model selected > select #3/A:81-90 72 atoms, 74 bonds, 10 residues, 1 model selected > color sel red > color sel orange > color sel forest green > color sel blue > color sel orange red > select clear > select #3/A:92 11 atoms, 11 bonds, 1 residue, 1 model selected > select #3/A:92-101 80 atoms, 82 bonds, 10 residues, 1 model selected > color sel forest green > color sel orange > undo > color sel forest green > select clear > surface #3 > surface hidePatches #3 > select #3/A:92-93 18 atoms, 18 bonds, 2 residues, 1 model selected > select #3/A:92-101 80 atoms, 82 bonds, 10 residues, 1 model selected > surface (#!3 & sel) > select #3/A:81 11 atoms, 10 bonds, 1 residue, 1 model selected > select #3/A:81-89 68 atoms, 70 bonds, 9 residues, 1 model selected > select #3/A:81-82 18 atoms, 17 bonds, 2 residues, 1 model selected > select #3/A:81-90 72 atoms, 74 bonds, 10 residues, 1 model selected > surface (#!3 & sel) > select clear > select :81-90, 92-101 1098 atoms, 1122 bonds, 140 residues, 6 models selected > surface (#!3 & sel) > surface hidePatches (#!3 & sel) > select :81-90, 92-101 1098 atoms, 1122 bonds, 140 residues, 6 models selected > select add #2 2396 atoms, 2453 bonds, 298 residues, 10 models selected > select subtract #2 945 atoms, 965 bonds, 120 residues, 9 models selected > select add #1 2345 atoms, 2397 bonds, 310 residues, 8 models selected > select subtract #1 624 atoms, 638 bonds, 80 residues, 7 models selected > select add #4 1922 atoms, 1969 bonds, 238 residues, 5 models selected > select subtract #4 473 atoms, 483 bonds, 60 residues, 4 models selected > select add #5 1226 atoms, 1255 bonds, 163 residues, 4 models selected > select subtract #5 308 atoms, 317 bonds, 40 residues, 3 models selected > select add #6 955 atoms, 977 bonds, 127 residues, 3 models selected > select subtract #6 152 atoms, 156 bonds, 20 residues, 2 models selected > select add #3 1450 atoms, 1487 bonds, 178 residues, 2 models selected > select subtract #3 1 model selected > select add #3 1450 atoms, 1487 bonds, 178 residues, 1 model selected > select subtract #3 1 model selected > select :81-90, 92-101 1098 atoms, 1122 bonds, 140 residues, 6 models selected > surface (#!3 & sel) > select :81-90 558 atoms, 568 bonds, 70 residues, 6 models selected > select clear > surface hidePatches #3 > select :81-90 558 atoms, 568 bonds, 70 residues, 6 models selected > surface (#!3 & sel) > color (#!3 & sel) orange red > select clear > select :92-101 540 atoms, 554 bonds, 70 residues, 6 models selected > surface (#!3 & sel) > select clear > surface hidePatches #3 > surface #3 > select :92-101 540 atoms, 554 bonds, 70 residues, 6 models selected > color (#!3 & sel) forest green > hide #!3 models > show #4 models > select :1 61 atoms, 54 bonds, 7 residues, 6 models selected > select clear > select :71-90 1165 atoms, 1193 bonds, 140 residues, 6 models selected > color (#4 & sel) orange red > select clear > select : 95-105 567 atoms, 576 bonds, 77 residues, 6 models selected > color (#4 & sel) forest green > color (#4 & sel) blue > select clear > surface #4 > surface hidePatches #4 > surface #4 > select : 95-105 567 atoms, 576 bonds, 77 residues, 6 models selected > color (#!4 & sel) blue > select clear > select : 71-90 1165 atoms, 1193 bonds, 140 residues, 6 models selected > color (#!4 & sel) orange > color (#!4 & sel) orange red > hide #!4 models > show #!1 models > select clear > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A #5/A Alignment identifier is 1 > sequence chain #1/B #6/A Alignment identifier is 2 > select #1/A:122-123 #5/A:122-123 24 atoms, 22 bonds, 4 residues, 2 models selected > select #1/A:122-123 #5/A:122-123 24 atoms, 22 bonds, 4 residues, 2 models selected 1 [ID: 1] region 2 chains [122-123] RMSD: 2.951 > select clear > select #5/A 918 atoms, 938 bonds, 123 residues, 1 model selected > select clear > select #1/A 918 atoms, 938 bonds, 123 residues, 1 model selected > color (#!1 & sel) orange > select clear > select #1/B 803 atoms, 821 bonds, 107 residues, 1 model selected > color (#!1 & sel) cyan > select clear > select strand 3505 atoms, 3540 bonds, 424 residues, 6 models selected > color (#!1 & sel) magenta > select clear > select #1/A:104 #5/A:104 16 atoms, 14 bonds, 2 residues, 2 models selected > select #1/A:104-116 #5/A:104-116 216 atoms, 228 bonds, 26 residues, 2 models selected 1 [ID: 1] region 2 chains [104-116] RMSD: 1.927 > select clear > surface #1 > surface hidePatches #1 > select #1/A:1 #5/A:1 18 atoms, 16 bonds, 2 residues, 2 models selected > select #1/A:1-2 #5/A:1-2 32 atoms, 30 bonds, 4 residues, 2 models selected 1 [ID: 1] region 2 chains [1-2] RMSD: 0.996 > select clear > select #1/A:122 #5/A:122 12 atoms, 10 bonds, 2 residues, 2 models selected > select #1/A:122-123 #5/A:122-123 24 atoms, 22 bonds, 4 residues, 2 models selected 1 [ID: 1] region 2 chains [122-123] RMSD: 2.951 > select clear > hide #!1 models > show #5 models > show #6 models > surface #5-6 > surface hidePatches #5-6 > surface #5-6 > hide #!5 models > hide #!6 models > show #!1 models > hide #!1 models > show #!5 models > show #!6 models > hide #!6 models > show #!6 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > hide #!6 models > show #!1 models > select #1/A:122 #5/A:122 12 atoms, 10 bonds, 2 residues, 2 models selected > select #1/A:122-123 #5/A:122-123 24 atoms, 22 bonds, 4 residues, 2 models selected 1 [ID: 1] region 2 chains [122-123] RMSD: 2.951 > select clear > surface #1 > surface hidePatches #1 > surface #1 > surface hidePatches #1 > surface #1 > surface hidePatches #1 > surface #1 > surface hidePatches #1 > select #1/A:28 #5/A:28 12 atoms, 10 bonds, 2 residues, 2 models selected > select #1/A:28-35 #5/A:28-35 114 atoms, 114 bonds, 16 residues, 2 models selected 1 [ID: 1] region 2 chains [28-35] RMSD: 2.803 > color (#!1 & sel) red > select #1/A:55-56 #5/A:55-56 20 atoms, 18 bonds, 4 residues, 2 models selected > select #1/A:55-60 #5/A:55-60 60 atoms, 58 bonds, 12 residues, 2 models selected 1 [ID: 1] region 2 chains [55-60] RMSD: 0.266 > color (#!1 & sel) red > select clear > select strand 3505 atoms, 3540 bonds, 424 residues, 6 models selected > select clear > select strand 3505 atoms, 3540 bonds, 424 residues, 6 models selected > color (#!1 & sel) light gray > color (#!1 & sel) lime > color (#!1 & sel) cornflower blue > color (#!1 & sel) lime > color (#!1 & sel) medium blue > color (#!1 & sel) forest green > select clear > select #1/A:104 #5/A:104 16 atoms, 14 bonds, 2 residues, 2 models selected > select #1/A:104-108 #5/A:104-108 72 atoms, 76 bonds, 10 residues, 2 models selected 1 [ID: 1] region 2 chains [104-108] RMSD: 2.746 > color (#!1 & sel) red > select #1/B:26-27 #6/A:26-27 30 atoms, 28 bonds, 4 residues, 2 models selected > select #1/B:26-32 #6/A:26-32 106 atoms, 106 bonds, 14 residues, 2 models selected 2 [ID: 2] region chains A,B [26-32] RMSD: 0.172 > color (#!1 & sel) red > select #1/B:99 #6/A:99 8 atoms, 6 bonds, 2 residues, 2 models selected > select #1/B:91-99 #6/A:91-99 126 atoms, 130 bonds, 18 residues, 2 models selected 2 [ID: 2] region chains A,B [91-99] RMSD: 0.390 > color (#!1 & sel) red > select #1/B:49 #6/A:49 24 atoms, 24 bonds, 2 residues, 2 models selected > select #1/B:49-61 #6/A:49-61 184 atoms, 186 bonds, 26 residues, 2 models selected 2 [ID: 2] region chains A,B [49-61] RMSD: 0.261 > color (#!1 & sel) red > select strand 3505 atoms, 3540 bonds, 424 residues, 6 models selected > select clear > hide #!1 models > open ""/Users/kelvinchung/Desktop/BPHM Year 4 Sem 2 Files/BPHM4142 Mol. Pharm > Document/Lab 3 document/BPHM4142 Lab 3 Report.docx"" Unrecognized file suffix '.docx' > open ""/Users/kelvinchung/Desktop/BPHM Year 4 Sem 2 Files/BPHM4142 Mol. Pharm > Document/Lab 3 document/Antibody_hLcn2_rank_1.pdb"" Chain information for Antibody_hLcn2_rank_1.pdb #7 --- Chain | Description A | No description available B | No description available C | No description available > ui tool show Contacts > help help:user/tools/clashes.html > alphafold contacts /A toResidues /B distance 5 Interface PAE pseudobonds can only be computed for a single structure, got 7. > ui tool show Contacts > hide #!1 target m > hide #!2 target m > hide #!3 target m > hide #!4 target m > hide #!5 target m > hide #!6 target m > show #7 target m > alphafold contacts /A toResidues /B distance 5 Interface PAE pseudobonds can only be computed for a single structure, got 7. > hide #7 models > show #!1 models > save ""/Users/kelvinchung/Desktop/BPHM Year 4 Sem 2 Files/BPHM4142 Mol. Pharm > Document/Lab 3 document/BPHM4142 Lab 3 Antibody CDR prediction.pdb"" models > #1 relModel #1 > show #!2 models > show #!3 models > hide #!3 models > hide #!2 models > close #1 > close #2 > close #3 > close #4 > close #5 > close #6 > show #7 models > alphafold contacts /A toResidues /B distance 5 Structure Antibody_hLcn2_rank_1.pdb #7 does not have PAE data opened > ui tool show Contacts > ui tool show ""Selection Inspector"" > ui tool show ""AlphaFold Error Plot"" > help help:user/tools/alphafold.html#pae Must choose path to predicted aligned file > ui tool show ""AlphaFold Error Plot"" > help help:user/tools/alphafold.html#pae > surface > surface hidePatches > alphafold contacts /A toResidues /B Structure Antibody_hLcn2_rank_1.pdb #7 does not have PAE data opened > ui tool show Contacts > ui tool show AlphaFold Must choose path to predicted aligned file > close #7 > open ""/Users/kelvinchung/Desktop/BPHM Year 4 Sem 2 Files/BPHM4142 Mol. Pharm > Document/Lab 3 document/Antibody_hLcn2_rank_1.pdb"" Chain information for Antibody_hLcn2_rank_1.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available > ui tool show ""AlphaFold Error Plot"" > alphafold pae #1 uniprotId Missing ""uniprotId"" keyword's argument > ui tool show Contacts > help help:user/tools/clashes.html > contacts sel distanceOnly 4.9999999999999964 intraModel false intraMol false > ignoreHiddenModels true showDist true reveal true No atoms match given atom specifier > ui tool show Contacts > alphafold contacts /A toResidues /B Structure Antibody_hLcn2_rank_1.pdb #1 does not have PAE data opened > alphafold contacts /A toResidues /B Structure Antibody_hLcn2_rank_1.pdb #1 does not have PAE data opened > alphafold contacts /A toResidues /B Structure Antibody_hLcn2_rank_1.pdb #1 does not have PAE data opened > alphafold contacts /A toResidues /B Structure Antibody_hLcn2_rank_1.pdb #1 does not have PAE data opened > alphafold contacts /A toResidues /B Structure Antibody_hLcn2_rank_1.pdb #1 does not have PAE data opened > alphafold contacts /A toResidues /B Structure Antibody_hLcn2_rank_1.pdb #1 does not have PAE data opened > alphafold contacts /A toResidues /B Structure Antibody_hLcn2_rank_1.pdb #1 does not have PAE data opened > select /A 918 atoms, 938 bonds, 123 residues, 1 model selected > select /B 803 atoms, 821 bonds, 107 residues, 1 model selected > alphafold contacts /C toResidues /B Structure Antibody_hLcn2_rank_1.pdb #1 does not have PAE data opened > select clear > ui tool show ""AlphaFold Error Plot"" File ""iojoih"" does not exist. > help help:user/tools/alphafold.html#pae > select clear > select /C 1451 atoms, 1488 bonds, 178 residues, 1 model selected > hide sel cartoons > show sel atoms > hide sel atoms > show sel cartoons > hide sel cartoons > select clear > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > sequence chain /B Alignment identifier is 1/B > select clear > select /C 1451 atoms, 1488 bonds, 178 residues, 1 model selected > show sel cartoons > hide sel cartoons > select /A:122 6 atoms, 5 bonds, 1 residue, 1 model selected > select /A:122-123 12 atoms, 11 bonds, 2 residues, 1 model selected > select clear > select /C 1451 atoms, 1488 bonds, 178 residues, 1 model selected > show sel cartoons > hide sel cartoons > select clear > select /A:122-123 12 atoms, 11 bonds, 2 residues, 1 model selected > select /A:122-123 12 atoms, 11 bonds, 2 residues, 1 model selected > select clear > select /C 1451 atoms, 1488 bonds, 178 residues, 1 model selected > show sel cartoons > select clear > ui tool show Contacts > contacts sel distanceOnly 5.0 interModel false ignoreHiddenModels true > showDist true reveal true No atoms match given atom specifier > ui tool show Contacts > contacts sel distanceOnly 5.0 intraRes true ignoreHiddenModels true showDist > true reveal true No atoms match given atom specifier > ui tool show Contacts > contacts sel intraRes true ignoreHiddenModels true showDist true reveal true No atoms match given atom specifier > ui tool show Contacts > contacts sel intraRes true ignoreHiddenModels true showDist true reveal true No atoms match given atom specifier > select /C 1451 atoms, 1488 bonds, 178 residues, 1 model selected > ui tool show Contacts > contacts sel distanceOnly 5.0 intraRes true ignoreHiddenModels true showDist > true reveal true 9784 distances ===== 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 ATI-4.14.1 OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine OpenGL vendor: ATI Technologies 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: MacBookPro16,1 Processor Name: 8-Core Intel Core i9 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 1968.140.7.0.0 (iBridge: 20.16.6072.0.0,0) OS Loader Version: 577.140.2~15 Software: System Software Overview: System Version: macOS 13.5.1 (22G90) Kernel Version: Darwin 22.6.0 Time since boot: 12日5小時57分鐘 Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0002 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 AMD Radeon Pro 5500M: Chipset Model: AMD Radeon Pro 5500M Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0040 ROM Revision: 113-D3220E-190 VBIOS Version: 113-D32206U1-020 Option ROM Version: 113-D32206U1-020 EFI Driver Version: 01.A1.190 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 3072 x 1920 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal 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-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-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 Core duplicate Tom Goddard all ChimeraX