id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16418 Crash opening mmCIF chimerax-bug-report@… Greg Couch "{{{ The following bug report has been submitted: Platform: macOS-14.6.1-x86_64-i386-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x0000700007cc8000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00007ff84857cdc0 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mmcif/__init__.py"", line 54 in open File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 484 in remember_data_format File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 513 in collated_open File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 213 in provider_open File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 3213 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 131 in cmd_open File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 3213 in run File ""/Applications/ChimeraX-1.8.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-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 2075 in _open_dropped_file File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 278 in event File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, 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""648c94d4ebdf9e3e398fa708"", ""factorPackIds"" : { ""SIRI_UNDERSTANDING_NL_OVERRIDES"" : ""65a8104b6712a43e7922cab8"" }, ""deploymentId"" : 240000171 } ], ""experiments"" : [ { ""treatmentId"" : ""45f4e2a5-551b-4bc2-a2dc-19c244dda8f8"", ""experimentId"" : ""6643969b3099cf28e049862f"", ""deploymentId"" : 400000007 } ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/stellabrenman/Downloads/ChimeraX/AlphaFold/Q13951_ELOB/best_model.pdb > format pdb Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available > close > open ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q13033/Q13033_CTTNBP2NL/fold_q13033_cttnbp2nl_model_0.cif"" Chain information for fold_q13033_cttnbp2nl_model_0.cif #1 --- Chain | Description A | . B | . > set bgColor white > select /b 4915 atoms, 4995 bonds, 639 residues, 1 model selected > select /A 6137 atoms, 6266 bonds, 797 residues, 1 model selected > color sel hot pink > select /A:1,797 /B:1,639 31 atoms, 27 bonds, 4 residues, 1 model selected > label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code} > label height 3 > ui tool show ""AlphaFold Error Plot"" > alphafold pae #1 file ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q13033/Q13033_CTTNBP2NL/fold_q13033_cttnbp2nl_full_data_0.json"" > alphafold contacts /A toAtoms /B distance 8 Found 1866 residue or atom pairs within distance 8 > save /Users/stellabrenman/Desktop/image2.png supersample 3 > close > open ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q13033/Q13033-2_CTTNBP2NL/fold_q13033_2_cttnbp2nl_model_0.cif"" Chain information for fold_q13033_2_cttnbp2nl_model_0.cif #1 --- Chain | Description A | . B | . > select /A 5473 atoms, 5593 bonds, 713 residues, 1 model selected > color sel hot pink > select /A:1,713 /B:1,639 31 atoms, 27 bonds, 4 residues, 1 model selected > label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code} > label height 3 > alphafold pae #1 file ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q13033/Q13033-2_CTTNBP2NL/fold_q13033_2_cttnbp2nl_full_data_0.json"" > alphafold contacts /A toAtoms /B distance 8 Found 1224 residue or atom pairs within distance 8 > save /Users/stellabrenman/Desktop/image3.png supersample 3 > close > open ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q13033/Q13033_STRN/fold_q13033_strn_model_0.cif"" Chain information for fold_q13033_strn_model_0.cif #1 --- Chain | Description A | . B | . > select /A 6137 atoms, 6266 bonds, 797 residues, 1 model selected > color sel hot pink > close > open ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q13033/Q13033-2_STRN/fold_q13033_2_strn_model_0.cif"" Chain information for fold_q13033_2_strn_model_0.cif #1 --- Chain | Description A | . B | . > select /b 6059 atoms, 6178 bonds, 780 residues, 1 model selected > select /A 5473 atoms, 5593 bonds, 713 residues, 1 model selected > color sel hot pink > select /A:1,713 /B:1,780 32 atoms, 28 bonds, 4 residues, 1 model selected > label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code} > label height 3 > alphafold pae #1 file ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q13033/Q13033-2_STRN/fold_q13033_2_strn_full_data_0.json"" > alphafold contacts /A toAtoms /B distance 8 Found 907 residue or atom pairs within distance 8 > save /Users/stellabrenman/Desktop/image1.png supersample 3 > close > open ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q13561/Q13561_CCDC172/fold_q13561_ccdc172_model_0.cif"" Chain information for fold_q13561_ccdc172_model_0.cif #1 --- Chain | Description A | . B | . > select /b 2173 atoms, 2195 bonds, 258 residues, 1 model selected > select /A 3104 atoms, 3142 bonds, 401 residues, 1 model selected > color sel hot pink > select /A:1,401 /B:1,258 36 atoms, 32 bonds, 4 residues, 1 model selected > label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code} > label height 3 > alphafold pae #1 file ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q13561/Q13561_CCDC172/fold_q13561_ccdc172_full_data_0.json"" > alphafold contacts /A toAtoms /B distance 8 Found 854 residue or atom pairs within distance 8 > save /Users/stellabrenman/Desktop/image1.png supersample 3 > close > open ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q13561/Q13561-3_CCDC172/fold_q13561_3_ccdc172_model_0.cif"" Chain information for fold_q13561_3_ccdc172_model_0.cif #1 --- Chain | Description A | . B | . > select /A 3121 atoms, 3159 bonds, 403 residues, 1 model selected > color sel hot pink > select /A:1,403 /B:1,258 36 atoms, 32 bonds, 4 residues, 1 model selected > label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code} > label height 3 > alphafold pae #1 file ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q13561/Q13561-3_CCDC172/fold_q13561_3_ccdc172_full_data_0.json"" > alphafold contacts /A toAtoms /B distance 8 Found 814 residue or atom pairs within distance 8 > save /Users/stellabrenman/Desktop/image2.png supersample 3 > close > open ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q14978/Q14978_ARRB1/fold_q14978_p49407_model_0.cif"" Chain information for fold_q14978_p49407_model_0.cif #1 --- Chain | Description A | . B | . > select /b 3312 atoms, 3379 bonds, 418 residues, 1 model selected > select /A 5166 atoms, 5245 bonds, 699 residues, 1 model selected > color sel hot pink > select /A:1,699 /B:1,418 38 atoms, 34 bonds, 4 residues, 1 model selected > label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code} > label height 3 > alphafold pae #1 file ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q14978/Q14978_ARRB1/fold_q14978_p49407_full_data_0.json"" > alphafold contacts /A toAtoms /B distance 8 Found 111 residue or atom pairs within distance 8 > save /Users/stellabrenman/Desktop/image1.png supersample 3 > close > open ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q14978/Q14978-2_ARRB1/fold_q14978_2_p49407_model_0.cif"" Chain information for fold_q14978_2_p49407_model_0.cif #1 --- Chain | Description A | . B | . > select /A 5247 atoms, 5328 bonds, 709 residues, 1 model selected > color sel hot pink > select /A:1,709 /B:1,418 38 atoms, 34 bonds, 4 residues, 1 model selected > label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code} > label height 3 > alphafold pae #1 file ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q14978/Q14978-2_ARRB1/fold_q14978_2_p49407_full_data_0.json"" > alphafold contacts /A toAtoms /B distance 8 Found 87 residue or atom pairs within distance 8 > save /Users/stellabrenman/Desktop/image2.png supersample 3 > close > open ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q14978/Q14978_ARRB2/fold_q14978_p32121_model_0.cif"" Chain information for fold_q14978_p32121_model_0.cif #1 --- Chain | Description A | . B | . > select /b 3247 atoms, 3322 bonds, 409 residues, 1 model selected > select /A 5166 atoms, 5245 bonds, 699 residues, 1 model selected > color sel hot pink > select /A:1,699 /B:1,409 33 atoms, 29 bonds, 4 residues, 1 model selected > label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code} > label height 3 > alphafold pae #1 file ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q14978/Q14978_ARRB2/fold_q14978_p32121_full_data_0.json"" > alphafold contacts /A toAtoms /B distance 8 Found 136 residue or atom pairs within distance 8 > save /Users/stellabrenman/Desktop/image1.png supersample 3 > close > open ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q14978/Q14978-2_ARRB2/fold_q14978_2_p32121_model_0.cif"" Chain information for fold_q14978_2_p32121_model_0.cif #1 --- Chain | Description A | . B | . > select /A 5247 atoms, 5328 bonds, 709 residues, 1 model selected > color sel hot pink > select /A:1,709 /B:1,409 33 atoms, 29 bonds, 4 residues, 1 model selected > label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code} > label height 3 > alphafold pae #1 file ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q14978/Q14978-2_ARRB2/fold_q14978_2_p32121_full_data_0.json"" > alphafold contacts /A toAtoms /B distance 8 Found 52 residue or atom pairs within distance 8 > save /Users/stellabrenman/Desktop/image2.png supersample 3 > close > open ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q15366/Q15366_SRSF3/fold_q15366_p84103_model_0.cif"" Chain information for fold_q15366_p84103_model_0.cif #1 --- Chain | Description A | . B | . > select /b 1360 atoms, 1389 bonds, 164 residues, 1 model selected > select /A 2695 atoms, 2738 bonds, 365 residues, 1 model selected > color sel hot pink > select /A:1,365 /B:1,164 33 atoms, 29 bonds, 4 residues, 1 model selected > label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code} > label height 3 > alphafold pae #1 file ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q15366/Q15366_SRSF3/fold_q15366_p84103_full_data_0.json"" > alphafold contacts /A toAtoms /B distance 8 Found 206 residue or atom pairs within distance 8 > save /Users/stellabrenman/Desktop/image1.png supersample 3 > close > open ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q15366/Q15366-J5_SRSF3/fold_q15366_j5_p84103_model_0.cif"" Chain information for fold_q15366_j5_p84103_model_0.cif #1 --- Chain | Description A | . B | . > select /A 2354 atoms, 2385 bonds, 320 residues, 1 model selected > color sel hot pink > select /A:1,320 /B:1,164 33 atoms, 29 bonds, 4 residues, 1 model selected > label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code} > label height 3 > alphafold pae #1 file ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q15366/Q15366-J5_SRSF3/fold_q15366_j5_p84103_full_data_0.json"" > alphafold contacts /A toAtoms /B distance 8 Found 254 residue or atom pairs within distance 8 > save /Users/stellabrenman/Desktop/image2.png supersample 3 > close > open ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q32MZ4/Q32MZ4_TMOD1/fold_q32mz4_p28289_model_0.cif"" Chain information for fold_q32mz4_p28289_model_0.cif #1 --- Chain | Description A | . B | . > select /b 2846 atoms, 2889 bonds, 359 residues, 1 model selected > select /A 6238 atoms, 6307 bonds, 808 residues, 1 model selected > color sel hot pink > select /A:1,808 /B:1,359 31 atoms, 27 bonds, 4 residues, 1 model selected > label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code} > label height 3 > alphafold pae #1 file ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q32MZ4/Q32MZ4_TMOD1/fold_q32mz4_p28289_full_data_0.json"" > alphafold contacts /A toAtoms /B distance 8 Found 422 residue or atom pairs within distance 8 > save /Users/stellabrenman/Desktop/image1.png supersample 3 > close > open ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q32MZ4/Q32MZ4-3_TMOD1/fold_q32mz4_3_p28289_model_0.cif"" Chain information for fold_q32mz4_3_p28289_model_0.cif #1 --- Chain | Description A | . B | . > select /A 5781 atoms, 5848 bonds, 752 residues, 1 model selected > color sel hot pink > select /A:1,752 /B:1,359 31 atoms, 27 bonds, 4 residues, 1 model selected > label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code} > label height 3 > alphafold pae #1 file ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q32MZ4/Q32MZ4-3_TMOD1/fold_q32mz4_3_p28289_full_data_0.json"" > alphafold contacts /A toAtoms /B distance 8 Found 123 residue or atom pairs within distance 8 > save /Users/stellabrenman/Desktop/image2.png supersample 3 > close > open ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q32MZ4/Q32MZ4-4_TMOD1/fold_q32mz4_4_p28289_model_0.cif"" Chain information for fold_q32mz4_4_p28289_model_0.cif #1 --- Chain | Description A | . B | . > select /A 5119 atoms, 5168 bonds, 640 residues, 1 model selected > color sel hot pink > select /A:1,640 /B:1,359 34 atoms, 30 bonds, 4 residues, 1 model selected > label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code} > label height 3 > alphafold pae #1 file ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q32MZ4/Q32MZ4-4_TMOD1/fold_q32mz4_4_p28289_full_data_0.json"" > alphafold contacts /A toAtoms /B distance 8 Found 0 residue or atom pairs within distance 8 > alphafold contacts /A toAtoms /B distance 13 Found 17 residue or atom pairs within distance 13 > save /Users/stellabrenman/Desktop/image3.png supersample 3 > close > open ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q32MZ4/Q32MZ4_CEP44/fold_q32mz4_q9c0f1_model_0.cif"" Chain information for fold_q32mz4_q9c0f1_model_0.cif #1 --- Chain | Description A | . B | . > select /b 3085 atoms, 3129 bonds, 390 residues, 1 model selected > select /A 6238 atoms, 6307 bonds, 808 residues, 1 model selected > color sel hot pink > select /A:1,808 /B:1,390 32 atoms, 28 bonds, 4 residues, 1 model selected > label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code} > label height 3 > alphafold pae #1 file ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q32MZ4/Q32MZ4_CEP44/fold_q32mz4_q9c0f1_full_data_0.json"" > alphafold contacts /A toAtoms /B distance 8 Found 482 residue or atom pairs within distance 8 > save /Users/stellabrenman/Desktop/image1.png supersample 3 > close > open ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q32MZ4/Q32MZ4-3_CEP44/fold_q32mz4_3_q9c0f1_model_0.cif"" Chain information for fold_q32mz4_3_q9c0f1_model_0.cif #1 --- Chain | Description A | . B | . > select /A 5781 atoms, 5848 bonds, 752 residues, 1 model selected > color sel hot pink > select /A:1,752 /B:1,390 32 atoms, 28 bonds, 4 residues, 1 model selected > label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code} > label height 3 > alphafold pae #1 file ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q32MZ4/Q32MZ4-3_CEP44/fold_q32mz4_3_q9c0f1_full_data_0.json"" > alphafold contacts /A toAtoms /B distance 8 Found 408 residue or atom pairs within distance 8 > save /Users/stellabrenman/Desktop/image2.png supersample 3 > close > open ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q32MZ4/Q32MZ4-4_CEP44/fold_q32mz4_4_q9c0f1_model_0.cif"" Chain information for fold_q32mz4_4_q9c0f1_model_0.cif #1 --- Chain | Description A | . B | . > select /A 5119 atoms, 5168 bonds, 640 residues, 1 model selected > color sel hot pink > select /A:1,640 /B:1,390 35 atoms, 31 bonds, 4 residues, 1 model selected > label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code} > label height 3 > alphafold pae #1 file ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q32MZ4/Q32MZ4-4_CEP44/fold_q32mz4_4_q9c0f1_full_data_0.json"" > alphafold contacts /A toAtoms /B distance 8 Found 678 residue or atom pairs within distance 8 > save /Users/stellabrenman/Desktop/image3.png supersample 3 > close > open ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q3KQU3/Q3KQU3_MAPRE1/fold_q3kqu3_q15691_model_0.cif"" Chain information for fold_q3kqu3_q15691_model_0.cif #1 --- Chain | Description A | . B | . > select /b 2112 atoms, 2154 bonds, 268 residues, 1 model selected > select /A 6523 atoms, 6667 bonds, 841 residues, 1 model selected > color sel hot pink > select /A:1,841 /B:1,268 38 atoms, 35 bonds, 4 residues, 1 model selected > label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code} > label height 3 > alphafold pae #1 file ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q3KQU3/Q3KQU3_MAPRE1/fold_q3kqu3_q15691_full_data_0.json"" > alphafold contacts /A toAtoms /B distance 8 Found 315 residue or atom pairs within distance 8 > save /Users/stellabrenman/Desktop/image1.png supersample 3 > close > open ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q3KQU3/Q3KQU3-4_MAPRE1/fold_q3kqu3_4_q15691_model_0.cif"" Chain information for fold_q3kqu3_4_q15691_model_0.cif #1 --- Chain | Description A | . B | . > select /A 6287 atoms, 6423 bonds, 808 residues, 1 model selected > color sel hot pink > select /A:1,808 /B:1,268 38 atoms, 35 bonds, 4 residues, 1 model selected > label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code} > label height 3 > alphafold pae #1 file ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q3KQU3/Q3KQU3-4_MAPRE1/fold_q3kqu3_4_q15691_full_data_0.json"" > alphafold contacts /A toAtoms /B distance 8 Found 337 residue or atom pairs within distance 8 > save /Users/stellabrenman/Desktop/image2.png supersample 3 > close > open ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q3KQU3/Q3KQU3_KIF2A/fold_q3kqu3_o00139_model_0.cif"" Chain information for fold_q3kqu3_o00139_model_0.cif #1 --- Chain | Description A | . B | . > select /b 5608 atoms, 5698 bonds, 706 residues, 1 model selected > select /A 6523 atoms, 6667 bonds, 841 residues, 1 model selected > color sel hot pink > select /A:1,841 /B:1,706 34 atoms, 30 bonds, 4 residues, 1 model selected > label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code} > label height 3 > alphafold pae #1 file ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q3KQU3/Q3KQU3_KIF2A/fold_q3kqu3_o00139_full_data_0.json"" > alphafold contacts /A toAtoms /B distance 8 Found 425 residue or atom pairs within distance 8 > save /Users/stellabrenman/Desktop/image1.png supersample 3 > close > open ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q3KQU3/Q3KQU3-4_KIF2A/fold_q3kqu3_4_o00139_model_0.cif"" Chain information for fold_q3kqu3_4_o00139_model_0.cif #1 --- Chain | Description A | . B | . > select /A 6287 atoms, 6423 bonds, 808 residues, 1 model selected > color sel hot pink > select /A:1,808 /B:1,706 34 atoms, 30 bonds, 4 residues, 1 model selected > label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code} > label height 3 > alphafold pae #1 file ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q3KQU3/Q3KQU3-4_KIF2A/fold_q3kqu3_4_o00139_full_data_0.json"" > alphafold contacts /A toAtoms /B distance 8 Found 733 residue or atom pairs within distance 8 > save /Users/stellabrenman/Desktop/image2.png supersample 3 > close > open ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q8NE71/Q8NE71_RPS23/fold_q8ne71_p62266_model_0.cif"" Chain information for fold_q8ne71_p62266_model_0.cif #1 --- Chain | Description A | . B | . > select /b 1113 atoms, 1131 bonds, 143 residues, 1 model selected > select /A 6287 atoms, 6423 bonds, 808 residues, 1 model selected > color sel hot pink > select /A:1,808 /B:1,143 32 atoms, 28 bonds, 4 residues, 1 model selected > label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code} > label height 3 > alphafold pae #1 file ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q8NE71/Q8NE71_RPS23/fold_q8ne71_p62266_full_data_0.json"" > alphafold contacts /A toAtoms /B distance 8 Found 23 residue or atom pairs within distance 8 > save /Users/stellabrenman/Desktop/image1.png supersample 3 > close > open ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q8NE71/Q8NE71-J1_RPS23/fold_q8ne71_j1_p62266_model_0.cif"" Chain information for fold_q8ne71_j1_p62266_model_0.cif #1 --- Chain | Description A | . B | . > select /A 6750 atoms, 6857 bonds, 846 residues, 1 model selected > color sel hot pink > select /A:1,846 /B:1,143 33 atoms, 29 bonds, 4 residues, 1 model selected > label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code} > label height 3 > alphafold pae #1 file ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q8NE71/Q8NE71-J1_RPS23/fold_q8ne71_j1_p62266_full_data_0.json"" > alphafold contacts /A toAtoms /B distance 8 Found 125 residue or atom pairs within distance 8 > save /Users/stellabrenman/Desktop/image2.png supersample 3 > close > open ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q8NE71/Q8NE71_RPL10A/fold_q8ne71_p62906_model_0.cif"" Chain information for fold_q8ne71_p62906_model_0.cif #1 --- Chain | Description A | . B | . > select /b 1744 atoms, 1772 bonds, 217 residues, 1 model selected > select /A 6287 atoms, 6423 bonds, 808 residues, 1 model selected > color sel hot pink > select /A:1,808 /B:1,217 38 atoms, 35 bonds, 4 residues, 1 model selected > label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code} > label height 3 > alphafold pae #1 file ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q8NE71/Q8NE71_RPL10A/fold_q8ne71_p62906_full_data_0.json"" > alphafold contacts /A toAtoms /B distance 8 Found 33 residue or atom pairs within distance 8 > save /Users/stellabrenman/Desktop/image1.png supersample 3 > close > open ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q8NE71/Q8NE71-J1_RPL10A/fold_q8ne71_j1_p62906_model_0.cif"" Chain information for fold_q8ne71_j1_p62906_model_0.cif #1 --- Chain | Description A | . B | . > select /A 6750 atoms, 6857 bonds, 846 residues, 1 model selected > color sel hot pink > select /A:1,846 /B:1,217 39 atoms, 36 bonds, 4 residues, 1 model selected > label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code} > label height 3 > alphafold pae #1 file ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q8NE71/Q8NE71-J1_RPL10A/fold_q8ne71_j1_p62906_full_data_0.json"" > alphafold contacts /A toAtoms /B distance 8 Found 365 residue or atom pairs within distance 8 > save /Users/stellabrenman/Desktop/image2.png supersample 3 > close > open ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q8NE71/Q8NE71_RPL11/fold_q8ne71_p62913_model_0.cif"" Chain information for fold_q8ne71_p62913_model_0.cif #1 --- Chain | Description A | . B | . > select /b 1424 atoms, 1447 bonds, 178 residues, 1 model selected > select /A 6287 atoms, 6423 bonds, 808 residues, 1 model selected > color sel hot pink > select /A:1,808 /B:1,178 35 atoms, 31 bonds, 4 residues, 1 model selected > label sel text /{0.chain_id}{0.name}{0.number}{0.insertion_code} > label height 3 > alphafold pae #1 file ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q8NE71/Q8NE71_RPL11/fold_q8ne71_p62913_full_data_0.json"" > alphafold contacts /A toAtoms /B distance 8 Found 171 residue or atom pairs within distance 8 > save /Users/stellabrenman/Desktop/image1.png supersample 3 > close > open ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q8NE71/Q8NE71-J1_RPL11/fold_q8ne71_j1_p62913_model_0.cif"" Failed opening file /Volumes/Omics-Shared/Struc_Func_Predict/Alphafold 3/Q8NE71/Q8NE71-J1_RPL11/fold_q8ne71_j1_p62913_model_0.cif: mmCIF parsing error: not enough data values, foundEnd of input on line 10433 > open ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q9NUQ6/Q9NUQ6_IFI16/fold_q9nuq6_q16666_model_0.cif"" ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Volumes/Omics-Shared/Struc_Func_Predict/Alphafold > 3/Q9NUQ6/Q9NUQ6-2_IFI16/fold_q9nuq6_2_q16666_model_0.cif"" Chain information for fold_q9nuq6_2_q16666_model_0.cif #1 --- Chain | Description A | . B | . OpenGL version: 4.1 INTEL-22.5.11 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645 OpenGL vendor: Intel Inc. Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,3 Processor Name: Quad-Core Intel Core i5 Processor Speed: 1.4 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: 8 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: 5 hours Graphics/Displays: Intel Iris Plus Graphics 645: Chipset Model: Intel Iris Plus Graphics 645 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3ea6 Revision ID: 0x0001 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL P2415Q: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 30.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: 59JJ48BG0V3B Mirror: Off Online: Yes Rotation: Supported Connection Type: Thunderbolt/DisplayPort Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Input/Output duplicate all ChimeraX