id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14691 Crash in garbage collection o.bozkurt@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.3.1-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 0x0000000314b89000 (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 0x000000020279f240 (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/geometry/plane.py"", line 44 in __init__ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/bond_geom.py"", line 222 in tetra_pos File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/bond_geom.py"", line 89 in bond_positions File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/hbond.py"", line 220 in add_hydrogens File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/cmd.py"", line 184 in hbond_add_hydrogens File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/cmd.py"", line 77 in cmd_addh File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/coulombic.py"", line 95 in assign_charges File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/cmd.py"", line 99 in cmd_coulombic 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/shortcuts/shortcuts.py"", line 525 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 582 in run_expanded_command File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 72 in func_plus_tip File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 339 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 420 in run_shortcut File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 402 in try_shortcut File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 1376 in run_provider File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/__init__.py"", line 66 in run_provider File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py"", line 1302 in run_provider File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/info.py"", line 397 in run_provider File 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2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/obozkurt/Downloads/D8674_029218PyrusussuriensisxPyruscommunis_a7342/D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb Chain information for D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1 --- Chain | Description A B C D E | No description available > set bgColor white > select all 7570 atoms, 7635 bonds, 965 residues, 1 model selected > hide sel atoms > show sel cartoons > lighting soft > graphics silhouettes true > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_A SES surface #1.1: minimum, -17.03, mean -1.57, maximum 11.40 Coulombic values for D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_B SES surface #1.2: minimum, -26.43, mean -1.58, maximum 11.30 Coulombic values for D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_C SES surface #1.3: minimum, -20.67, mean -1.62, maximum 11.55 Coulombic values for D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_D SES surface #1.4: minimum, -16.20, mean -1.59, maximum 11.37 Coulombic values for D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_E SES surface #1.5: minimum, -32.71, mean -1.59, maximum 13.65 To also show corresponding color key, enter the above coulombic command and add key true > open > /Users/obozkurt/Downloads/D8674_029218PyrusussuriensisxPyruscommunis_a7342/D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb Chain information for D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #2 --- Chain | Description A B C D E | No description available > select clear > close #2 > mlp Map values for surface ""D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_A SES surface"": minimum -28.83, mean -3.559, maximum 22.03 Map values for surface ""D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_B SES surface"": minimum -26.89, mean -3.532, maximum 22.68 Map values for surface ""D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_C SES surface"": minimum -30.07, mean -3.56, maximum 22.84 Map values for surface ""D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_D SES surface"": minimum -29.46, mean -3.536, maximum 22.06 Map values for surface ""D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_E SES surface"": minimum -29.36, mean -3.582, maximum 22 To also show corresponding color key, enter the above mlp command and add key true > coulombic Coulombic values for D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_A SES surface #1.1: minimum, -17.03, mean -1.57, maximum 11.40 Coulombic values for D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_B SES surface #1.2: minimum, -26.43, mean -1.58, maximum 11.30 Coulombic values for D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_C SES surface #1.3: minimum, -20.67, mean -1.62, maximum 11.55 Coulombic values for D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_D SES surface #1.4: minimum, -16.20, mean -1.59, maximum 11.37 Coulombic values for D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_E SES surface #1.5: minimum, -32.71, mean -1.59, maximum 13.65 To also show corresponding color key, enter the above coulombic command and add key true Alignment identifier is 1 > select /A-E:1 40 atoms, 35 bonds, 5 residues, 1 model selected > select /A-E:1-49 1845 atoms, 1870 bonds, 245 residues, 1 model selected > color (#!1 & sel) black > select clear > color bfactor 7570 atoms, 965 residues, 5 surfaces, atom bfactor range 24.3 to 93.3 > coulombic Coulombic values for D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_A SES surface #1.1: minimum, -17.03, mean -1.57, maximum 11.40 Coulombic values for D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_B SES surface #1.2: minimum, -26.43, mean -1.58, maximum 11.30 Coulombic values for D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_C SES surface #1.3: minimum, -20.67, mean -1.62, maximum 11.55 Coulombic values for D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_D SES surface #1.4: minimum, -16.20, mean -1.59, maximum 11.37 Coulombic values for D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_E SES surface #1.5: minimum, -32.71, mean -1.59, maximum 13.65 To also show corresponding color key, enter the above coulombic command and add key true > color bynucleotide > coulombic Coulombic values for D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_A SES surface #1.1: minimum, -17.03, mean -1.57, maximum 11.40 Coulombic values for D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_B SES surface #1.2: minimum, -26.43, mean -1.58, maximum 11.30 Coulombic values for D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_C SES surface #1.3: minimum, -20.67, mean -1.62, maximum 11.55 Coulombic values for D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_D SES surface #1.4: minimum, -16.20, mean -1.59, maximum 11.37 Coulombic values for D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_E SES surface #1.5: minimum, -32.71, mean -1.59, maximum 13.65 To also show corresponding color key, enter the above coulombic command and add key true > rainbow > color bypolymer > color bychain > color byhetero > color bychain > color bypolymer > rainbow > coulombic Coulombic values for D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_A SES surface #1.1: minimum, -17.03, mean -1.57, maximum 11.40 Coulombic values for D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_B SES surface #1.2: minimum, -26.43, mean -1.58, maximum 11.30 Coulombic values for D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_C SES surface #1.3: minimum, -20.67, mean -1.62, maximum 11.55 Coulombic values for D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_D SES surface #1.4: minimum, -16.20, mean -1.59, maximum 11.37 Coulombic values for D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_E SES surface #1.5: minimum, -32.71, mean -1.59, maximum 13.65 To also show corresponding color key, enter the above coulombic command and add key true > mlp Map values for surface ""D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_A SES surface"": minimum -28.83, mean -3.559, maximum 22.03 Map values for surface ""D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_B SES surface"": minimum -26.89, mean -3.532, maximum 22.68 Map values for surface ""D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_C SES surface"": minimum -30.07, mean -3.56, maximum 22.84 Map values for surface ""D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_D SES surface"": minimum -29.46, mean -3.536, maximum 22.06 Map values for surface ""D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_E SES surface"": minimum -29.36, mean -3.582, maximum 22 To also show corresponding color key, enter the above mlp command and add key true > coulombic Coulombic values for D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_A SES surface #1.1: minimum, -17.03, mean -1.57, maximum 11.40 Coulombic values for D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_B SES surface #1.2: minimum, -26.43, mean -1.58, maximum 11.30 Coulombic values for D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_C SES surface #1.3: minimum, -20.67, mean -1.62, maximum 11.55 Coulombic values for D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_D SES surface #1.4: minimum, -16.20, mean -1.59, maximum 11.37 Coulombic values for D8674_029218PyrusussuriensisxPyruscommunis_a7342_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_E SES surface #1.5: minimum, -32.71, mean -1.59, maximum 13.65 To also show corresponding color key, enter the above coulombic command and add key true > close > open > /Users/obozkurt/Downloads/D8674_029218Pyrus_6X_4bc3d/D8674_029218Pyrus_6X_4bc3d_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb Chain information for D8674_029218Pyrus_6X_4bc3d_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1 --- Chain | Description A B C D E F | No description available > hide atoms > show cartoons > coulombic Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for D8674_029218Pyrus_6X_4bc3d_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_A SES surface #1.1: minimum, -16.28, mean -1.57, maximum 14.88 Coulombic values for D8674_029218Pyrus_6X_4bc3d_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_B SES surface #1.2: minimum, -16.46, mean -1.58, maximum 11.67 Coulombic values for D8674_029218Pyrus_6X_4bc3d_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_C SES surface #1.3: minimum, -26.51, mean -1.58, maximum 11.67 Coulombic values for D8674_029218Pyrus_6X_4bc3d_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_D SES surface #1.4: minimum, -16.41, mean -1.55, maximum 12.05 Coulombic values for D8674_029218Pyrus_6X_4bc3d_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_E SES surface #1.5: minimum, -16.72, mean -1.58, maximum 11.70 Coulombic values for D8674_029218Pyrus_6X_4bc3d_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_F SES surface #1.6: minimum, -16.68, mean -1.56, maximum 14.51 To also show corresponding color key, enter the above coulombic command and add key true > mlp Map values for surface ""D8674_029218Pyrus_6X_4bc3d_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_A SES surface"": minimum -28.59, mean -3.514, maximum 22.73 Map values for surface ""D8674_029218Pyrus_6X_4bc3d_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_B SES surface"": minimum -28.92, mean -3.513, maximum 23.34 Map values for surface ""D8674_029218Pyrus_6X_4bc3d_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_C SES surface"": minimum -28.26, mean -3.455, maximum 22.08 Map values for surface ""D8674_029218Pyrus_6X_4bc3d_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_D SES surface"": minimum -27.62, mean -3.463, maximum 21.84 Map values for surface ""D8674_029218Pyrus_6X_4bc3d_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_E SES surface"": minimum -29.62, mean -3.49, maximum 21.74 Map values for surface ""D8674_029218Pyrus_6X_4bc3d_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb_F SES surface"": minimum -27.87, mean -3.489, maximum 23.08 To also show corresponding color key, enter the above mlp command and add key true > open > /Users/obozkurt/Downloads/RPW81_335dd/RPW81_335dd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb Chain information for RPW81_335dd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb #2 --- Chain | Description A B C D E | No description available > close #1 > hide atoms > show cartoons > coulombic Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for RPW81_335dd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb_A SES surface #2.1: minimum, -18.58, mean 0.17, maximum 17.75 Coulombic values for RPW81_335dd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb_B SES surface #2.2: minimum, -15.25, mean 0.19, maximum 17.05 Coulombic values for RPW81_335dd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb_C SES surface #2.3: minimum, -15.52, mean 0.17, maximum 18.35 Coulombic values for RPW81_335dd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb_D SES surface #2.4: minimum, -16.50, mean 0.14, maximum 17.42 Coulombic values for RPW81_335dd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb_E SES surface #2.5: minimum, -22.76, mean 0.16, maximum 22.42 To also show corresponding color key, enter the above coulombic command and add key true > hide cartoons > show atoms > hide atoms > mlp Map values for surface ""RPW81_335dd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb_A SES surface"": minimum -27.39, mean -2.52, maximum 25.26 Map values for surface ""RPW81_335dd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb_B SES surface"": minimum -27.18, mean -2.512, maximum 25.19 Map values for surface ""RPW81_335dd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb_C SES surface"": minimum -27.08, mean -2.49, maximum 25.31 Map values for surface ""RPW81_335dd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb_D SES surface"": minimum -27.8, mean -2.463, maximum 26.42 Map values for surface ""RPW81_335dd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb_E SES surface"": minimum -27.33, mean -2.558, maximum 25.03 To also show corresponding color key, enter the above mlp command and add key true > hide surfaces > show cartoons > coulombic Coulombic values for RPW81_335dd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb_A SES surface #2.1: minimum, -18.58, mean 0.17, maximum 17.75 Coulombic values for RPW81_335dd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb_B SES surface #2.2: minimum, -15.25, mean 0.19, maximum 17.05 Coulombic values for RPW81_335dd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb_C SES surface #2.3: minimum, -15.52, mean 0.17, maximum 18.35 Coulombic values for RPW81_335dd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb_D SES surface #2.4: minimum, -16.50, mean 0.14, maximum 17.42 Coulombic values for RPW81_335dd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb_E SES surface #2.5: minimum, -22.76, mean 0.16, maximum 22.42 To also show corresponding color key, enter the above coulombic command and add key true > hide surfaces > color bypolymer > close > open > /Users/obozkurt/Downloads/DAR5_Arabidopsis_5X_a674c/DAR5_Arabidopsis_5X_a674c_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb Chain information for DAR5_Arabidopsis_5X_a674c_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #1 --- Chain | Description A B C D E | No description available > hide cartoons > hide atoms > show cartoons > close > open > /Users/obozkurt/Downloads/LOC112180138_Rosa_chinensis_a919e/LOC112180138_Rosa_chinensis_a919e_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb Chain information for LOC112180138_Rosa_chinensis_a919e_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #1 --- Chain | Description A B C D E | No description available > hide atoms > show cartoons > coulombic ===== 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 > open > /Users/obozkurt/Downloads/LOC112180138_Rosa_chinensis_a919e/LOC112180138_Rosa_chinensis_a919e_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb Chain information for LOC112180138_Rosa_chinensis_a919e_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #1 --- Chain | Description A B C D E | No description available OpenGL version: 4.1 Metal - 88 OpenGL renderer: Apple M3 Max OpenGL vendor: Apple 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: Mac Model Identifier: Mac15,10 Model Number: MRX53B/A Chip: Unknown Total Number of Cores: 14 (10 performance and 4 efficiency) Memory: 36 GB System Firmware Version: 10151.81.1 OS Loader Version: 10151.81.1 Software: System Software Overview: System Version: macOS 14.3.1 (23D60) Kernel Version: Darwin 23.3.0 Time since boot: 3 hours, 30 minutes Graphics/Displays: Apple M3 Max: Chipset Model: Apple M3 Max Type: GPU Bus: Built-In Total Number of Cores: 30 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina 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