id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14839 Crash in garbage collection shakeel.s@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.1.1-x86_64-i386-64bit ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x00007ff84de0cb40 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/serialize.py"", line 81 in msgpack_deserialize File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py"", line 721 in restore File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py"", line 1017 in open File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py"", line 37 in open File ""/Applications/ChimeraX-1.7.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-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 514 in collated_open File ""/Applications/ChimeraX-1.7.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-1.7.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.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-1.7.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.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/dialog.py"", line 334 in _qt_safe File ""/Applications/ChimeraX-1.7.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.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.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, 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Bytes before following region: 140737487167319\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffede000-7fffffedf000 [ 4K] r-x\/r-x SM=SHM "", ""exception"" : {""codes"":""0x0000000000000001, 0x00000000000000a9"",""rawCodes"":[1,169],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x00000000000000a9""}, ""termination"" : {""flags"":0,""code"":11,""namespace"":""SIGNAL"",""indicator"":""Segmentation fault: 11"",""byProc"":""ChimeraX"",""byPid"":36940}, ""ktriageinfo"" : ""VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n"", ""vmregioninfo"" : ""0xa9 is not in any region. 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""632c763c58740028737bfdd2"", ""factorPackIds"" : { ""SIRI_DIALOG_ASSETS"" : ""64a57d23fa6fd41b2353e2ae"" }, ""deploymentId"" : 240000034 }, { ""rolloutId"" : ""5f72dc58705eff005a46b3a9"", ""factorPackIds"" : { }, ""deploymentId"" : 240000015 } ], ""experiments"" : [ { ""treatmentId"" : ""a3f9ec09-b145-49f3-8142-da4a1f338456"", ""experimentId"" : ""65f21aa774b6f500a45abd7d"", ""deploymentId"" : 400000002 } ] } } ===== 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 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/alphafold_MORC2dimer/relaxed_model_1_multimer_v3_pred_2.pdb Chain information for relaxed_model_1_multimer_v3_pred_2.pdb #1 --- Chain | Description A B | No description available > set bgColor white > color /B hot pink > color /A cornflower blue > select :899-1068 5396 atoms, 5446 bonds, 340 residues, 1 model selected > hide sel cartoons > show sel cartoons > hide sel cartoons > show sel cartoons > select up 6746 atoms, 6810 bonds, 434 residues, 1 model selected > select up 34268 atoms, 34612 bonds, 2136 residues, 1 model selected > select :605-783 5668 atoms, 5730 bonds, 358 residues, 1 model selected > hide sel cartoons > show sel cartoons > ui tool show XMAS Peptide pair mapping of Xi evidence file: /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/ampvapo_XMAS.csv Unique peptide pairs: 29 out of 31 Unique peptide pairs with pseudobonds: 29 Pseudobonds are stored in /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/ampvapo_XMAS_1.pb Mapping information is stored in /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/ampvapo_XMAS_1.tsv Peptide pair mapping of Xi evidence file: /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/ampvdna_XMAS.csv Unique peptide pairs: 25 out of 26 Unique peptide pairs with pseudobonds: 25 Pseudobonds are stored in /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/ampvdna_XMAS_1.pb Mapping information is stored in /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/ampvdna_XMAS_1.tsv Peptide pair mapping of Xi evidence file: /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/apo_XMAS.csv Unique peptide pairs: 20 out of 21 Unique peptide pairs with pseudobonds: 20 Pseudobonds are stored in /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/apo_XMAS_1.pb Mapping information is stored in /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/apo_XMAS_1.tsv Peptide pair mapping of Xi evidence file: /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/DNA_XMAS.csv Unique peptide pairs: 24 out of 24 Unique peptide pairs with pseudobonds: 24 /Users/shakeel.s/Library/Application Support/ChimeraX/1.7/lib/python/site- packages/chimerax/XMAS/info_file.py:46: FutureWarning: The behavior of DataFrame concatenation with empty or all-NA entries is deprecated. In a future version, this will no longer exclude empty or all-NA columns when determining the result dtypes. To retain the old behavior, exclude the relevant entries before the concat operation. self.df = pd.concat([self.df, df_add], ignore_index=True) Pseudobonds are stored in /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/DNA_XMAS_1.pb Mapping information is stored in /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/DNA_XMAS_1.tsv Pseudobonds are stored in /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/EnrichedAMPinAMPvsApo_20A.pb Pseudobonds are stored in /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/EnrichedAMPinAMPvsApo_20A.pb > hide #5 models > hide #4 models > hide #3 models > hide #2 models > hide #6 models > close session > open > /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/alphafold_MORC2dimer/relaxed_model_1_multimer_v3_pred_2.pdb Chain information for relaxed_model_1_multimer_v3_pred_2.pdb #1 --- Chain | Description A B | No description available > color /B hot pink > color /A cornflower blue > ui tool show XMAS Peptide pair mapping of Xi evidence file: /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/ampvapo_XMAS.csv Unique peptide pairs: 29 out of 31 Unique peptide pairs with pseudobonds: 29 Pseudobonds are stored in /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/ampvapo_XMAS_1.pb Mapping information is stored in /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/ampvapo_XMAS_1.tsv Peptide pair mapping of Xi evidence file: /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/ampvdna_XMAS.csv Unique peptide pairs: 25 out of 26 Unique peptide pairs with pseudobonds: 25 Pseudobonds are stored in /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/ampvdna_XMAS_1.pb Mapping information is stored in /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/ampvdna_XMAS_1.tsv Peptide pair mapping of Xi evidence file: /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/apo_XMAS.csv Unique peptide pairs: 20 out of 21 Unique peptide pairs with pseudobonds: 20 Pseudobonds are stored in /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/apo_XMAS_1.pb Mapping information is stored in /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/apo_XMAS_1.tsv Peptide pair mapping of Xi evidence file: /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/DNA_XMAS.csv Unique peptide pairs: 24 out of 24 Unique peptide pairs with pseudobonds: 24 /Users/shakeel.s/Library/Application Support/ChimeraX/1.7/lib/python/site- packages/chimerax/XMAS/info_file.py:46: FutureWarning: The behavior of DataFrame concatenation with empty or all-NA entries is deprecated. In a future version, this will no longer exclude empty or all-NA columns when determining the result dtypes. To retain the old behavior, exclude the relevant entries before the concat operation. self.df = pd.concat([self.df, df_add], ignore_index=True) Pseudobonds are stored in /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/DNA_XMAS_1.pb Mapping information is stored in /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/DNA_XMAS_1.tsv > hide #5 models > hide #4 models > hide #3 models Please select pseudobonds Pseudobonds are stored in /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/EnrichedAMPinAMPvsDNA_20A.pb > hide #2 models > hide #6 models > show #4 models Pseudobonds are stored in /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/EnrichedAPOinAMPvsAPO_20A.pb > hide #7 models > hide #4 models > color #4 #8efa00ff models > show #4 models > hide #4 models > color #7 #8efa00ff models > select subtract #4 Nothing selected > show #7 models > hide #7 models > show #3 models Pseudobonds are stored in /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/EnrichedAMPinAMPvsDNA_20A.pb > close session > open > /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/alphafold_MORC2dimer/relaxed_model_1_multimer_v3_pred_2.pdb > format pdb Chain information for relaxed_model_1_multimer_v3_pred_2.pdb #1 --- Chain | Description A B | No description available > color /A cornflower blue > color /B hot pink > open > /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/ampvapo_XMAS.csv > /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/ampvdna_XMAS.csv > /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/apo_XMAS.csv > /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/DNA_XMAS.csv Unrecognized file suffix '.csv' > ui tool show XMAS Peptide pair mapping of Xi evidence file: /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/ampvapo_XMAS.csv Unique peptide pairs: 29 out of 31 Unique peptide pairs with pseudobonds: 29 Pseudobonds are stored in /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/ampvapo_XMAS_1.pb Mapping information is stored in /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/ampvapo_XMAS_1.tsv Peptide pair mapping of Xi evidence file: /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/ampvdna_XMAS.csv Unique peptide pairs: 25 out of 26 Unique peptide pairs with pseudobonds: 25 Pseudobonds are stored in /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/ampvdna_XMAS_1.pb Mapping information is stored in /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/ampvdna_XMAS_1.tsv Peptide pair mapping of Xi evidence file: /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/apo_XMAS.csv Unique peptide pairs: 20 out of 21 Unique peptide pairs with pseudobonds: 20 Pseudobonds are stored in /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/apo_XMAS_1.pb Mapping information is stored in /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/apo_XMAS_1.tsv Peptide pair mapping of Xi evidence file: /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/DNA_XMAS.csv Unique peptide pairs: 24 out of 24 Unique peptide pairs with pseudobonds: 24 /Users/shakeel.s/Library/Application Support/ChimeraX/1.7/lib/python/site- packages/chimerax/XMAS/info_file.py:46: FutureWarning: The behavior of DataFrame concatenation with empty or all-NA entries is deprecated. In a future version, this will no longer exclude empty or all-NA columns when determining the result dtypes. To retain the old behavior, exclude the relevant entries before the concat operation. self.df = pd.concat([self.df, df_add], ignore_index=True) Pseudobonds are stored in /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/DNA_XMAS_1.pb Mapping information is stored in /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/DNA_XMAS_1.tsv > hide #3 models > hide #4 models > hide #5 models Pseudobonds are stored in /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/EnrichedAMPinAMPvsAPO_20A.pb Pseudobonds are stored in /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/EnrichedAMPinAMPvsDNA_20A.pb Pseudobonds are stored in /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/EnrichedAPOinAMPvsAPO_20A.pb Pseudobonds are stored in /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/EnrichedDNAinAMPvsDNA_20A.pb > color #8 #8efa00ff models > color #9 #8efa00ff models > hide #7 models > hide #9 models > hide #2 models > hide #6 models > hide #8 models > show #6 models > show #7 models > hide #7 models > show #8 models > hide #6 models > hide #8 models > show #6 models > show #8 models Peptide pair mapping of Xi evidence file: /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/P4383_apo.csv Unique peptide pairs: 286 out of 359 Unique peptide pairs with pseudobonds: 260 Pseudobonds are stored in /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/P4383_apo_1.pb Mapping information is stored in /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/P4383_apo_1.tsv Pseudobonds are stored in /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/Apo_chain_interlinks_25A.pb > hide #10 models > hide #8 models > hide #6 models > show #10 models > hide #11 models Pseudobonds are stored in /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/Apo_chain_interlinks_25A.pb > hide #10 models Pseudobonds are stored in /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/Apo_chain_interlinks_20A.pb > hide #12 models > select ~sel & ##selected 892 pseudobonds, 1 model selected > hide #13 models > show #6 models > show #8 models > select subtract #10 Nothing selected > color :82-103 white > hide #8 models > hide #6 models > show #9 models > show #7 models > hide #9 models > hide #7 models > color :67-109 red > color :82-103 white > color /A cornflower blue > color /B hot pink > color :81-109 red > show #9 models > show #7 models > color #7 #fffc79ff models > color #7 #ffd479ff models > color #7 #fffb00ff models > color #9 #8efa00ff models > color :495-545 dark red > color /A steelblue > color /B mercury Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color /A steelblue > color /B snow > color /A steelblue > color /A iron Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color /B darkred white Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color /A lead Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color /A fern Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #10 #5e5e5eff models > select /A 17134 atoms, 17306 bonds, 367 pseudobonds, 1068 residues, 10 models selected > color (#1 & sel) gray > color :495-545 dark red > color :67-109 red > color /B snow > select /A 17134 atoms, 17306 bonds, 367 pseudobonds, 1068 residues, 10 models selected > color /A grey > color :495-545 dark red > color :81-109 red > color :266-494 magenta > color #9 #8efa00ff models > color #7 #8efa00ff models > color #7 #fffb00ff models > color :547-584 cyan > hide #9 models > hide #7 models > show #7 models > color #7 #8efa00ff models > color #7 #fffb00ff models > color #7 #8efa00ff models > color #7 #fffb00ff models > color #9 #0096ffff models > color #9 #8efa00ff models > show #9 models > color :786-851 ff7f00 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color :786-851 #ff7f00 > color :966-1016 #cf597e > color :903-1016 #cf597e > color #9 #00f900ff models > color #9 #8efa00ff models > color #7 #8efa00ff models > color #7 #fffb00ff models > color :741-761 blue > open > /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/XiaominProject/Neuropilin_project/alphafold/alphafold_OmiSpike_NRP1/Omi_NRP/unrelaxed_model_1_multimer_v3_pred_0.pdb Chain information for unrelaxed_model_1_multimer_v3_pred_0.pdb #14 --- Chain | Description B C D | No description available E | No description available > open > /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/XiaominProject/Neuropilin_project/alphafold/alphafold_OmiSpike_NRP1/Omi_NRP/unrelaxed_model_2_multimer_v3_pred_0.pdb Chain information for unrelaxed_model_2_multimer_v3_pred_0.pdb #15 --- Chain | Description B C D | No description available E | No description available > open > /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/XiaominProject/Neuropilin_project/alphafold/alphafold_OmiSpike_NRP1/Omi_NRP/unrelaxed_model_3_multimer_v3_pred_0.pdb Chain information for unrelaxed_model_3_multimer_v3_pred_0.pdb #16 --- Chain | Description B C D | No description available E | No description available > open > /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/XiaominProject/Neuropilin_project/alphafold/alphafold_OmiSpike_NRP1/Omi_NRP/unrelaxed_model_4_multimer_v3_pred_0.pdb Chain information for unrelaxed_model_4_multimer_v3_pred_0.pdb #17 --- Chain | Description B C D | No description available E | No description available > open > /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/XiaominProject/Neuropilin_project/alphafold/alphafold_OmiSpike_NRP1/Omi_NRP/unrelaxed_model_5_multimer_v3_pred_0.pdb Chain information for unrelaxed_model_5_multimer_v3_pred_0.pdb #18 --- Chain | Description B C D | No description available E | No description available > hide #1 models > hide #7 models > hide #9 models > hide #15 models > hide #16 models > hide #17 models > hide #18 models > color bychain #14-18 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color #14-18 bychain > hide #14 models > show #15 models > hide #15 models > show #16 models > hide #16 models > show #17 models > hide #17 models > show #18 models > select down 17134 atoms, 17306 bonds, 367 pseudobonds, 1068 residues, 10 models selected > select down 17134 atoms, 17306 bonds, 367 pseudobonds, 1068 residues, 10 models selected > select down 17134 atoms, 17306 bonds, 367 pseudobonds, 1068 residues, 10 models selected > close #14-18 > open > /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/XiaominProject/Neuropilin_project/alphafold/alphafold_OmiSpike_NRP1/Omi_NRP/unrelaxed_model_1_multimer_v3_pred_0.pdb Chain information for unrelaxed_model_1_multimer_v3_pred_0.pdb #14 --- Chain | Description B C D | No description available E | No description available > open > /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/XiaominProject/Neuropilin_project/alphafold/alphafold_OmiSpike_NRP1/Omi_NRP/unrelaxed_model_2_multimer_v3_pred_0.pdb Chain information for unrelaxed_model_2_multimer_v3_pred_0.pdb #15 --- Chain | Description B C D | No description available E | No description available > open > /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/XiaominProject/Neuropilin_project/alphafold/alphafold_OmiSpike_NRP1/Omi_NRP/unrelaxed_model_3_multimer_v3_pred_0.pdb Chain information for unrelaxed_model_3_multimer_v3_pred_0.pdb #16 --- Chain | Description B C D | No description available E | No description available > open > /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/XiaominProject/Neuropilin_project/alphafold/alphafold_OmiSpike_NRP1/Omi_NRP/unrelaxed_model_4_multimer_v3_pred_0.pdb Chain information for unrelaxed_model_4_multimer_v3_pred_0.pdb #17 --- Chain | Description B C D | No description available E | No description available > open > /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/XiaominProject/Neuropilin_project/alphafold/alphafold_OmiSpike_NRP1/Omi_NRP/unrelaxed_model_5_multimer_v3_pred_0.pdb Chain information for unrelaxed_model_5_multimer_v3_pred_0.pdb #18 --- Chain | Description B C D | No description available E | No description available > hide #14 models > hide #15 models > hide #16 models > hide #17 models > hide #18 models > show #14 models > color #14-18 bychain > show #15 models > hide #14 models > hide #15 models > show #16 models > hide #16 models > show #17 models > hide #17 models > show #18 models > toolshed show Peptide pair mapping of Xi evidence file: /Users/shakeel.s/Downloads/P4699_Xi1.7.6.7_CSM_xiFDR2.1.5.5.csv Unique peptide pairs: 195 out of 549 Unique peptide pairs with pseudobonds: 149 Pseudobonds are stored in /Users/shakeel.s/Downloads/P4699_Xi1.7.6.7_CSM_xiFDR2.1.5.5_14.pb Mapping information is stored in /Users/shakeel.s/Downloads/P4699_Xi1.7.6.7_CSM_xiFDR2.1.5.5_14.tsv > select add #19 17134 atoms, 17306 bonds, 794 pseudobonds, 1068 residues, 11 models selected > hide #19 models > select subtract #19 17134 atoms, 17306 bonds, 367 pseudobonds, 1068 residues, 10 models selected > show #19 models > show #14 models > hide #18 models > hide #19 models Pseudobonds are stored in /Users/shakeel.s/Downloads/spikenrp1_model1.pb > hide #14 models > show #15 models Peptide pair mapping of Xi evidence file: /Users/shakeel.s/Downloads/P4699_Xi1.7.6.7_CSM_xiFDR2.1.5.5.csv Unique peptide pairs: 195 out of 549 Unique peptide pairs with pseudobonds: 149 Pseudobonds are stored in /Users/shakeel.s/Downloads/P4699_Xi1.7.6.7_CSM_xiFDR2.1.5.5_15.pb Mapping information is stored in /Users/shakeel.s/Downloads/P4699_Xi1.7.6.7_CSM_xiFDR2.1.5.5_15.tsv Pseudobonds are stored in /Users/shakeel.s/Downloads/spikenrp1_model2.pb > hide #21 models > hide #20 models > hide #22 models > show #21 models > hide #15 models > show #14 models > hide #21 models > show #20 models > hide #20 models > hide #14 models > show #16 models Peptide pair mapping of Xi evidence file: /Users/shakeel.s/Downloads/P4699_Xi1.7.6.7_CSM_xiFDR2.1.5.5.csv Unique peptide pairs: 195 out of 549 Unique peptide pairs with pseudobonds: 149 Pseudobonds are stored in /Users/shakeel.s/Downloads/P4699_Xi1.7.6.7_CSM_xiFDR2.1.5.5_16.pb Mapping information is stored in /Users/shakeel.s/Downloads/P4699_Xi1.7.6.7_CSM_xiFDR2.1.5.5_16.tsv Pseudobonds are stored in /Users/shakeel.s/Downloads/spikenrp1_model3.pb > hide #23 models > show #20 models > hide #24 models > hide #20 models > show #14 models > hide #16 models > ui tool show ""Show Sequence Viewer"" > sequence chain #14/B #14/C #14/D #15/B #15/C #15/D #16/B #16/C #16/D #17/B > #17/C #17/D #18/B #18/C #18/D Alignment identifier is 1 > select #14/B-D:841 #15/B-D:841 #16/B-D:841 #17/B-D:841 #18/B-D:841 120 atoms, 105 bonds, 15 residues, 5 models selected > select #14/B-D:841-927 #15/B-D:841-927 #16/B-D:841-927 #17/B-D:841-927 > #18/B-D:841-927 9945 atoms, 10155 bonds, 1305 residues, 5 models selected 1 [ID: 1] region 15 chains [841-927] RMSD: 63.226 > select down 9945 atoms, 10155 bonds, 1305 residues, 5 models selected > select down 9945 atoms, 10155 bonds, 1305 residues, 5 models selected > select down 9945 atoms, 10155 bonds, 1305 residues, 5 models selected > select down 9945 atoms, 10155 bonds, 1305 residues, 5 models selected > select down 9945 atoms, 10155 bonds, 1305 residues, 5 models selected > close #14 > close #15 > close #16 > close #17 > close #18 > close #19 > close #20 > close #21 > close #22 > close #23 > close #24 > show #1 models > close session > open > /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/CLMS_analysis.cxs ===== 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 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 ATI-5.1.35 OpenGL renderer: AMD Radeon Pro 5300 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: iMac Model Identifier: iMac20,1 Processor Name: 6-Core Intel Core i5 Processor Speed: 3.3 GHz Number of Processors: 1 Total Number of Cores: 6 L2 Cache (per Core): 256 KB L3 Cache: 12 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 2020.41.1.0.0 (iBridge: 21.16.1069.0.0,0) OS Loader Version: 580~743 Software: System Software Overview: System Version: macOS 14.1.1 (23B81) Kernel Version: Darwin 23.1.0 Time since boot: 9 days, 1 hour, 43 minutes Graphics/Displays: AMD Radeon Pro 5300: Chipset Model: AMD Radeon Pro 5300 Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0047 ROM Revision: 113-D3220I-231 VBIOS Version: 113-D322A1XL-012 Option ROM Version: 113-D322A1XL-012 EFI Driver Version: 01.01.231 Metal Support: Metal 3 Displays: iMac: Display Type: Built-In Retina LCD Resolution: Retina 5K (5120 x 2880) Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.1 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: 2.12.1 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.3 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 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 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: 1.5.13 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: 1.0.3 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: 1.12.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 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: 1.33.2 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-XMAS: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.0 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 et-xmlfile: 1.1.0 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.0 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: 5.5.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.8 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openpyxl: 3.1.2 openvr: 1.23.701 packaging: 21.3 pandas: 2.2.1 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.9.0 pickleshare: 0.7.5 Pillow: 10.0.1 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 QtRangeSlider: 0.1.5 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 seaborn: 0.13.2 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: 1.0.7 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.5 sphinxcontrib-htmlhelp: 2.0.4 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.6 sphinxcontrib-serializinghtml: 1.1.9 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: 2023.3 urllib3: 2.1.0 wcwidth: 0.2.12 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