id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19379 Crash in Qt destructor during traceback release chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-13.6.5-arm64-arm-64bit ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 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 0x00000001f173e100 (most recent call first): File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 368 in event_loop File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1057 in init File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1220 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, 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""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""64c17a9925d75a7281053d4c"", ""factorPackIds"" : { ""SIRI_AUDIO_DISABLE_MEDIA_ENTITY_SYNC"" : ""64d29746ad29a465b3bbeace"" }, ""deploymentId"" : 240000002 }, { ""rolloutId"" : ""6410af69ed1e1e7ab93ed169"", ""factorPackIds"" : { }, ""deploymentId"" : 240000011 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.10.1 (2025-07-24) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/kurscheidt/Documents/MassSpec core facility/Crosslinking- > MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251110_Analysis_XL- > MS_SMG5-SMG6-RNA_high-BS3-conc.cxs"" > set bgColor #ffffff00 > view name session-start opened ChimeraX session > close #9-27 > close #2 > close #32 > close #31 > hide #3 models > show #6 models > show #7 models > show #8 models > mmaker #6-8 to #1.8/B Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker Session_Export.cif, chain B (#1.8) with ranked_0.pdb, chain B (#6), sequence alignment score = 1090.5 RMSD between 197 pruned atom pairs is 0.813 angstroms; (across all 217 pairs: 1.696) Matchmaker Session_Export.cif, chain B (#1.8) with ranked_1.pdb, chain B (#7), sequence alignment score = 1098.3 RMSD between 181 pruned atom pairs is 0.745 angstroms; (across all 217 pairs: 2.210) Matchmaker Session_Export.cif, chain B (#1.8) with ranked_2.pdb, chain B (#8), sequence alignment score = 1091.1 RMSD between 200 pruned atom pairs is 0.694 angstroms; (across all 217 pairs: 1.628) > mmaker #6-8 to #1.8/A:700-900 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker Session_Export.cif, chain A (#1.8) with ranked_0.pdb, chain A (#6), sequence alignment score = 994.1 RMSD between 185 pruned atom pairs is 0.722 angstroms; (across all 201 pairs: 1.196) Matchmaker Session_Export.cif, chain A (#1.8) with ranked_1.pdb, chain A (#7), sequence alignment score = 1026.5 RMSD between 190 pruned atom pairs is 0.648 angstroms; (across all 201 pairs: 0.973) Matchmaker Session_Export.cif, chain A (#1.8) with ranked_2.pdb, chain A (#8), sequence alignment score = 1003.1 RMSD between 190 pruned atom pairs is 0.658 angstroms; (across all 201 pairs: 0.993) > mmaker #28-30 to #1.8/A:700-900 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker Session_Export.cif, chain A (#1.8) with ranked_22.pdb, chain A (#28), sequence alignment score = 997.7 RMSD between 185 pruned atom pairs is 0.803 angstroms; (across all 201 pairs: 1.176) Matchmaker Session_Export.cif, chain A (#1.8) with ranked_23.pdb, chain A (#29), sequence alignment score = 997.7 RMSD between 182 pruned atom pairs is 0.765 angstroms; (across all 201 pairs: 1.202) Matchmaker Session_Export.cif, chain A (#1.8) with ranked_24.pdb, chain A (#30), sequence alignment score = 1015.7 RMSD between 187 pruned atom pairs is 0.821 angstroms; (across all 201 pairs: 1.132) > show #28 models > show #29 models > show #30 models > show #4 models > show #5 models > hide #4 models > show #4 models > hide #4 models > hide #29 models > hide #30 models > hide #7 models > hide #8 models > hide #6 models > hide #28 models > show #28 models > hide #28 models > ui tool show XMAS > show #4 models > hide #5 models > hide #4 models > show #5 models > hide #5 models > select subtract #5 Nothing selected > show #4 models > close #7-8 > close #29-30 > show #3 models > hide #3 models > show #3 models > hide #3 models > save ""/Users/kurscheidt/Documents/MassSpec core facility/Crosslinking- > MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251117_Analysis_XL- > MS_SMG5-SMG6-RNA_high-BS3-conc.cxs"" Pseudobonds are stored in /Users/kurscheidt/Documents/MassSpec core facility/Crosslinking- MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251117_Intralinks_cut- off_AF3-pred_sample-04.pb > hide #4 models > select subtract #4 Nothing selected > select add #2 56 pseudobonds, 1 model selected > show #5 models > hide #2 models > save ""/Users/kurscheidt/Documents/MassSpec core facility/Crosslinking- > MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251117_Analysis_XL- > MS_Comparison_SMG5-SMG6-RNA_high-BS3-conc.cxs"" > select add #5 12 pseudobonds, 1 model selected > select add #4 175 pseudobonds, 2 models selected > close #2-5 > close #1.1-7 > close #1.10-11#1.9 > rename #1.8 id #1 > hide #!1 models > show #!1 models > rename #6 id #2 > rename #28 id #3 Peptide pair mapping of XlinkX evidence file: /Users/kurscheidt/Documents/MassSpec core facility/Crosslinking- MS/20251022_SMG5-SMG6+RNA_BS3/Results/20251024_ECL1_ENO9_68min_NiKr_SA_F-45-55_Orbi5918_Sample02_Crosslinks.txt Unique peptide pairs: 194 out of 194 Unique peptide pairs with pseudobonds: 188 Pseudobonds are stored in /Users/kurscheidt/Documents/MassSpec core facility/Crosslinking- MS/20251022_SMG5-SMG6+RNA_BS3/Results/20251024_ECL1_ENO9_68min_NiKr_SA_F-45-55_Orbi5918_Sample02_Crosslinks_1.8.pb Mapping information is stored in /Users/kurscheidt/Documents/MassSpec core facility/Crosslinking- MS/20251022_SMG5-SMG6+RNA_BS3/Results/20251024_ECL1_ENO9_68min_NiKr_SA_F-45-55_Orbi5918_Sample02_Crosslinks_1.8.tsv Peptide pair mapping of XlinkX evidence file: /Users/kurscheidt/Documents/MassSpec core facility/Crosslinking- MS/20251022_SMG5-SMG6+RNA_BS3/Results/20251024_ECL1_ENO9_68min_NiKr_SA_F-45-55_Orbi5918_Sample04_Crosslinks.txt Unique peptide pairs: 183 out of 183 Unique peptide pairs with pseudobonds: 177 Pseudobonds are stored in /Users/kurscheidt/Documents/MassSpec core facility/Crosslinking- MS/20251022_SMG5-SMG6+RNA_BS3/Results/20251024_ECL1_ENO9_68min_NiKr_SA_F-45-55_Orbi5918_Sample04_Crosslinks_1.8.pb Mapping information is stored in /Users/kurscheidt/Documents/MassSpec core facility/Crosslinking- MS/20251022_SMG5-SMG6+RNA_BS3/Results/20251024_ECL1_ENO9_68min_NiKr_SA_F-45-55_Orbi5918_Sample04_Crosslinks_1.8.tsv > rename #4 20251024_Orbi5918_02_Crosslinks_1.8.pb > rename #5 20251024_Orbi5918_04_Crosslinks_1.8.pb > hide #5 models Please select pseudobonds Please select pseudobonds > select add #4 187 pseudobonds, 1 model selected > show #5 models > select add #5 362 pseudobonds, 2 models selected > hide #4 models > select subtract #4 175 pseudobonds, 1 model selected > select add #4 362 pseudobonds, 2 models selected > show #4 models > hide #5 models > hide #4 models > select subtract #5 187 pseudobonds, 1 model selected > select subtract #4 Nothing selected > hide #1.8 models > show #1.8 models > hide #7 models > show #7 models > hide #7 models > show #7 models > hide #7 models > show #7 models > hide #7 models > hide #6 models > show #7 models > show #6 models > select add #6 187 pseudobonds, 1 model selected > select add #7 362 pseudobonds, 2 models selected > close #6-7 Traceback (most recent call last): File ""/Users/kurscheidt/Library/Application Support/ChimeraX/1.10/lib/python/site-packages/chimerax/XMAS/tool.py"", line 1015, in self.get_names(names_menu, pbs_dict, f)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Users/kurscheidt/Library/Application Support/ChimeraX/1.10/lib/python/site-packages/chimerax/XMAS/tool.py"", line 1246, in get_names function(pbs_dict, names) File ""/Users/kurscheidt/Library/Application Support/ChimeraX/1.10/lib/python/site-packages/chimerax/XMAS/tool.py"", line 1115, in create_distance_plot plt.yticks(plt.yticks()[0], names) File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/matplotlib/pyplot.py"", line 2324, in yticks labels_out = ax.set_yticklabels(labels, minor=minor, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/matplotlib/axes/_base.py"", line 74, in wrapper return get_method(self)(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/matplotlib/axis.py"", line 2106, in set_ticklabels raise ValueError( ValueError: The number of FixedLocator locations (6), usually from a call to set_ticks, does not match the number of labels (2). ValueError: The number of FixedLocator locations (6), usually from a call to set_ticks, does not match the number of labels (2). File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/matplotlib/axis.py"", line 2106, in set_ticklabels raise ValueError( See log for complete Python traceback. > select add #4 187 pseudobonds, 1 model selected > select add #5 362 pseudobonds, 2 models selected Traceback (most recent call last): File ""/Users/kurscheidt/Library/Application Support/ChimeraX/1.10/lib/python/site-packages/chimerax/XMAS/tool.py"", line 1015, in self.get_names(names_menu, pbs_dict, f)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Users/kurscheidt/Library/Application Support/ChimeraX/1.10/lib/python/site-packages/chimerax/XMAS/tool.py"", line 1246, in get_names function(pbs_dict, names) File ""/Users/kurscheidt/Library/Application Support/ChimeraX/1.10/lib/python/site-packages/chimerax/XMAS/tool.py"", line 1115, in create_distance_plot plt.yticks(plt.yticks()[0], names) File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/matplotlib/pyplot.py"", line 2324, in yticks labels_out = ax.set_yticklabels(labels, minor=minor, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/matplotlib/axes/_base.py"", line 74, in wrapper return get_method(self)(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/matplotlib/axis.py"", line 2106, in set_ticklabels raise ValueError( ValueError: The number of FixedLocator locations (6), usually from a call to set_ticks, does not match the number of labels (2). ValueError: The number of FixedLocator locations (6), usually from a call to set_ticks, does not match the number of labels (2). File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/matplotlib/axis.py"", line 2106, in set_ticklabels raise ValueError( See log for complete Python traceback. > show #4 models > show #5 models > save ""/Users/kurscheidt/Documents/MassSpec core facility/Crosslinking- > MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251117_Visualization_02-vs-04_CO-31A.pb"" > #4,5 Saved 362 pseudobonds to file /Users/kurscheidt/Documents/MassSpec core facility/Crosslinking- MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251117_Visualization_02-vs-04_CO-31A.pb > save ""/Users/kurscheidt/Documents/MassSpec core facility/Crosslinking- > MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251117_Visualization_02-vs-04_CO-31A.pb"" > #4,5 Saved 362 pseudobonds to file /Users/kurscheidt/Documents/MassSpec core facility/Crosslinking- MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251117_Visualization_02-vs-04_CO-31A.pb > open ""/Users/kurscheidt/Documents/MassSpec core facility/Crosslinking- > MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251117_Visualization_02-vs-04_CO-31A.pb"" Opened Pseudobonds 20251117_Visualization_02-vs-04_CO-31A.pb, 362 bonds > hide #5 models > hide #4 models > select subtract #5 187 pseudobonds, 1 model selected > select subtract #4 Nothing selected > select add #5 175 pseudobonds, 1 model selected > select add #4 362 pseudobonds, 2 models selected > select subtract #4 175 pseudobonds, 1 model selected > select subtract #5 Nothing selected > close #6 > show #4 models > show #5 models > select add #5 175 pseudobonds, 1 model selected > select add #4 362 pseudobonds, 2 models selected Pseudobonds are stored in /Users/kurscheidt/Documents/MassSpec core facility/Crosslinking- MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251117_Crosslinks_02-vs-04_AF3-model_CO-31A.pb > hide #5 models > hide #4 models > select add #6 433 pseudobonds, 3 models selected > select subtract #5 258 pseudobonds, 2 models selected > select subtract #4 71 pseudobonds, 1 model selected Venn diagrams can only be plotted for two or three groups > select add #5 246 pseudobonds, 2 models selected > select add #4 433 pseudobonds, 3 models selected > select subtract #6 362 pseudobonds, 2 models selected > hide #6 models > show #5 models > show #4 models > hide #5 models > select subtract #5 187 pseudobonds, 1 model selected Pseudobonds are stored in /Users/kurscheidt/Documents/MassSpec core facility/Crosslinking- MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251117_Crosslinks_02_AF3-model_CO-31A.pb > select add #5 362 pseudobonds, 2 models selected > show #5 models > hide #4 models > select subtract #4 175 pseudobonds, 1 model selected Pseudobonds are stored in /Users/kurscheidt/Documents/MassSpec core facility/Crosslinking- MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251117_Crosslinks_04_AF3-model_CO-31A.pb > hide #5 models > select subtract #5 Nothing selected > select add #7 66 pseudobonds, 1 model selected > select add #8 124 pseudobonds, 2 models selected > save ""/Users/kurscheidt/Documents/MassSpec core facility/Crosslinking- > MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251117_Analysis_XL- > MS_Comparison_SMG5-SMG6-RNA_high-BS3-conc.cxs"" > show #6 models > hide #7 models > hide #8 models > select subtract #8 66 pseudobonds, 1 model selected > select subtract #7 Nothing selected > hide #6 models > show #6 models > select subtract #6 66 pseudobonds, 1 model selected > select subtract #7 Nothing selected > hide #6 models > show #7 models > select add #7 66 pseudobonds, 1 model selected > show #8 models > select add #8 124 pseudobonds, 2 models selected > select intersect #7 & #8 Nothing selected > show #6 models > hide #8 models > hide #7 models > hide #6 models > show #8 models > show #6 models > hide #6 models > show #6 models > hide #6 models > show #6 models > hide #8 models > hide #6 models > show #6 models > select add #6 71 pseudobonds, 1 model selected Pseudobonds are stored in /Users/kurscheidt/Documents/MassSpec core facility/Crosslinking- MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251117_Crosslinks_02-vs-04_Intralinks_AF3-model_CO-31A.pb > hide #6 models > select subtract #6 Nothing selected > select add #6 71 pseudobonds, 1 model selected > show #6 models > hide #9 models Pseudobonds are stored in /Users/kurscheidt/Documents/MassSpec core facility/Crosslinking- MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251117_Crosslinks_02-vs-04_Interlinks_AF3-model_CO-31A.pb > color #10 #ffd479ff models > hide #6 models > show #9 models > hide #10 models > show #10 models > select add #10 73 pseudobonds, 2 models selected > select add #9 142 pseudobonds, 3 models selected > select subtract #6 71 pseudobonds, 2 models selected > hide #10 models > select subtract #10 69 pseudobonds, 1 model selected > save ""/Users/kurscheidt/Documents/MassSpec core facility/Crosslinking- > MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251117_Analysis_XL- > MS_Comparison_SMG5-SMG6-RNA_high-BS3-conc.cxs"" > show #10 models > hide #9 models > select #1.8/B 1716 atoms, 1744 bonds, 44 pseudobonds, 217 residues, 7 models selected > ui tool show ""Renumber Residues"" > renumber #1.8/B start 800 217 residues renumbered > select #1.8/A 6859 atoms, 6981 bonds, 556 pseudobonds, 855 residues, 7 models selected > ui tool show ""Renumber Residues"" > renumber #1.8/A start 565 855 residues renumbered > select clear > select add #7 66 pseudobonds, 1 model selected > hide #10 models Pseudobonds are stored in /Users/kurscheidt/Documents/MassSpec core facility/Crosslinking- MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251117_Crosslinks_02_Interlinks_AF3-model_CO-31A.pb > select add #8 124 pseudobonds, 2 models selected > select subtract #7 58 pseudobonds, 1 model selected Pseudobonds are stored in /Users/kurscheidt/Documents/MassSpec core facility/Crosslinking- MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251117_Crosslinks_04_Interlinks_AF3-model_CO-31A.pb > select subtract #8 Nothing selected > hide #12 models > show #12 models > hide #11 models > show #11 models > hide #12 models > show #12 models > select add #11 1 pseudobond, 1 model selected > select add #12 3 pseudobonds, 2 models selected > hide #12 models > hide #11 models > show #9 models > select subtract #11 2 pseudobonds, 1 model selected > select subtract #12 Nothing selected > select add #7 66 pseudobonds, 1 model selected Pseudobonds are stored in /Users/kurscheidt/Documents/MassSpec core facility/Crosslinking- MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251117_Crosslinks_02_Intralinks_AF3-model_CO-31A.pb > select add #8 124 pseudobonds, 2 models selected > select subtract #7 58 pseudobonds, 1 model selected Pseudobonds are stored in /Users/kurscheidt/Documents/MassSpec core facility/Crosslinking- MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251117_Crosslinks_04_Intralinks_AF3-model_CO-31A.pb > hide #9 models > select add #13 123 pseudobonds, 2 models selected > select add #14 179 pseudobonds, 3 models selected > ui mousemode right select > select clear > select add #13 65 pseudobonds, 1 model selected > select subtract #13 Nothing selected > hide #14 models > show #14 models > hide #14 models > show #14 models > hide #14 models > show #14 models > hide #14 models > select add #13 65 pseudobonds, 1 model selected > select add #14 121 pseudobonds, 2 models selected > show #14 models > hide #13 models > select subtract #13 56 pseudobonds, 1 model selected > select add #13 121 pseudobonds, 2 models selected > show #13 models > hide #14 models > select subtract #14 65 pseudobonds, 1 model selected > select clear > select #1.8/B & #13 7 pseudobonds, 1 model selected > hide #13 models > select add #13 65 pseudobonds, 1 model selected > select subtract #13 Nothing selected > select add #13 65 pseudobonds, 1 model selected > select add #14 121 pseudobonds, 2 models selected > show #13 models > show #14 models > select add #14 57 pseudobonds, 2 models selected > select subtract #14 1 pseudobond, 1 model selected > select add #13 65 pseudobonds, 1 model selected > select subtract #13 Nothing selected > select add #14 56 pseudobonds, 1 model selected > hide #14 models > hide #13 models > select subtract #14 Nothing selected > show #13 models > select add #13 65 pseudobonds, 1 model selected Pseudobonds are stored in /Users/kurscheidt/Documents/MassSpec core facility/Crosslinking- MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251117_Crosslinks_02_Intralinks_Interdomain- links_AF3-model_CO-31A.pb > hide #13 models > select subtract #13 Nothing selected > delete sel > hide sel pseudobonds > show sel pseudobonds > delete sel pseudobond Expected a keyword > delete sel pseudobonds Expected a keyword > hide sel pseudobonds Venn diagrams can only be plotted for two or three groups > select pbond delete Expected an objects specifier or a keyword > save ""/Users/kurscheidt/Documents/MassSpec core facility/Crosslinking- > MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251117_Analysis_XL- > MS_Comparison_SMG5-SMG6-RNA_high-BS3-conc.cxs"" > pbond delete sel Must specify exactly 2 atoms to delete pseudobond between; you specified 0 > pbond delete Missing or invalid ""atoms"" argument: empty atom specifier > hide sel pseudobonds ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.10.1 (2025-07-24) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 83.1 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.8.1, Qt 6.8.2 Qt runtime version: 6.8.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro17,1 Model Number: MYDA2D/A Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 10151.101.3 OS Loader Version: 8422.141.2.700.1 Software: System Software Overview: System Version: macOS 13.6.5 (22G621) Kernel Version: Darwin 22.6.0 Time since boot: 3 days, 18 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal ASUS PA279: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 50.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 babel: 2.17.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.6.1 build: 1.2.2.post1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.2 ChimeraX-AddCharge: 1.5.19 ChimeraX-AddH: 2.2.7 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.20.2 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.1.4 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.7 ChimeraX-AtomicLibrary: 14.1.19 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.5.1 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 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: 1.4.1 ChimeraX-Hbonds: 2.5.1 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.6.2 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 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: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.10.1 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.19 ChimeraX-ModelPanel: 1.5.1 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-MutationScores: 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: 1.14.1 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.10 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: 1.1.3 ChimeraX-ProfileGrids: 1.1.3 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.3 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 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: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.7 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.1 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 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: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.45.2 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 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: 1.1.5 ChimeraX-XMAS: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.2 coverage: 7.10.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.15 decorator: 5.2.1 docutils: 0.21.2 et_xmlfile: 2.0.0 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.59.0 funcparserlib: 2.0.0a0 glfw: 2.9.0 grako: 3.16.5 h5py: 3.14.0 html2text: 2024.2.26 idna: 3.10 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.1.0 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.7 jedi: 0.19.1 Jinja2: 3.1.6 jupyter_client: 8.6.3 jupyter_core: 5.8.1 jupyterlab_widgets: 3.0.15 kiwisolver: 1.4.8 line_profiler: 4.2.0 lxml: 5.3.1 lz4: 4.3.2 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib-inline: 0.1.7 msgpack: 1.1.0 ndindex: 1.10.0 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.11.0 numpy: 1.26.4 OpenMM: 8.2.0 openpyxl: 3.1.5 openvr: 1.26.701 packaging: 24.2 pandas: 2.3.3 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.4.0 pip: 25.0.1 pkginfo: 1.11.1 platformdirs: 4.3.8 pluggy: 1.6.0 prompt_toolkit: 3.0.51 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.3.5 pynrrd: 1.0.0 PyOpenGL: 3.1.9 PyOpenGL-accelerate: 3.1.9 pyopenxr: 1.1.4501 pyparsing: 3.2.3 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.8.1 PyQt6-Qt6: 6.8.2 PyQt6-WebEngine-commercial: 6.8.0 PyQt6-WebEngine-Qt6: 6.8.2 PyQt6_sip: 13.10.0 pytest: 8.4.1 pytest-cov: 6.2.1 python-dateutil: 2.9.0.post0 pytz: 2025.2 pyzmq: 27.0.0 qtconsole: 5.5.2 QtPy: 2.4.3 QtRangeSlider: 0.1.5 qtshim: 1.1 RandomWords: 0.4.0 requests: 2.32.3 roman-numerals-py: 3.1.0 scipy: 1.14.0 seaborn: 0.13.2 setuptools: 78.1.0 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.7 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.1.0 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.7.1 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.4 tornado: 6.5.1 traitlets: 5.14.3 typing_extensions: 4.14.1 tzdata: 2025.2 urllib3: 2.5.0 wcwidth: 0.2.13 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.14 }}} " defect closed normal Window Toolkit can't reproduce Tom Goddard all ChimeraX