id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20445 H-Bonds: acc_phi_psi() bad number of arguments bhogeba@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-26.5-arm64-arm-64bit ChimeraX Version: 1.10rc202506100450 (2025-06-10 04:50:02 UTC) Description Replace this text with list of actions that caused this problem to occur Log: UCSF ChimeraX version: 1.10rc202506100450 (2025-06-10) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/bhogeba/T4_dimeric > tRNA/Ecoli_M1RNP/3'CCA_T4_tRNA/5mM_Ca/Reextracted > /5mM_Ca_3CCA_Ser_J2562/5mM_Ca- > holoM1-3CCAT4-J2562-M1-RMSD_10_ions_coot-1.pdb"" format pdb Chain information for 5mM_Ca-holoM1-3CCAT4-J2562-M1-RMSD_10_ions_coot-1.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available > open ""/Users/bhogeba/T4_dimeric tRNA/Gst_RNP/10mM_Ca_GstRNaseP_T4 > complex_J635_P21/J635Pro-coot-0.pdb"" Summary of feedback from opening /Users/bhogeba/T4_dimeric tRNA/Gst_RNP/10mM_Ca_GstRNaseP_T4 complex_J635_P21/J635Pro-coot-0.pdb --- warnings | Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 1910 messages similar to the above omitted PDB SEQRES record for chain C is incomplete. Ignoring input sequence records as basis for sequence. Chain information for J635Pro-coot-0.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available > open ""/Users/bhogeba/T4_dimeric tRNA/Gst_RNP/10mM_Ca_GstRNaseP_T4 > complex_J635_P21/GstRNaseP_T4 complex_J635_P21_1.mrc"" Opened GstRNaseP_T4 complex_J635_P21_1.mrc as #3, grid size 312,312,312, pixel 1.36, shown at level 0.0145, step 2, values float32 > open ""/Users/bhogeba/T4_dimeric tRNA/Gst_RNP/10mM_Ca_GstRNaseP_T4 > complex_J635_P21/GstRNP_T4_complex_J635REP.pdb"" Chain information for GstRNP_T4_complex_J635REP.pdb #4 --- Chain | Description A | No description available B | No description available C | No description available F | No description available > hide #1 models > volume #3 level 0.1461 > hide #!3 models > show #!3 models > hide #4 models > show #4 models > hide #!3 models > show #!3 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #4 models > volume #3 level 0.2752 > show #4 models > hide #4 models > hide #!3 models > show #!3 models > hide #2 models > volume #3 level 0.08868 > show #4 models > hide #!3 models > show #!3 models > hide #!3 models > color #4 bychain > show #1 models > hide #4 models > color #1 bychain > nucleotides #1 atoms > style nucleic & #1 stick Changed 11611 atom styles > select #1/B:43 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 37 atoms, 36 bonds, 5 residues, 1 model selected > select up 941 atoms, 956 bonds, 115 residues, 1 model selected > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > show sel atoms > select clear > open ""/Users/bhogeba/T4_dimeric tRNA/Ecoli_M1RNP/Published > structure/Published_7uo1.pdb"" Chain information for Published_7uo1.pdb #5 --- Chain | Description A | No description available B | No description available C | No description available > hide #1 models > color #!5 bychain > nucleotides #!5 atoms > style nucleic & #!5 stick Changed 14693 atom styles > select #5/A:14 11 atoms, 10 bonds, 1 residue, 1 model selected > select up 163 atoms, 166 bonds, 10 residues, 1 model selected > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > show sel atoms > select clear > select add #5 16588 atoms, 17761 bonds, 20 pseudobonds, 577 residues, 2 models selected > select H 5894 atoms, 567 residues, 1 model selected > delete atoms sel > delete bonds sel > select #1/A#2/A#4/A#5/A 26894 atoms, 30029 bonds, 1320 residues, 4 models selected > ui tool show Matchmaker > matchmaker #2,4#!5 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 5mM_Ca-holoM1-3CCAT4-J2562-M1-RMSD_10_ions_coot-1.pdb, chain A (#1) with J635Pro-coot-0.pdb, chain A (#2), sequence alignment score = 1343.1 RMSD between 39 pruned atom pairs is 1.150 angstroms; (across all 348 pairs: 36.851) Matchmaker 5mM_Ca-holoM1-3CCAT4-J2562-M1-RMSD_10_ions_coot-1.pdb, chain A (#1) with GstRNP_T4_complex_J635REP.pdb, chain A (#4), sequence alignment score = 1343.1 RMSD between 37 pruned atom pairs is 1.051 angstroms; (across all 348 pairs: 36.824) Matchmaker 5mM_Ca-holoM1-3CCAT4-J2562-M1-RMSD_10_ions_coot-1.pdb, chain A (#1) with Published_7uo1.pdb, chain B (#5), sequence alignment score = 2219.3 RMSD between 183 pruned atom pairs is 1.256 angstroms; (across all 373 pairs: 3.686) > show #2 models > hide #2 models > show #1 models > hide sel & #1#!5 atoms > select clear > hide #1#!5 atoms > color #1#!5 bychain > select #5/C:-4 20 atoms, 21 bonds, 1 residue, 1 model selected > select add #5/C:-3 40 atoms, 42 bonds, 2 residues, 1 model selected > select add #5/C:-2 60 atoms, 63 bonds, 3 residues, 1 model selected > select add #5/C:-1 82 atoms, 87 bonds, 4 residues, 1 model selected > select add #1/C:76 102 atoms, 108 bonds, 5 residues, 2 models selected > select add #5/C:1 125 atoms, 133 bonds, 6 residues, 2 models selected > select add #5/C:0 145 atoms, 154 bonds, 7 residues, 2 models selected > select subtract #5/C:-1 123 atoms, 130 bonds, 6 residues, 2 models selected > select add #5/C:-1 145 atoms, 154 bonds, 7 residues, 2 models selected > select add #1/C:74 167 atoms, 178 bonds, 8 residues, 2 models selected > select add #1/C:73 190 atoms, 203 bonds, 9 residues, 2 models selected > select add #1/C:72 212 atoms, 227 bonds, 10 residues, 2 models selected > select add #1/C:71 235 atoms, 252 bonds, 11 residues, 2 models selected > select add #1/C:75 255 atoms, 273 bonds, 12 residues, 2 models selected > select add #1/C:77 278 atoms, 298 bonds, 13 residues, 2 models selected > show sel atoms > nucleotides sel atoms > style nucleic & sel stick Changed 278 atom styles > hbonds sel reveal true 141 hydrogen bonds found > select clear [Repeated 1 time(s)] > hide #1 models > show #1 models > hide #!5 models > hide #6 models > show #6 models > show #!5 models > hide #!5 models > hide #1 models > show #!5 models > select #5/A:13 7 atoms, 7 bonds, 1 residue, 1 model selected > select add #5/A:14 13 atoms, 12 bonds, 2 residues, 1 model selected > select add #5/A:15 22 atoms, 20 bonds, 3 residues, 1 model selected > select add #5/A:16 33 atoms, 31 bonds, 4 residues, 1 model selected > select add #5/A:17 40 atoms, 37 bonds, 5 residues, 1 model selected > select add #5/A:18 51 atoms, 48 bonds, 6 residues, 1 model selected > select add #5/A:19 58 atoms, 54 bonds, 7 residues, 1 model selected > select add #5/A:20 69 atoms, 65 bonds, 8 residues, 1 model selected > select add #5/A:21 78 atoms, 73 bonds, 9 residues, 1 model selected > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > show sel atoms > select #5/B:352 22 atoms, 24 bonds, 1 residue, 1 model selected > show sel atoms > select #5/B:247 20 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > select #5/B:248 22 atoms, 24 bonds, 1 residue, 1 model selected > select #5/B:247 20 atoms, 21 bonds, 1 residue, 1 model selected > select #5/B:248 22 atoms, 24 bonds, 1 residue, 1 model selected > select #5/C:-1 22 atoms, 24 bonds, 1 residue, 1 model selected > select add #5/B:333 44 atoms, 48 bonds, 2 residues, 1 model selected > select add #5/B:332 67 atoms, 73 bonds, 3 residues, 1 model selected > select clear > show #1 models > hide #6 models > show #6 models > hide #6 models > hide #!5 models > show #!5 models > select add #1/B:11 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #1/B:10 17 atoms, 15 bonds, 2 residues, 1 model selected > select add #1/B:13 28 atoms, 26 bonds, 3 residues, 1 model selected > select add #1/B:12 37 atoms, 34 bonds, 4 residues, 1 model selected > select add #1/B:14 46 atoms, 42 bonds, 5 residues, 1 model selected > select add #1/B:15 55 atoms, 50 bonds, 6 residues, 1 model selected > select add #1/B:16 62 atoms, 56 bonds, 7 residues, 1 model selected > select add #1/B:17 73 atoms, 67 bonds, 8 residues, 1 model selected > select add #1/B:18 82 atoms, 75 bonds, 9 residues, 1 model selected > select add #1/B:19 91 atoms, 83 bonds, 10 residues, 1 model selected > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > show sel atoms > select clear > hide #1 models > hide #!5 models > show #1 models > open ""/Users/bhogeba/T4_dimeric > tRNA/Ecoli_M1RNP/3'CCA_T4_tRNA/5mM_Ca/Reextracted > /5mM_Ca_3CCA_Ser_J2562/5mM_Ca- > holoM1-3CCAT4-J2562-M1-RMSD_10_ions_coot-1.pdb"" Chain information for 5mM_Ca-holoM1-3CCAT4-J2562-M1-RMSD_10_ions_coot-1.pdb #7 --- Chain | Description A | No description available B | No description available C | No description available > nucleotides #1,7 atoms > style nucleic & #1,7 stick Changed 23222 atom styles > color #1,7 bychain > close #1 > select add #7 12594 atoms, 13953 bonds, 698 residues, 1 model selected > nucleotides sel atoms > style nucleic & sel stick Changed 11611 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 11611 atom styles > show sel atoms > select subtract #7 Nothing selected > hide #7 atoms > select #7/C:76 20 atoms, 21 bonds, 1 residue, 1 model selected > select add #7/C:75 40 atoms, 42 bonds, 2 residues, 1 model selected > select add #7/C:74 62 atoms, 66 bonds, 3 residues, 1 model selected > select add #7/C:73 85 atoms, 91 bonds, 4 residues, 1 model selected > select add #7/C:72 107 atoms, 115 bonds, 5 residues, 1 model selected > select add #7/C:71 130 atoms, 140 bonds, 6 residues, 1 model selected > show sel atoms > hbonds sel reveal true 82 hydrogen bonds found > show #6 models > select #7/C:75 20 atoms, 21 bonds, 1 residue, 1 model selected > select #7/B:14 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 91 atoms, 92 bonds, 10 residues, 1 model selected > select up 941 atoms, 956 bonds, 115 residues, 1 model selected > show sel atoms > select #7/A:352 22 atoms, 24 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > show sel atoms > select #7/C:77 23 atoms, 25 bonds, 1 residue, 1 model selected > select #7/C:76 20 atoms, 21 bonds, 1 residue, 1 model selected > select #7/C:77 23 atoms, 25 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select #7/C:76 20 atoms, 21 bonds, 1 residue, 1 model selected > select #7/C:77 23 atoms, 25 bonds, 1 residue, 1 model selected > hbonds sel reveal true 18 hydrogen bonds found > select #7/A:330 22 atoms, 24 bonds, 1 residue, 1 model selected > select clear > select #7/A:353 20 atoms, 21 bonds, 1 residue, 1 model selected > nucleotides sel atoms > style nucleic & sel stick Changed 20 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 20 atom styles > show sel atoms > open ""/Users/bhogeba/T4_dimeric tRNA/Gst_RNP/10mM_Ca_GstRNaseP_T4 > complex_J635_P21/J635Pro.pdb"" Summary of feedback from opening /Users/bhogeba/T4_dimeric tRNA/Gst_RNP/10mM_Ca_GstRNaseP_T4 complex_J635_P21/J635Pro.pdb --- warnings | Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 1910 messages similar to the above omitted PDB SEQRES record for chain C is incomplete. Ignoring input sequence records as basis for sequence. Chain information for J635Pro.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available > hide #6 models > hide #7 models > show #7 models > select add #7 12594 atoms, 13953 bonds, 6 pseudobonds, 698 residues, 2 models selected > select subtract #7 Nothing selected > hide #!1 models > hide #7 models > show #!1 models > color #!1 bychain > show #2 models > color #2#!1 bychain > hide #!1 models > open ""/Users/bhogeba/T4_dimeric > tRNA/Ecoli_M1RNP/3'CCA_T4_tRNA/5mM_Ca/Reextracted > /5mM_Ca_3CCA_Ser_J2562/J2562_no_Metals.pdb"" Chain information for J2562_no_Metals.pdb #8 --- Chain | Description A | No description available B | No description available C | No description available > hide #2 models > color #8 bychain > buriedArea #1/A,B #1/C Unknown command: measure buriedArea #1/A,B #1/C > buriedArea #8/A,B #8/C Unknown command: measure buriedArea #8/A,B #8/C > buriedArea #8/A #8/C Unknown command: measure buriedArea #8/A #8/C > buriedArea #8/A with #8/C distance 4.0 Unknown command: measure buriedArea #8/A with #8/C distance 4.0 > measure buriedarea #8/A withAtoms2 #8/B Buried area between #8/A and #8/B = 1235.2 area #8/A = 54424, area #8/B = 6440.1, area both = 58394 > measure buriedarea #8/A,B withAtoms2 #8/C Buried area between #8/A,B and #8/C = 2596.5 area #8/A,B = 58394, area #8/C = 26800, area both = 80001 > measure buriedarea #8/A,B withAtoms2 #8/C distance 4.0 Expected a keyword > surface #8 > measure buriedarea #8/A,B withAtoms2 #8/C select true cutoffArea 4 Buried area between #8/A,B and #8/C = 2596.5 area #8/A,B = 58394, area #8/C = 26800, area both = 80001 > color sel yellow target s > hide sel surfaces [Repeated 1 time(s)] > show sel surfaces > select clear > hide #!8 surfaces > show #!8 surfaces > hide #!8 surfaces > measure buriedarea #8/A,B withAtoms2 #8/C select true cutoffArea 4 Buried area between #8/A,B and #8/C = 2596.5 area #8/A,B = 58394, area #8/C = 26800, area both = 80001 > color sel yellow target s > color (#!8 & sel) cyan > show sel surfaces > hide sel surfaces > select clear > nucleotides #!8 atoms > style nucleic & #!8 stick Changed 11611 atom styles > measure buriedarea #8/A,B withAtoms2 #8/C select true cutoffArea 4 Buried area between #8/A,B and #8/C = 2596.5 area #8/A,B = 58394, area #8/C = 26800, area both = 80001 > hbonds sel reveal true Skipping possible acceptor with bad geometry: J635Pro.pdb #1/C U 155 O4 Wrong number of grandchild atoms for phi/psi acceptor J635Pro.pdb #1/C U 155 O4 donor: J635Pro.pdb #1/C A 139 N6 acceptor: J635Pro.pdb #1/C C 156 N3 Traceback (most recent call last): File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/toolbar/tool.py"", line 230, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py"", line 397, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/__init__.py"", line 1419, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/__init__.py"", line 66, in run_provider shortcuts.run_provider(session, name) File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 1394, in run_provider keyboard_shortcuts(session).try_shortcut(name) File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 403, in try_shortcut self.run_shortcut(keys) File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 421, in run_shortcut sc.run(self.session, status = self._enabled) File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 340, in run f(s) File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 594, in run_expanded_command run(session, cmd) File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 537, in run run_command(session, command, **kw) File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3219, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/hbonds/cmd.py"", line 94, in cmd_hbonds result = hb_func(session, struct_info, dist_slop=dist_slop, angle_slop=angle_slop, **base_kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/hbonds/hbond.py"", line 615, in find_hbonds if not geom_func(donor_atom, donor_hyds, *args): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/hbonds/hbond.py"", line 615, in find_hbonds if not geom_func(donor_atom, donor_hyds, *args): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. > hbonds sel reveal true Skipping possible acceptor with bad geometry: J635Pro.pdb #1/C U 155 O4 Wrong number of grandchild atoms for phi/psi acceptor J635Pro.pdb #1/C U 155 O4 donor: J635Pro.pdb #1/C A 139 N6 acceptor: J635Pro.pdb #1/C C 156 N3 Traceback (most recent call last): File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/toolbar/tool.py"", line 230, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py"", line 397, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/__init__.py"", line 1419, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/__init__.py"", line 66, in run_provider shortcuts.run_provider(session, name) File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 1394, in run_provider keyboard_shortcuts(session).try_shortcut(name) File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 403, in try_shortcut self.run_shortcut(keys) File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 421, in run_shortcut sc.run(self.session, status = self._enabled) File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 340, in run f(s) File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 594, in run_expanded_command run(session, cmd) File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 537, in run run_command(session, command, **kw) File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3219, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/hbonds/cmd.py"", line 94, in cmd_hbonds result = hb_func(session, struct_info, dist_slop=dist_slop, angle_slop=angle_slop, **base_kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/hbonds/hbond.py"", line 615, in find_hbonds if not geom_func(donor_atom, donor_hyds, *args): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/hbonds/hbond.py"", line 615, in find_hbonds if not geom_func(donor_atom, donor_hyds, *args): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. > select clear > select #8/C:145 20 atoms, 21 bonds, 1 residue, 1 model selected > select add #8/C:144 40 atoms, 42 bonds, 2 residues, 2 models selected > select add #8/C:146 60 atoms, 63 bonds, 3 residues, 2 models selected > select add #8/C:143 83 atoms, 88 bonds, 4 residues, 2 models selected > select add #8/C:142 106 atoms, 113 bonds, 5 residues, 2 models selected > select add #8/C:151 126 atoms, 134 bonds, 6 residues, 2 models selected > select add #8/C:152 146 atoms, 155 bonds, 7 residues, 2 models selected > select add #8/C:153 166 atoms, 176 bonds, 8 residues, 2 models selected > select add #8/A:118 188 atoms, 200 bonds, 9 residues, 2 models selected > select add #8/A:233 210 atoms, 224 bonds, 10 residues, 3 models selected > select add #8/A:234 232 atoms, 248 bonds, 11 residues, 3 models selected > select add #8/A:5 252 atoms, 269 bonds, 12 residues, 3 models selected > select subtract #8/A:5 232 atoms, 248 bonds, 11 residues, 3 models selected > select add #8/C:154 254 atoms, 272 bonds, 12 residues, 3 models selected > select add #8/C:155 274 atoms, 293 bonds, 13 residues, 3 models selected > select add #8/C:156 294 atoms, 314 bonds, 14 residues, 3 models selected > select add #8/A:359 314 atoms, 335 bonds, 15 residues, 3 models selected > select add #8/A:70 334 atoms, 356 bonds, 16 residues, 3 models selected > select add #8/A:69 354 atoms, 377 bonds, 17 residues, 3 models selected > select add #8/A:360 374 atoms, 398 bonds, 18 residues, 3 models selected > hbonds sel reveal true Skipping possible acceptor with bad geometry: J635Pro.pdb #1/C U 155 O4 Wrong number of grandchild atoms for phi/psi acceptor J635Pro.pdb #1/C U 155 O4 donor: J635Pro.pdb #1/C A 139 N6 acceptor: J635Pro.pdb #1/C C 156 N3 Traceback (most recent call last): File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/toolbar/tool.py"", line 230, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py"", line 397, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/__init__.py"", line 1419, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/__init__.py"", line 66, in run_provider shortcuts.run_provider(session, name) File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 1394, in run_provider keyboard_shortcuts(session).try_shortcut(name) File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 403, in try_shortcut self.run_shortcut(keys) File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 421, in run_shortcut sc.run(self.session, status = self._enabled) File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 340, in run f(s) File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 594, in run_expanded_command run(session, cmd) File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 537, in run run_command(session, command, **kw) File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3219, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/hbonds/cmd.py"", line 94, in cmd_hbonds result = hb_func(session, struct_info, dist_slop=dist_slop, angle_slop=angle_slop, **base_kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/hbonds/hbond.py"", line 615, in find_hbonds if not geom_func(donor_atom, donor_hyds, *args): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given File ""/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/hbonds/hbond.py"", line 615, in find_hbonds if not geom_func(donor_atom, donor_hyds, *args): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M3 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.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: Mac15,6 Model Number: Z1AU00299LL/A Chip: Apple M3 Pro Total Number of Cores: 11 (5 Performance and 6 Efficiency) Memory: 18 GB System Firmware Version: 18000.120.36 OS Loader Version: 18000.120.36 Software: System Software Overview: System Version: macOS 26.5 (25F71) Kernel Version: Darwin 25.5.0 Time since boot: 6 hours, 13 minutes Graphics/Displays: Apple M3 Pro: Chipset Model: Apple M3 Pro Type: GPU Bus: Built-In Total Number of Cores: 14 Vendor: Apple (0x106b) Metal Support: Metal 4 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 DELL P2715Q: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported DELL P2715Q: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 30.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.4.0 babel: 2.17.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.3.4 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: 14.1.18 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: 1.10rc202506100450 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: 2.2.1 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: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-QScore: 1.2 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: 1.45.1 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-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.2 coverage: 7.8.2 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.14 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.58.2 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: 4.4.4 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib-inline: 0.1.7 msgpack: 1.1.0 narwhals: 2.21.2 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: 2.4.6 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 24.2 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 plotly: 6.7.0 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 pyelftools: 0.32 Pygments: 2.18.0 pyKVFinder: 0.9.2 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: 8.4.0 pytest-cov: 6.1.1 python-dateutil: 2.9.0.post0 pytz: 2025.2 pyzmq: 26.4.0 qtconsole: 5.5.2 QtPy: 2.4.3 qtshim: 1.1 RandomWords: 0.4.0 requests: 2.32.3 roman-numerals-py: 3.1.0 scipy: 1.14.0 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 tomlkit: 0.15.0 tornado: 6.5.1 traitlets: 5.14.3 typing_extensions: 4.14.0 tzdata: 2025.2 urllib3: 2.4.0 wcwidth: 0.2.13 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.14 }}} " defect closed normal Structure Analysis not a bug all ChimeraX