id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2713 "Clashes: ""Include intramolecule"" option throws error" Elaine Meng Eric Pettersen "{{{ The following bug report has been submitted: Platform: Darwin-17.7.0-x86_64-i386-64bit ChimeraX Version: 0.92 (2019-12-24) Description trying to use Clashes dialog after unchecking ""Include intramolecule"" gives traceback Log: UCSF ChimeraX version: 0.92 (2019-12-24) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 6bkl Summary of feedback from opening 6bkl fetched from pdb --- notes | Fetching compressed mmCIF 6bkl from http://files.rcsb.org/download/6bkl.cif Fetching CCD EU7 from http://ligand-expo.rcsb.org/reports/E/EU7/EU7.cif Fetching CCD RIM from http://ligand-expo.rcsb.org/reports/R/RIM/RIM.cif 6bkl title: Influenza A M2 transmembrane domain bound to rimantadine [more info...] Chain information for 6bkl #1 --- Chain | Description A B C D E F G H | Matrix protein 2 Non-standard residues in 6bkl #1 --- EU7 — (1S)-1-[(3R,5R,7R)-tricyclo[3.3.1.1~3,7~]decan-1-yl]ethan-1-amine (S-rimantadine) RIM — rimantadine (1-(1-adamantyl)ethanamine) 6bkl mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > sym #1 assembly 2 > view > show #2 atoms > style #2 stick Changed 767 atom styles > mlp Map values for surface ""6bkl_A SES surface"": minimum -21.78, mean 1.875, maximum 22.14 Map values for surface ""6bkl_B SES surface"": minimum -21.11, mean 2.503, maximum 22.49 Map values for surface ""6bkl_C SES surface"": minimum -21.15, mean 2.547, maximum 21.52 Map values for surface ""6bkl_D SES surface"": minimum -20.92, mean 2.507, maximum 21.14 Map values for surface ""6bkl_E SES surface"": minimum -21.29, mean 1.889, maximum 21.9 Map values for surface ""6bkl_F SES surface"": minimum -21.19, mean 2.543, maximum 21.97 Map values for surface ""6bkl_G SES surface"": minimum -21.61, mean 2.499, maximum 21.53 Map values for surface ""6bkl_H SES surface"": minimum -21.17, mean 2.462, maximum 21.51 Map values for surface ""6bkl assembly 2_E SES surface"": minimum -21.29, mean 1.889, maximum 21.9 Map values for surface ""6bkl assembly 2_F SES surface"": minimum -21.19, mean 2.543, maximum 21.97 Map values for surface ""6bkl assembly 2_G SES surface"": minimum -21.61, mean 2.499, maximum 21.53 Map values for surface ""6bkl assembly 2_H SES surface"": minimum -21.17, mean 2.462, maximum 21.51 > select #2/E:32@CG2 1 atom, 1 model selected > select up 8 atoms, 7 bonds, 2 models selected > select up 180 atoms, 183 bonds, 2 models selected > hide sel surfaces > select #2/F:39@N 1 atom, 1 model selected > select #2/F:39@N 1 atom, 1 model selected > select up 8 atoms, 7 bonds, 2 models selected > select up 172 atoms, 175 bonds, 2 models selected > hide sel surfaces Expected an objects specifier or a keyword > select ligand 78 atoms, 90 bonds, 2 models selected > hbonds sel 36 hydrogen bonds found > select up 2 atoms, 1 bond, 1 model selected > select up 7 atoms, 6 bonds, 2 models selected > select up 180 atoms, 183 bonds, 2 models selected > select up 188 atoms, 189 bonds, 2 models selected > hide sel surfaces > lighting shadows false > close #2,3 > show #!1 models > style stick Changed 1536 atom styles > delete /a-d > ~surface > close > open 6bkl 6bkl title: Influenza A M2 transmembrane domain bound to rimantadine [more info...] Chain information for 6bkl #1 --- Chain | Description A B C D E F G H | Matrix protein 2 Non-standard residues in 6bkl #1 --- EU7 — (1S)-1-[(3R,5R,7R)-tricyclo[3.3.1.1~3,7~]decan-1-yl]ethan-1-amine (S-rimantadine) RIM — rimantadine (1-(1-adamantyl)ethanamine) 6bkl mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > delete /e-h > style stick Changed 769 atom styles > lighting shadows false > close > open 6bkl format mmCIF fromDatabase pdb 6bkl title: Influenza A M2 transmembrane domain bound to rimantadine [more info...] Chain information for 6bkl #1 --- Chain | Description A B C D E F G H | Matrix protein 2 Non-standard residues in 6bkl #1 --- EU7 — (1S)-1-[(3R,5R,7R)-tricyclo[3.3.1.1~3,7~]decan-1-yl]ethan-1-amine (S-rimantadine) RIM — rimantadine (1-(1-adamantyl)ethanamine) 6bkl mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > style stick Changed 1536 atom styles > preset ""initial styles"" sticks Preset implemented in Python; no expansion to individual ChimeraX commands available. > select ::name=""EU7"" 26 atoms, 30 bonds, 1 model selected > hide protein > ~select Nothing selected > hide :eu7 > show :eu7 > close > open 1gta format mmCIF fromDatabase pdb 1gta title: Crystal structures of A schistosomal drug and vaccine target: glutathione S-transferase from schistosoma japonica and its complex with the leading antischistosomal drug praziquantel [more info...] Chain information for 1gta #1 --- Chain | Description A | glutathione S-transferase 1gta mmCIF Assemblies --- 1| author_and_software_defined_assembly > close > open 6nec Summary of feedback from opening 6nec fetched from pdb --- notes | Fetching compressed mmCIF 6nec from http://files.rcsb.org/download/6nec.cif Fetching CCD XIN from http://ligand-expo.rcsb.org/reports/X/XIN/XIN.cif Fetching CCD FMT from http://ligand-expo.rcsb.org/reports/F/FMT/FMT.cif 6nec title: Structure of ret protein tyrosine kinase domain In complex with nintedanib [more info...] Chain information for 6nec #1 --- Chain | Description A C | Proto-oncogene tyrosine-protein kinase receptor Ret Non-standard residues in 6nec #1 --- FMT — formic acid XIN — methyl (3Z)-3-{[(4-{methyl[(4-methylpiperazin-1-yl)acetyl]amino}phenyl)amino](phenyl)methylidene}-2-oxo-2,3-dihydro-1H-indole-6-carboxylate 6nec mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly > sym #1 assembly 1 > view > sym #1 assembly 2 > view > hide #!2 models > show #!2 models > hide #!3 models > show #!3 models > show #!1 models > close #2,3 > delete /c > select :xin 40 atoms, 44 bonds, 1 model selected Unknown command: start H-Bonds > open startup.cxc > alias reset view orient; view initial > alias start toolshed show $1 > alias whereprefs info path user unversioned config > alias previewts toolshed url https://cxtoolshed- > preview.rbvi.ucsf.edu;toolshed reload available > alias normalts toolshed url https://cxtoolshed.rbvi.ucsf.edu;toolshed reload > available executed startup.cxc > start H-Bonds > hbonds sel interModel false reveal true log true Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 6nec 4 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): /A LYS 758 NZ /A XIN 1101 O26 no hydrogen 2.805 N/A /A ALA 807 N /A XIN 1101 O10 no hydrogen 2.865 N/A /A ASP 892 N /A XIN 1101 O26 no hydrogen 3.073 N/A /A XIN 1101 N9 /A GLU 805 O no hydrogen 2.801 N/A 4 hydrogen bonds found > mlp Map values for surface ""6nec_A SES surface"": minimum -27.86, mean -4.635, maximum 24.27 > surface hide > open 6nja Summary of feedback from opening 6nja fetched from pdb --- notes | Fetching compressed mmCIF 6nja from http://files.rcsb.org/download/6nja.cif Fetching CCD ADE from http://ligand-expo.rcsb.org/reports/A/ADE/ADE.cif 6nja title: Structure of WT RET protein tyrosine kinase domain at 1.92A resolution. [more info...] Chain information for 6nja #2 --- Chain | Description A | Proto-oncogene tyrosine-protein kinase receptor Ret Non-standard residues in 6nja #2 --- FMT — formic acid > mmaker #2 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 6nec, chain A (#1) with 6nja, chain A (#2), sequence alignment score = 1521.2 RMSD between 271 pruned atom pairs is 0.396 angstroms; (across all 280 pairs: 1.290) > show :ade > hide #!2 models > hide #!1 models > show #!2 models > select :ade 10 atoms, 11 bonds, 1 model selected > hbonds sel interModel false reveal true log true Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 2 6nja 5 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 6nja #2/A ALA 807 N 6nja #2/A ADE 1101 N1 no hydrogen 2.912 N/A 6nja #2/A ADE 1101 N6 6nja #2/A GLU 805 O no hydrogen 3.139 N/A 6nja #2/A ADE 1101 N6 6nja #2/A HOH 1302 O no hydrogen 3.165 N/A 6nja #2/A HOH 1302 O 6nja #2/A ADE 1101 N7 no hydrogen 3.429 N/A 6nja #2/A HOH 1345 O 6nja #2/A ADE 1101 N3 no hydrogen 3.345 N/A 5 hydrogen bonds found > cartoon suppressBackboneDisplay false > close #2 > open 6ne7 Summary of feedback from opening 6ne7 fetched from pdb --- note | Fetching compressed mmCIF 6ne7 from http://files.rcsb.org/download/6ne7.cif 6ne7 title: Structure of G810A mutant of RET protein tyrosine kinase domain. [more info...] Chain information for 6ne7 #2 --- Chain | Description A | Proto-oncogene tyrosine-protein kinase receptor Ret Non-standard residues in 6ne7 #2 --- AMP — adenosine monophosphate FMT — formic acid > mmaker #2 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 6nec, chain A (#1) with 6ne7, chain A (#2), sequence alignment score = 1511 RMSD between 272 pruned atom pairs is 0.362 angstroms; (across all 281 pairs: 1.524) > show #!1 models > hide #!1 models > mlp Map values for surface ""6nec_A SES surface"": minimum -27.86, mean -4.635, maximum 24.27 Map values for surface ""6ne7_A SES surface"": minimum -26.8, mean -4.409, maximum 23.73 > surface hide > mmaker #1 to #2 show t 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 6ne7, chain A (#2) with 6nec, chain A (#1), sequence alignment score = 1511 Alignment identifier is 1 RMSD between 272 pruned atom pairs is 0.362 angstroms; (across all 281 pairs: 1.524) Seqview [ID: 1] region 6ne7, chain A..6nec, chain A [111] RMSD: 0.433 > show #!1 models > show sel > cartoon suppressBackboneDisplay false > select :xin 40 atoms, 44 bonds, 1 model selected > hbonds sel intraModel false reveal true log true Finding intermodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 6nec 2 6ne7 4 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 6nec #1/A XIN 1101 N9 6ne7 #2/A GLU 805 O no hydrogen 2.927 N/A 6ne7 #2/A LYS 758 NZ 6nec #1/A XIN 1101 O26 no hydrogen 2.348 N/A 6ne7 #2/A ALA 807 N 6nec #1/A XIN 1101 O10 no hydrogen 2.847 N/A 6ne7 #2/A ASP 892 N 6nec #1/A XIN 1101 O26 no hydrogen 3.103 N/A 4 hydrogen bonds found > hbonds sel interModel false reveal true log true Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 6nec 4 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 6nec #1/A LYS 758 NZ 6nec #1/A XIN 1101 O26 no hydrogen 2.805 N/A 6nec #1/A ALA 807 N 6nec #1/A XIN 1101 O10 no hydrogen 2.865 N/A 6nec #1/A ASP 892 N 6nec #1/A XIN 1101 O26 no hydrogen 3.073 N/A 6nec #1/A XIN 1101 N9 6nec #1/A GLU 805 O no hydrogen 2.801 N/A 4 hydrogen bonds found > close > open 6bkk Summary of feedback from opening 6bkk fetched from pdb --- notes | Fetching compressed mmCIF 6bkk from http://files.rcsb.org/download/6bkk.cif Fetching CCD 308 from http://ligand-expo.rcsb.org/reports/3/308/308.cif 6bkk title: Influenza A M2 transmembrane domain bound to amantadine [more info...] Chain information for 6bkk #1 --- Chain | Description A B C D E F G H | Matrix protein 2 Non-standard residues in 6bkk #1 --- 308 — (3S,5S,7S)-tricyclo[3.3.1.1~3,7~]decan-1-amine (Amantadine) ACE — acetyl group CL — chloride ion 6bkk mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > delete /e-h > style stick Changed 833 atom styles > select ligand 11 atoms, 13 bonds, 1 model selected > hbonds sel interModel false reveal true log true Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 6bkk 1 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): /B 308 101 N1 /A HOH 103 O no hydrogen 3.202 N/A 1 hydrogen bonds found > close > open 6nec 6nec title: Structure of ret protein tyrosine kinase domain In complex with nintedanib [more info...] Chain information for 6nec #1 --- Chain | Description A C | Proto-oncogene tyrosine-protein kinase receptor Ret Non-standard residues in 6nec #1 --- FMT — formic acid XIN — methyl (3Z)-3-{[(4-{methyl[(4-methylpiperazin-1-yl)acetyl]amino}phenyl)amino](phenyl)methylidene}-2-oxo-2,3-dihydro-1H-indole-6-carboxylate 6nec mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly Associated 6nec chain A to 6nec, chain A with 0 mismatches Associated 6nec chain C to 6nec, chain A with 0 mismatches > mlp Map values for surface ""6nec_A SES surface"": minimum -27.86, mean -4.635, maximum 24.27 Map values for surface ""6nec_C SES surface"": minimum -26.84, mean -4.353, maximum 22.31 > delete /c > select :810 4 atoms, 3 bonds, 1 model selected > transparency 50 > show sel > show :810 > select :810 4 atoms, 3 bonds, 1 model selected > label sel > open 6ne7 6ne7 title: Structure of G810A mutant of RET protein tyrosine kinase domain. [more info...] Chain information for 6ne7 #2 --- Chain | Description A | Proto-oncogene tyrosine-protein kinase receptor Ret Non-standard residues in 6ne7 #2 --- AMP — adenosine monophosphate FMT — formic acid Associated 6ne7 chain A to 6ne7, chain A with 0 mismatches > mmaker #2 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 6nec, chain A (#1) with 6ne7, chain A (#2), sequence alignment score = 1511 RMSD between 272 pruned atom pairs is 0.362 angstroms; (across all 281 pairs: 1.524) > show :810 > mlp Map values for surface ""6nec_A SES surface"": minimum -27.86, mean -4.635, maximum 24.27 Map values for surface ""6ne7_A SES surface"": minimum -26.8, mean -4.409, maximum 23.73 > select :xin 40 atoms, 44 bonds, 1 model selected > start Clashes > clashes sel intraMol false Traceback (most recent call last): File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/clashes/tool.py"", line 55, in run_command run(self.session, "" "".join(self.gui.get_command())) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2837, in run result = ci.function(session, **kw_args) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/clashes/cmd.py"", line 22, in cmd_clashes return _cmd(session, test_atoms, name, hbond_allowance, overlap_cutoff, ""clashes"", color, radius, **kw) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/clashes/cmd.py"", line 127, in _cmd intra_mol=intra_mol, res_separation=res_separation, restrict=restrict) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/clashes/clashes.py"", line 140, in find_clashes if not intra_mol and a.molecule.rootForAtom(a, File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/attr_registration.py"", line 39, in _getattr_ return look_in_class._attr_registration.get_attr(attr_name) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/attr_registration.py"", line 67, in get_attr raise AttributeError(""'%s' object has no attribute '%s'"" % (self.class_.__name__, attr_name)) from None AttributeError: 'Atom' object has no attribute 'molecule' AttributeError: 'Atom' object has no attribute 'molecule' File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/attr_registration.py"", line 67, in get_attr raise AttributeError(""'%s' object has no attribute '%s'"" % (self.class_.__name__, attr_name)) from None See log for complete Python traceback. > clashes sel 80 clashes > hide #1 & protein > hide surfaces > ~cartoon #1 > clashes sel intraMol false Traceback (most recent call last): File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/clashes/tool.py"", line 55, in run_command run(self.session, "" "".join(self.gui.get_command())) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2837, in run result = ci.function(session, **kw_args) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/clashes/cmd.py"", line 22, in cmd_clashes return _cmd(session, test_atoms, name, hbond_allowance, overlap_cutoff, ""clashes"", color, radius, **kw) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/clashes/cmd.py"", line 127, in _cmd intra_mol=intra_mol, res_separation=res_separation, restrict=restrict) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/clashes/clashes.py"", line 140, in find_clashes if not intra_mol and a.molecule.rootForAtom(a, File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/attr_registration.py"", line 39, in _getattr_ return look_in_class._attr_registration.get_attr(attr_name) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/attr_registration.py"", line 67, in get_attr raise AttributeError(""'%s' object has no attribute '%s'"" % (self.class_.__name__, attr_name)) from None AttributeError: 'Atom' object has no attribute 'molecule' AttributeError: 'Atom' object has no attribute 'molecule' File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/attr_registration.py"", line 67, in get_attr raise AttributeError(""'%s' object has no attribute '%s'"" % (self.class_.__name__, attr_name)) from None See log for complete Python traceback. > start Contacts > clashes sel intraMol false Traceback (most recent call last): File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/clashes/tool.py"", line 55, in run_command run(self.session, "" "".join(self.gui.get_command())) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2837, in run result = ci.function(session, **kw_args) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/clashes/cmd.py"", line 22, in cmd_clashes return _cmd(session, test_atoms, name, hbond_allowance, overlap_cutoff, ""clashes"", color, radius, **kw) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/clashes/cmd.py"", line 127, in _cmd intra_mol=intra_mol, res_separation=res_separation, restrict=restrict) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/clashes/clashes.py"", line 140, in find_clashes if not intra_mol and a.molecule.rootForAtom(a, File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/attr_registration.py"", line 39, in _getattr_ return look_in_class._attr_registration.get_attr(attr_name) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/attr_registration.py"", line 67, in get_attr raise AttributeError(""'%s' object has no attribute '%s'"" % (self.class_.__name__, attr_name)) from None AttributeError: 'Atom' object has no attribute 'molecule' AttributeError: 'Atom' object has no attribute 'molecule' File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/attr_registration.py"", line 67, in get_attr raise AttributeError(""'%s' object has no attribute '%s'"" % (self.class_.__name__, attr_name)) from None See log for complete Python traceback. OpenGL version: 4.1 NVIDIA-10.32.0 355.11.10.10.40.102 OpenGL renderer: NVIDIA GeForce GTX 675MX OpenGL Engine OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Structure Analysis fixed all ChimeraX