id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9002 Build Structure: wrong residue names for complementary base pairs erik.marklund@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC) Description Using Build Structure to make a series of small nucleotide BPs for subsequent MD simulations. With 'nucleic double helix', 'DNA', 'B-form' all checked, I input 'AT' as the sequence. When saving as a pdb file, the residues in the first chain get residue names 'DA' and 'DT', but in the second chain they get 'A' and 'T'. This confuses my MD software, but more generally it is an unmotivated inconsistency that looks like a bug. Log: UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > ui tool show ""Build Structure"" > build start nucleic dAT A type dna form B Traceback (most recent call last): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molarray.py"", line 113, in __init__ pointers = numpy.array([i._c_pointer.value for i in items], cptr) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molarray.py"", line 113, in pointers = numpy.array([i._c_pointer.value for i in items], cptr) AttributeError: 'NoneType' object has no attribute '_c_pointer' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/build_structure/tool.py"", line 386, in apply_but.clicked.connect(lambda checked: self._ss_apply_cb()) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/build_structure/tool.py"", line 547, in _ss_apply_cb run(self.session, "" "".join([""build start"", provider_name, struct_arg, subcmd_string])) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/build_structure/cmd.py"", line 51, in cmd_start_structure ret_val = manager.execute_command(method, model, subargs) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/build_structure/manager.py"", line 63, in execute_command return self._get_provider(name).execute_command(structure, args) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/build_structure/providers.py"", line 272, in execute_command return cmd.run(self.name + ' ' + args, log=False)[0] File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/build_structure/providers.py"", line 539, in shim_place_nucleic_acid chains = place_nucleic_acid(_structure, sequence, **kw) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/build_structure/start.py"", line 253, in place_nucleic_acid chains = Chains([residues1[0].chain, residues2[0].chain]) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molarray.py"", line 1422, in __init__ Collection.__init__(self, chain_pointers, molobject.Chain, Chains) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molarray.py"", line 118, in __init__ raise ValueError('Collection items of unrecognized type ""%s""' % t) ValueError: Collection items of unrecognized type """" ValueError: Collection items of unrecognized type """" File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molarray.py"", line 118, in __init__ raise ValueError('Collection items of unrecognized type ""%s""' % t) See log for complete Python traceback. > build start nucleic dAT A type dna form B Traceback (most recent call last): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molarray.py"", line 113, in __init__ pointers = numpy.array([i._c_pointer.value for i in items], cptr) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molarray.py"", line 113, in pointers = numpy.array([i._c_pointer.value for i in items], cptr) AttributeError: 'NoneType' object has no attribute '_c_pointer' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/build_structure/tool.py"", line 386, in apply_but.clicked.connect(lambda checked: self._ss_apply_cb()) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/build_structure/tool.py"", line 547, in _ss_apply_cb run(self.session, "" "".join([""build start"", provider_name, struct_arg, subcmd_string])) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/build_structure/cmd.py"", line 51, in cmd_start_structure ret_val = manager.execute_command(method, model, subargs) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/build_structure/manager.py"", line 63, in execute_command return self._get_provider(name).execute_command(structure, args) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/build_structure/providers.py"", line 272, in execute_command return cmd.run(self.name + ' ' + args, log=False)[0] File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/build_structure/providers.py"", line 539, in shim_place_nucleic_acid chains = place_nucleic_acid(_structure, sequence, **kw) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/build_structure/start.py"", line 253, in place_nucleic_acid chains = Chains([residues1[0].chain, residues2[0].chain]) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molarray.py"", line 1422, in __init__ Collection.__init__(self, chain_pointers, molobject.Chain, Chains) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molarray.py"", line 118, in __init__ raise ValueError('Collection items of unrecognized type ""%s""' % t) ValueError: Collection items of unrecognized type """" ValueError: Collection items of unrecognized type """" File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molarray.py"", line 118, in __init__ raise ValueError('Collection items of unrecognized type ""%s""' % t) See log for complete Python traceback. > build start nucleic dAT AT type dna form B Chain information for dAT #1 --- Chain | Description A B | No description available > build start nucleic dAT A type dna form B Traceback (most recent call last): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molarray.py"", line 113, in __init__ pointers = numpy.array([i._c_pointer.value for i in items], cptr) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molarray.py"", line 113, in pointers = numpy.array([i._c_pointer.value for i in items], cptr) AttributeError: 'NoneType' object has no attribute '_c_pointer' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/build_structure/tool.py"", line 386, in apply_but.clicked.connect(lambda checked: self._ss_apply_cb()) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/build_structure/tool.py"", line 547, in _ss_apply_cb run(self.session, "" "".join([""build start"", provider_name, struct_arg, subcmd_string])) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/build_structure/cmd.py"", line 51, in cmd_start_structure ret_val = manager.execute_command(method, model, subargs) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/build_structure/manager.py"", line 63, in execute_command return self._get_provider(name).execute_command(structure, args) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/build_structure/providers.py"", line 272, in execute_command return cmd.run(self.name + ' ' + args, log=False)[0] File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/build_structure/providers.py"", line 539, in shim_place_nucleic_acid chains = place_nucleic_acid(_structure, sequence, **kw) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/build_structure/start.py"", line 253, in place_nucleic_acid chains = Chains([residues1[0].chain, residues2[0].chain]) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molarray.py"", line 1422, in __init__ Collection.__init__(self, chain_pointers, molobject.Chain, Chains) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molarray.py"", line 118, in __init__ raise ValueError('Collection items of unrecognized type ""%s""' % t) ValueError: Collection items of unrecognized type """" ValueError: Collection items of unrecognized type """" File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molarray.py"", line 118, in __init__ raise ValueError('Collection items of unrecognized type ""%s""' % t) See log for complete Python traceback. > build start nucleic dAT AAA type dna form B Chain information for dAT #2 --- Chain | Description A | No description available B | No description available > build start nucleic dAT ATA type dna form B Chain information for dAT #3 --- Chain | Description A | No description available B | No description available > close > build start nucleic dAT A type dna form B Traceback (most recent call last): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molarray.py"", line 113, in __init__ pointers = numpy.array([i._c_pointer.value for i in items], cptr) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molarray.py"", line 113, in pointers = numpy.array([i._c_pointer.value for i in items], cptr) AttributeError: 'NoneType' object has no attribute '_c_pointer' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/build_structure/tool.py"", line 386, in apply_but.clicked.connect(lambda checked: self._ss_apply_cb()) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/build_structure/tool.py"", line 547, in _ss_apply_cb run(self.session, "" "".join([""build start"", provider_name, struct_arg, subcmd_string])) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/build_structure/cmd.py"", line 51, in cmd_start_structure ret_val = manager.execute_command(method, model, subargs) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/build_structure/manager.py"", line 63, in execute_command return self._get_provider(name).execute_command(structure, args) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/build_structure/providers.py"", line 272, in execute_command return cmd.run(self.name + ' ' + args, log=False)[0] File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/build_structure/providers.py"", line 539, in shim_place_nucleic_acid chains = place_nucleic_acid(_structure, sequence, **kw) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/build_structure/start.py"", line 253, in place_nucleic_acid chains = Chains([residues1[0].chain, residues2[0].chain]) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molarray.py"", line 1422, in __init__ Collection.__init__(self, chain_pointers, molobject.Chain, Chains) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molarray.py"", line 118, in __init__ raise ValueError('Collection items of unrecognized type ""%s""' % t) ValueError: Collection items of unrecognized type """" ValueError: Collection items of unrecognized type """" File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molarray.py"", line 118, in __init__ raise ValueError('Collection items of unrecognized type ""%s""' % t) See log for complete Python traceback. > build start nucleic dAT T type dna form B Traceback (most recent call last): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molarray.py"", line 113, in __init__ pointers = numpy.array([i._c_pointer.value for i in items], cptr) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molarray.py"", line 113, in pointers = numpy.array([i._c_pointer.value for i in items], cptr) AttributeError: 'NoneType' object has no attribute '_c_pointer' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/build_structure/tool.py"", line 386, in apply_but.clicked.connect(lambda checked: self._ss_apply_cb()) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/build_structure/tool.py"", line 547, in _ss_apply_cb run(self.session, "" "".join([""build start"", provider_name, struct_arg, subcmd_string])) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/build_structure/cmd.py"", line 51, in cmd_start_structure ret_val = manager.execute_command(method, model, subargs) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/build_structure/manager.py"", line 63, in execute_command return self._get_provider(name).execute_command(structure, args) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/build_structure/providers.py"", line 272, in execute_command return cmd.run(self.name + ' ' + args, log=False)[0] File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/build_structure/providers.py"", line 539, in shim_place_nucleic_acid chains = place_nucleic_acid(_structure, sequence, **kw) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/build_structure/start.py"", line 253, in place_nucleic_acid chains = Chains([residues1[0].chain, residues2[0].chain]) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molarray.py"", line 1422, in __init__ Collection.__init__(self, chain_pointers, molobject.Chain, Chains) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molarray.py"", line 118, in __init__ raise ValueError('Collection items of unrecognized type ""%s""' % t) ValueError: Collection items of unrecognized type """" ValueError: Collection items of unrecognized type """" File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molarray.py"", line 118, in __init__ raise ValueError('Collection items of unrecognized type ""%s""' % t) See log for complete Python traceback. > build start nucleic dAT AA type dna form B Chain information for dAT #1 --- Chain | Description A | No description available B | No description available > select #1 76 atoms, 84 bonds, 4 residues, 1 model selected > close > build start nucleic dAT AT type dna form B Chain information for dAT #1 --- Chain | Description A B | No description available > save /Users/ermar499/Projects/RNA/maketst/dAT.pdb relModel #1 > close > build start nucleic dAT TA type dna form B Chain information for dAT #1 --- Chain | Description A B | No description available > close > build start nucleic dTA TA type dna form B Chain information for dTA #1 --- Chain | Description A B | No description available > save /Users/ermar499/Projects/RNA/maketst/dTA.pdb relModel #1 OpenGL version: 4.1 Metal - 83.1 OpenGL renderer: Apple M1 Pro OpenGL vendor: AppleHardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,1 Model Number: Z14Z0000KKS/A Chip: Unknown Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 16 GB System Firmware Version: 8422.100.650 OS Loader Version: 8422.100.650 Software: System Software Overview: System Version: macOS 13.3.1 (22E261) Kernel Version: Darwin 22.4.0 Time since boot: 30 days, 1 hour, 54 minutes Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Thunderbolt Display: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 60.00Hz Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Thunderbolt Display: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 60.00Hz Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Locale: (None, 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.5.30 cftime: 1.5.1.1 charset-normalizer: 2.0.9 ChimeraX-AddCharge: 1.2.2 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.31 ChimeraX-AtomicLibrary: 4.2 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.2 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.5 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 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 ChimeraX-Label: 1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.4 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.4 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2.6 ChimeraX-ModelPanel: 1.2.1 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.7 ChimeraX-PDB: 2.6.5 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.6.1 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.13.7 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.24 decorator: 5.1.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.3.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.9.1 kiwisolver: 1.3.2 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 2.0.1 matplotlib: 3.4.3 matplotlib-inline: 0.1.3 msgpack: 1.0.2 netCDF4: 1.5.7 networkx: 2.6.3 numexpr: 2.8.0 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.0 ParmEd: 3.2.0 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.23 psutil: 5.8.0 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.6 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.3 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 setuptools: 57.5.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.2.0 sphinx-autodoc-typehints: 1.12.0 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-jurko: 0.6 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0 }}} " defect closed normal Structure Editing fixed all ChimeraX