id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3027 Peptide builder should remove whitespace and catch non-peptide characters SARA.IRANPARAST@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.17134 ChimeraX Version: 0.94 (2020-04-08) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.94 (2020-04-08) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > help help:credits.html > show sel cartoons > toolshed show ""Build Structure"" > build start peptide ""custom built"" > ""MYSFVSEETGTLIVNSVLLFLAFVVFLLVTLAILTALRLCAYCCNIVNVSLVKPSFYVYSRVKNLNSSRV\nPDLLV"" > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 rotLib Dunbrack Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\start.py"", line 79, in place_peptide r3 = Sequence.protein1to3[c] KeyError: '\n' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\tool.py"", line 252, in apply_but.clicked.connect(lambda checked: self._ss_apply_cb()) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\tool.py"", line 379, in _ss_apply_cb run(self.session, "" "".join([""build start"", provider_name, struct_arg, subcmd_string])) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py"", line 31, in run results = command.run(text, log=log) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2848, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\cmd.py"", line 33, in cmd_start_structure manager.execute_command(method, model, subargs) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\manager.py"", line 59, in execute_command self.providers[name].run_provider(self.session, name, self, command_info=(structure, args)) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\info.py"", line 453, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\\__init__.py"", line 1633, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\\__init__.py"", line 54, in run_provider process_command(session, name, structure, substring) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\providers.py"", line 293, in process_command cmd.run(name + ' ' + substring, log=False) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2848, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\providers.py"", line 307, in shim_place_peptide return place_peptide(_structure, sequence, phi_psis, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\start.py"", line 81, in place_peptide raise PeptideError(""Unrecognized protein 1-letter code: %s"" % c) chimerax.atomic.build_structure.start.PeptideError: Unrecognized protein 1-letter code: chimerax.atomic.build_structure.start.PeptideError: Unrecognized protein 1-letter code: File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\start.py"", line 81, in place_peptide raise PeptideError(""Unrecognized protein 1-letter code: %s"" % c) See log for complete Python traceback. > build start peptide ""custom built"" > ""MYSFVSEETGTLIVNSVLLFLAFVVFLLVTLAILTALRLCAYCCNIVNVSLVKPSFYVYSRVKNLNSSRV\nPDLLV"" > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 rotLib Dunbrack Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\start.py"", line 79, in place_peptide r3 = Sequence.protein1to3[c] KeyError: '\n' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\tool.py"", line 252, in apply_but.clicked.connect(lambda checked: self._ss_apply_cb()) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\tool.py"", line 379, in _ss_apply_cb run(self.session, "" "".join([""build start"", provider_name, struct_arg, subcmd_string])) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py"", line 31, in run results = command.run(text, log=log) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2848, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\cmd.py"", line 33, in cmd_start_structure manager.execute_command(method, model, subargs) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\manager.py"", line 59, in execute_command self.providers[name].run_provider(self.session, name, self, command_info=(structure, args)) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\info.py"", line 453, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\\__init__.py"", line 1633, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\\__init__.py"", line 54, in run_provider process_command(session, name, structure, substring) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\providers.py"", line 293, in process_command cmd.run(name + ' ' + substring, log=False) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2848, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\providers.py"", line 307, in shim_place_peptide return place_peptide(_structure, sequence, phi_psis, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\start.py"", line 81, in place_peptide raise PeptideError(""Unrecognized protein 1-letter code: %s"" % c) chimerax.atomic.build_structure.start.PeptideError: Unrecognized protein 1-letter code: chimerax.atomic.build_structure.start.PeptideError: Unrecognized protein 1-letter code: File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\start.py"", line 81, in place_peptide raise PeptideError(""Unrecognized protein 1-letter code: %s"" % c) See log for complete Python traceback. > build start peptide ""custom built"" "">YP_009724392.1 ENVELOPE PROTEIN [SEVERE > ACUTE RESPIRATORY SYNDROME CORONAVIRUS > 2]\nMYSFVSEETGTLIVNSVLLFLAFVVFLLVTLAILTALRLCAYCCNIVNVSLVKPSFYVYSRVKNLNSSRV\nPDLLV"" > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 rotLib > Dunbrack Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\start.py"", line 79, in place_peptide r3 = Sequence.protein1to3[c] KeyError: '>' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\tool.py"", line 252, in apply_but.clicked.connect(lambda checked: self._ss_apply_cb()) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\tool.py"", line 379, in _ss_apply_cb run(self.session, "" "".join([""build start"", provider_name, struct_arg, subcmd_string])) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py"", line 31, in run results = command.run(text, log=log) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2848, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\cmd.py"", line 33, in cmd_start_structure manager.execute_command(method, model, subargs) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\manager.py"", line 59, in execute_command self.providers[name].run_provider(self.session, name, self, command_info=(structure, args)) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\info.py"", line 453, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\\__init__.py"", line 1633, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\\__init__.py"", line 54, in run_provider process_command(session, name, structure, substring) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\providers.py"", line 293, in process_command cmd.run(name + ' ' + substring, log=False) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2848, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\providers.py"", line 307, in shim_place_peptide return place_peptide(_structure, sequence, phi_psis, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\start.py"", line 81, in place_peptide raise PeptideError(""Unrecognized protein 1-letter code: %s"" % c) chimerax.atomic.build_structure.start.PeptideError: Unrecognized protein 1-letter code: > chimerax.atomic.build_structure.start.PeptideError: Unrecognized protein 1-letter code: > File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\start.py"", line 81, in place_peptide raise PeptideError(""Unrecognized protein 1-letter code: %s"" % c) See log for complete Python traceback. > build start peptide ""custom built"" "">YP_009724392.1 ENVELOPE PROTEIN [SEVERE > ACUTE RESPIRATORY SYNDROME CORONAVIRUS > 2]\nMYSFVSEETGTLIVNSVLLFLAFVVFLLVTLAILTALRLCAYCCNIVNVSLVKPSFYVYSRVKNLNSSRV\nPDLLV"" > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 rotLib > Dunbrack Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\start.py"", line 79, in place_peptide r3 = Sequence.protein1to3[c] KeyError: '>' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\tool.py"", line 252, in apply_but.clicked.connect(lambda checked: self._ss_apply_cb()) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\tool.py"", line 379, in _ss_apply_cb run(self.session, "" "".join([""build start"", provider_name, struct_arg, subcmd_string])) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py"", line 31, in run results = command.run(text, log=log) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2848, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\cmd.py"", line 33, in cmd_start_structure manager.execute_command(method, model, subargs) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\manager.py"", line 59, in execute_command self.providers[name].run_provider(self.session, name, self, command_info=(structure, args)) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\info.py"", line 453, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\\__init__.py"", line 1633, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\\__init__.py"", line 54, in run_provider process_command(session, name, structure, substring) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\providers.py"", line 293, in process_command cmd.run(name + ' ' + substring, log=False) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2848, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\providers.py"", line 307, in shim_place_peptide return place_peptide(_structure, sequence, phi_psis, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\start.py"", line 81, in place_peptide raise PeptideError(""Unrecognized protein 1-letter code: %s"" % c) chimerax.atomic.build_structure.start.PeptideError: Unrecognized protein 1-letter code: > chimerax.atomic.build_structure.start.PeptideError: Unrecognized protein 1-letter code: > File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\start.py"", line 81, in place_peptide raise PeptideError(""Unrecognized protein 1-letter code: %s"" % c) See log for complete Python traceback. > build start peptide ""custom built"" > ""MYSFVSEETGTLIVNSVLLFLAFVVFLLVTLAILTALRLCAYCCNIVNVSLVKPSFYVYSRVKNLNSSRV\nPDLLV"" > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 rotLib Dunbrack Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\start.py"", line 79, in place_peptide r3 = Sequence.protein1to3[c] KeyError: '\n' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\tool.py"", line 252, in apply_but.clicked.connect(lambda checked: self._ss_apply_cb()) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\tool.py"", line 379, in _ss_apply_cb run(self.session, "" "".join([""build start"", provider_name, struct_arg, subcmd_string])) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py"", line 31, in run results = command.run(text, log=log) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2848, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\cmd.py"", line 33, in cmd_start_structure manager.execute_command(method, model, subargs) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\manager.py"", line 59, in execute_command self.providers[name].run_provider(self.session, name, self, command_info=(structure, args)) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\info.py"", line 453, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\\__init__.py"", line 1633, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\\__init__.py"", line 54, in run_provider process_command(session, name, structure, substring) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\providers.py"", line 293, in process_command cmd.run(name + ' ' + substring, log=False) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2848, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\providers.py"", line 307, in shim_place_peptide return place_peptide(_structure, sequence, phi_psis, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\start.py"", line 81, in place_peptide raise PeptideError(""Unrecognized protein 1-letter code: %s"" % c) chimerax.atomic.build_structure.start.PeptideError: Unrecognized protein 1-letter code: chimerax.atomic.build_structure.start.PeptideError: Unrecognized protein 1-letter code: File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\start.py"", line 81, in place_peptide raise PeptideError(""Unrecognized protein 1-letter code: %s"" % c) See log for complete Python traceback. > toolshed show ""Build Structure"" > toolshed show ""Segment Map"" > build start peptide ""custom built"" > ""MYSFVSEETGTLIVNSVLLFLAFVVFLLVTLAILTALRLCAYCCNIVNVSLVKPSFYVYSRVKNLNSSRV\nPDLLV"" > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 rotLib Dunbrack Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\start.py"", line 79, in place_peptide r3 = Sequence.protein1to3[c] KeyError: '\n' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\tool.py"", line 252, in apply_but.clicked.connect(lambda checked: self._ss_apply_cb()) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\tool.py"", line 379, in _ss_apply_cb run(self.session, "" "".join([""build start"", provider_name, struct_arg, subcmd_string])) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py"", line 31, in run results = command.run(text, log=log) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2848, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\cmd.py"", line 33, in cmd_start_structure manager.execute_command(method, model, subargs) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\manager.py"", line 59, in execute_command self.providers[name].run_provider(self.session, name, self, command_info=(structure, args)) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\info.py"", line 453, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\\__init__.py"", line 1633, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\\__init__.py"", line 54, in run_provider process_command(session, name, structure, substring) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\providers.py"", line 293, in process_command cmd.run(name + ' ' + substring, log=False) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2848, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\providers.py"", line 307, in shim_place_peptide return place_peptide(_structure, sequence, phi_psis, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\start.py"", line 81, in place_peptide raise PeptideError(""Unrecognized protein 1-letter code: %s"" % c) chimerax.atomic.build_structure.start.PeptideError: Unrecognized protein 1-letter code: chimerax.atomic.build_structure.start.PeptideError: Unrecognized protein 1-letter code: File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\start.py"", line 81, in place_peptide raise PeptideError(""Unrecognized protein 1-letter code: %s"" % c) See log for complete Python traceback. > select protein Nothing selected > select helix Nothing selected > select protein Nothing selected > ui autostart false ""Model Panel"" > ui mousemode rightMode select > show target ab Select a density map in the Segment map field > select sequence > ""MYSFVSEETGTLIVNSVLLFLAFVVFLLVTLAILTALRLCAYCCNIVNVSLVKPSFYVYSRVKNLNSSRV\nPDLLV"" Nothing selected > select sequence > ""MYSFVSEETGTLIVNSVLLFLAFVVFLLVTLAILTALRLCAYCCNIVNVSLVKPSFYVYSRVKNLNSSRV\nPDLLV"" Nothing selected > select sequence > ""MYSFVSEETGTLIVNSVLLFLAFVVFLLVTLAILTALRLCAYCCNIVNVSLVKPSFYVYSRVKNLNSSRV\nPDLLV"" Nothing selected > select sequence > ""MYSFVSEETGTLIVNSVLLFLAFVVFLLVTLAILTALRLCAYCCNIVNVSLVKPSFYVYSRVKNLNSSRV\nPDLLV"" Nothing selected > select sequence > ""MYSFVSEETGTLIVNSVLLFLAFVVFLLVTLAILTALRLCAYCCNIVNVSLVKPSFYVYSRVKNLNSSRV\nPDLLV"" Nothing selected > select sequence > ""MYSFVSEETGTLIVNSVLLFLAFVVFLLVTLAILTALRLCAYCCNIVNVSLVKPSFYVYSRVKNLNSSRV\nPDLLV"" Nothing selected > select sequence > ""MYSFVSEETGTLIVNSVLLFLAFVVFLLVTLAILTALRLCAYCCNIVNVSLVKPSFYVYSRVKNLNSSRV\nPDLLV"" Nothing selected > select sequence > ""MYSFVSEETGTLIVNSVLLFLAFVVFLLVTLAILTALRLCAYCCNIVNVSLVKPSFYVYSRVKNLNSSRV\nPDLLV"" Nothing selected > select sequence > ""MYSFVSEETGTLIVNSVLLFLAFVVFLLVTLAILTALRLCAYCCNIVNVSLVKPSFYVYSRVKNLNSSRV\nPDLLV"" Nothing selected > select sequence > ""MYSFVSEETGTLIVNSVLLFLAFVVFLLVTLAILTALRLCAYCCNIVNVSLVKPSFYVYSRVKNLNSSRV\nPDLLV"" Nothing selected > select sequence > ""MYSFVSEETGTLIVNSVLLFLAFVVFLLVTLAILTALRLCAYCCNIVNVSLVKPSFYVYSRVKNLNSSRV\nPDLLV"" Nothing selected > open 1a0m format mmCIF fromDatabase pdb 1a0m title: 1.1 angstrom crystal structure of A-conotoxin [TYR15]-epi [more info...] Chain information for 1a0m #1 --- Chain | Description A B | α-conotoxin [TYR15]-epi Non-standard residues in 1a0m #1 --- NH2 — amino group > select sequence > ""MYSFVSEETGTLIVNSVLLFLAFVVFLLVTLAILTALRLCAYCCNIVNVSLVKPSFYVYSRVKNLNSSRV\nPDLLV"" Nothing selected > select protein 234 atoms, 242 bonds, 1 model selected > toolshed show ""Modeller Comparative"" > toolshed show ""Build Structure"" > build start peptide ""custom built"" > ""MYSFVSEETGTLIVNSVLLFLAFVVFLLVTLAILTALRLCAYCCNIVNVSLVKPSFYVYSRVKNLNSSRV\nPDLLV"" > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 rotLib Dunbrack Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\start.py"", line 79, in place_peptide r3 = Sequence.protein1to3[c] KeyError: '\n' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\tool.py"", line 252, in apply_but.clicked.connect(lambda checked: self._ss_apply_cb()) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\tool.py"", line 379, in _ss_apply_cb run(self.session, "" "".join([""build start"", provider_name, struct_arg, subcmd_string])) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py"", line 31, in run results = command.run(text, log=log) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2848, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\cmd.py"", line 33, in cmd_start_structure manager.execute_command(method, model, subargs) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\manager.py"", line 59, in execute_command self.providers[name].run_provider(self.session, name, self, command_info=(structure, args)) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\info.py"", line 453, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\\__init__.py"", line 1633, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\\__init__.py"", line 54, in run_provider process_command(session, name, structure, substring) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\providers.py"", line 293, in process_command cmd.run(name + ' ' + substring, log=False) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2848, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\providers.py"", line 307, in shim_place_peptide return place_peptide(_structure, sequence, phi_psis, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\start.py"", line 81, in place_peptide raise PeptideError(""Unrecognized protein 1-letter code: %s"" % c) chimerax.atomic.build_structure.start.PeptideError: Unrecognized protein 1-letter code: chimerax.atomic.build_structure.start.PeptideError: Unrecognized protein 1-letter code: File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\start.py"", line 81, in place_peptide raise PeptideError(""Unrecognized protein 1-letter code: %s"" % c) See log for complete Python traceback. > delete atoms sel > delete bonds sel No atoms or bonds selected No atoms or bonds selected You must select exactly one atom to modify. > rainbow > volume showOutlineBox true No volumes specified > volume style surface No volumes specified No atoms or bonds selected No atoms or bonds selected > toolshed show ""Build Structure"" > build start atom ""custom built"" > build start peptide ""custom built"" > ""MYSFVSEETGTLIVNSVLLFLAFVVFLLVTLAILTALRLCAYCCNIVNVSLVKPSFYVYSRVKNLNSSRV\nPDLLV"" > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 rotLib Dunbrack Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\start.py"", line 79, in place_peptide r3 = Sequence.protein1to3[c] KeyError: '\n' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\tool.py"", line 252, in apply_but.clicked.connect(lambda checked: self._ss_apply_cb()) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\tool.py"", line 379, in _ss_apply_cb run(self.session, "" "".join([""build start"", provider_name, struct_arg, subcmd_string])) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py"", line 31, in run results = command.run(text, log=log) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2848, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\cmd.py"", line 33, in cmd_start_structure manager.execute_command(method, model, subargs) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\manager.py"", line 59, in execute_command self.providers[name].run_provider(self.session, name, self, command_info=(structure, args)) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\info.py"", line 453, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\\__init__.py"", line 1633, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\\__init__.py"", line 54, in run_provider process_command(session, name, structure, substring) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\providers.py"", line 293, in process_command cmd.run(name + ' ' + substring, log=False) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2848, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\providers.py"", line 307, in shim_place_peptide return place_peptide(_structure, sequence, phi_psis, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\start.py"", line 81, in place_peptide raise PeptideError(""Unrecognized protein 1-letter code: %s"" % c) chimerax.atomic.build_structure.start.PeptideError: Unrecognized protein 1-letter code: chimerax.atomic.build_structure.start.PeptideError: Unrecognized protein 1-letter code: File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\start.py"", line 81, in place_peptide raise PeptideError(""Unrecognized protein 1-letter code: %s"" % c) See log for complete Python traceback. > build start peptide ""custom built"" > ""MYSFVSEETGTLIVNSVLLFLAFVVFLLVTLAILTALRLCAYCCNIVNVSLVKPSFYVYSRVKNLNSSRV\nPDLLV"" > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 > -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, > -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 -57.0, -47.0 rotLib > Richardson.common Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\start.py"", line 79, in place_peptide r3 = Sequence.protein1to3[c] KeyError: '\n' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\tool.py"", line 252, in apply_but.clicked.connect(lambda checked: self._ss_apply_cb()) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\tool.py"", line 379, in _ss_apply_cb run(self.session, "" "".join([""build start"", provider_name, struct_arg, subcmd_string])) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py"", line 31, in run results = command.run(text, log=log) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2848, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\cmd.py"", line 33, in cmd_start_structure manager.execute_command(method, model, subargs) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\manager.py"", line 59, in execute_command self.providers[name].run_provider(self.session, name, self, command_info=(structure, args)) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\info.py"", line 453, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\\__init__.py"", line 1633, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\\__init__.py"", line 54, in run_provider process_command(session, name, structure, substring) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\providers.py"", line 293, in process_command cmd.run(name + ' ' + substring, log=False) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2848, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\providers.py"", line 307, in shim_place_peptide return place_peptide(_structure, sequence, phi_psis, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\start.py"", line 81, in place_peptide raise PeptideError(""Unrecognized protein 1-letter code: %s"" % c) chimerax.atomic.build_structure.start.PeptideError: Unrecognized protein 1-letter code: chimerax.atomic.build_structure.start.PeptideError: Unrecognized protein 1-letter code: File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\build_structure\start.py"", line 81, in place_peptide raise PeptideError(""Unrecognized protein 1-letter code: %s"" % c) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 388.57 OpenGL renderer: GeForce 920M/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: ASUSTeK COMPUTER INC. Model: TP301UJ OS: Microsoft Windows 10 Enterprise (Build 17134) Memory: 4,186,017,792 MaxProcessMemory: 137,438,953,344 CPU: 4 Intel(R) Core(TM) i7-6500U CPU @ 2.50GHz"" }}} " defect closed normal Structure Editing fixed all ChimeraX