Opened 6 years ago

Closed 6 years ago

#3027 closed defect (fixed)

Peptide builder should remove whitespace and catch non-peptide characters

Reported by: SARA.IRANPARAST@… Owned by: pett
Priority: normal Milestone:
Component: Structure Editing Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

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 <lambda>  
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 <lambda>  
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 <lambda>  
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 <lambda>  
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 <lambda>  
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 <lambda>  
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 <lambda>  
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 <lambda>  
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 <lambda>  
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"

Change History (3)

comment:1 by pett, 6 years ago

Component: Unassigned → Structure Editing
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Peptide builder should remove whitespace and catch non-peptide characters

comment:2 by pett, 6 years ago

Hi Sara,

Thanks for reporting this problem. It will be fixed in tomorrow's build, but you can get it to work before then by ensuring that the sequence you enter has no "carriage return" (new line) characters in it. The sequence you entered had such a character between the "SSRV" and "PDLLV" near the end of the sequence.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:3 by pett, 6 years ago

Resolution: → fixed
Status: accepted → closed
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