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Opened 6 years ago
Closed 6 years ago
#3026 closed defect (duplicate)
Peptide builder should remove whitespace and catch non-peptide characters
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| 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.
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 (2)
comment:1 by , 6 years ago
| Component: | Unassigned → Structure Editing |
|---|---|
| Owner: | set to |
| 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 , 6 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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Duplicate of #3027