Failure fetching UniProt sequence/info

[Eric Pettersen]

The following bug report has been submitted:
Platform:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.4.dev202111171953 (2021-11-17 19:53:21 UTC)
Description
Fetching UniProt sequence for 3m6j

Log:
UCSF ChimeraX version: 1.4.dev202111171953 (2021-11-17)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 3m6j

Summary of feedback from opening 3m6j fetched from pdb  
---  
note | Fetching compressed mmCIF 3m6j from
http://files.rcsb.org/download/3m6j.cif  
  
3m6j title:  
Crystal structure of unknown function protein from Leptospirillum rubarum
[more info...]  
  
Chain information for 3m6j #1  
---  
Chain | Description | UniProt  
A B C D | uncharacterized protein | A3ESP9_9BACT  
  
Non-standard residues in 3m6j #1  
---  
CL — chloride ion  
  
3m6j mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> coulombic

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
/A VAL 1  
/A SER 2  
/B VAL 70  
/C ASP 72  
/C GLN 74  
/C ASP 139  
/D ASP 139  
/D LYS 142  

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 3m6j_A SES surface #1.2: minimum, -14.91, mean -0.67,
maximum 14.08  
Coulombic values for 3m6j_B SES surface #1.3: minimum, -12.64, mean -0.99,
maximum 11.86  
Coulombic values for 3m6j_C SES surface #1.4: minimum, -13.18, mean -0.92,
maximum 14.63  
Coulombic values for 3m6j_D SES surface #1.5: minimum, -12.14, mean -0.75,
maximum 13.46  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide #1.4 models

> hide #1.5 models

> hide #1.3 models

> show #1.3 models

> hide #1.2 models

> sequence chain #1/A#1/B#1/C#1/D

Alignment identifier is 1  

> open A3ESP9_9BACT fromDatabase uniprot

Summary of feedback from opening A3ESP9_9BACT fetched from uniprot  
---  
notes | UniProt identifier A3ESP9_9BACT maps to entry A3ESP9  
Fetching A3ESP9_9BACT UniProt info from
https://www.uniprot.org/uniprot/A3ESP9_9BACT.xml  
  
Traceback (most recent call last):  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 333, in interceptRequest  
self._callback(info)  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/log/tool.py", line 205, in link_intercept  
chimerax_intercept(request_info, *args, session=self.session, view=self, **kw)  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 468, in chimerax_intercept  
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 397, in thread_safe  
func(*args, **kw)  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 459, in defer  
cxcmd(session, topic)  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 477, in cxcmd  
run(session, cmd)  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2875, in run  
result = ci.function(session, **kw_args)  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2875, in run  
result = ci.function(session, **kw_args)  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 153, in provider_open  
models, status = collated_open(session, database_name, ident,  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 457, in collated_open  
return remember_data_format()  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/uniprot/__init__.py", line 26, in fetch  
return fetch_uniprot(session, ident, ignore_cache=ignore_cache)  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/uniprot/fetch_uniprot.py", line 25, in fetch_uniprot  
seq_string, full_name, features = fetch_uniprot_accession_info(session,
accession,  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/uniprot/fetch_uniprot.py", line 81, in
fetch_uniprot_accession_info  
tree = xml.dom.minidom.parse(file_name)  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/xml/dom/minidom.py",
line 1988, in parse  
return expatbuilder.parse(file)  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/xml/dom/expatbuilder.py",
line 911, in parse  
result = builder.parseFile(fp)  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/xml/dom/expatbuilder.py",
line 211, in parseFile  
parser.Parse(b"", True)  
xml.parsers.expat.ExpatError: no element found: line 1, column 0  
  
xml.parsers.expat.ExpatError: no element found: line 1, column 0  
  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/xml/dom/expatbuilder.py",
line 211, in parseFile  
parser.Parse(b"", True)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-14.7.20
OpenGL renderer: Intel(R) Iris(TM) Pro Graphics 6200
OpenGL vendor: Intel Inc.Hardware:

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      SMC Version (system): 2.32f21

Software:

    System Software Overview:

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      Kernel Version: Darwin 19.6.0
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Graphics/Displays:

    Intel Iris Pro Graphics 6200:

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      Metal: Supported, feature set macOS GPUFamily1 v4
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Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
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[Eric Pettersen]

It's an obsolete UniProt accession ID. Reported it to the RCSB.