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#17348 closed defect (fixed)
SAXParseException reading markers
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.26100
ChimeraX Version: 1.9rc202412100036 (2024-12-10 00:36:39 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.9rc202412100036 (2024-12-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open D:/All_projects/Fousseyni-2024-2025/DENV1/Align.cxs
Log from Wed Apr 9 22:48:57 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.9rc202412100036 (2024-12-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open D:/All_projects/Fousseyni-2024-2025/DENV1/APB09654_DENV-1.cif
Chain information for APB09654_DENV-1.cif #1
---
Chain | Description
A | .
Computing secondary structure
> open D:/All_projects/Fousseyni-2024-2025/DENV1/UCRC003_prME_translation.cif
Chain information for UCRC003_prME_translation.cif #2
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #2 to #1
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker APB09654_DENV-1.cif, chain A (#1) with
UCRC003_prME_translation.cif, chain A (#2), sequence alignment score = 3327.7
RMSD between 428 pruned atom pairs is 1.139 angstroms; (across all 661 pairs:
3.515)
No reference and/or match structure/chain chosen
> matchmaker #2 to #1 showAlignment true
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker APB09654_DENV-1.cif, chain A (#1) with
UCRC003_prME_translation.cif, chain A (#2), sequence alignment score = 3327.7
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: APB09654_DENV-1.cif #1/A,
UCRC003_prME_translation.cif #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 428 pruned atom pairs is 1.139 angstroms; (across all 661 pairs:
3.515)
> select : 494
8 atoms, 6 bonds, 2 residues, 2 models selected
> show sel atoms
[Repeated 1 time(s)]
> select : 118
20 atoms, 18 bonds, 2 residues, 2 models selected
> show sel cartoons
> show sel atoms
> show sel target ab
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> label height 10
> label height 8
> label height 6
> color sel blue
> save D:/All_projects/Fousseyni-2024-2025/DENV1/Align.cxs
——— End of log from Wed Apr 9 22:48:57 2025 ———
opened ChimeraX session
> label height 5
> select : 122
20 atoms, 18 bonds, 2 residues, 2 models selected
> ~label sel residues
> select : 118
20 atoms, 18 bonds, 2 residues, 2 models selected
> ~label sel residues
> hide sel atoms
> hide #1 models
> color (#2 & sel) cornflower blue
> color (#2 & sel) medium blue
> select clear
> color #2 medium blue
> show #1 models
> hide #2 models
> color #1 forest green
> show #2 models
> ui tool show Matchmaker
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker APB09654_DENV-1.cif, chain A (#1) with
UCRC003_prME_translation.cif, chain A (#2), sequence alignment score = 3327.7
RMSD between 428 pruned atom pairs is 1.139 angstroms; (across all 661 pairs:
3.515)
> ui windowfill toggle
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker APB09654_DENV-1.cif, chain A (#1) with
UCRC003_prME_translation.cif, chain A (#2), sequence alignment score = 3327.7
RMSD between 428 pruned atom pairs is 1.139 angstroms; (across all 661 pairs:
3.515)
> ui windowfill toggle
> show surfaces
> hide surfaces
> save D:/All_projects/Fousseyni-2024-2025/DENV1/Align.cmm
Wrote 0 marker sets containing 0 markers
> save D:/All_projects/Fousseyni-2024-2025/DENV1/align.jpg width 943 height
> 569 supersample 3
> set bgColor white
> set bgColor #ffffff00
> save D:/All_projects/Fousseyni-2024-2025/DENV1/align.jpg width 943 height
> 569 supersample 3
[Repeated 1 time(s)]
> close session
> open D:\All_projects\Fousseyni-2024-2025\DENV1\Align.cmm format markers
Traceback (most recent call last):
File "C:\Program Files\ChimeraX
1.9rc202412100036\bin\Lib\xml\sax\expatreader.py", line 217, in feed
self._parser.Parse(data, isFinal)
xml.parsers.expat.ExpatError: no element found: line 1, column 0
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 320, in interceptRequest
self._callback(info)
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 353, in intercept
chimerax_intercept(*args, view=view, session=session)
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 455, in chimerax_intercept
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\ui\gui.py", line 438, in thread_safe
func(*args, **kw)
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 446, in defer
cxcmd(session, topic)
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 464, in cxcmd
run(session, cmd)
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 215, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 526, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 497, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\markers\\__init__.py", line 62, in open
return cmmfiles.read_cmm(session, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\markers\cmmfiles.py", line 7, in read_cmm
msets = load_markerset_xml(session, f)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\markers\cmmfiles.py", line 181, in load_markerset_xml
xml_parser.parse(input)
File "C:\Program Files\ChimeraX
1.9rc202412100036\bin\Lib\xml\sax\expatreader.py", line 111, in parse
xmlreader.IncrementalParser.parse(self, source)
File "C:\Program Files\ChimeraX
1.9rc202412100036\bin\Lib\xml\sax\xmlreader.py", line 127, in parse
self.close()
File "C:\Program Files\ChimeraX
1.9rc202412100036\bin\Lib\xml\sax\expatreader.py", line 240, in close
self.feed(b"", isFinal=True)
File "C:\Program Files\ChimeraX
1.9rc202412100036\bin\Lib\xml\sax\expatreader.py", line 221, in feed
self._err_handler.fatalError(exc)
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\xml\sax\handler.py",
line 38, in fatalError
raise exception
xml.sax._exceptions.SAXParseException:
D:\All_projects\Fousseyni-2024-2025\DENV1\Align.cmm:1:0: no element found
xml.sax._exceptions.SAXParseException:
D:\All_projects\Fousseyni-2024-2025\DENV1\Align.cmm:1:0: no element found
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\xml\sax\handler.py",
line 38, in fatalError
raise exception
See log for complete Python traceback.
> open D:\All_projects\Fousseyni-2024-2025\DENV1\Align.cmm format markers
Traceback (most recent call last):
File "C:\Program Files\ChimeraX
1.9rc202412100036\bin\Lib\xml\sax\expatreader.py", line 217, in feed
self._parser.Parse(data, isFinal)
xml.parsers.expat.ExpatError: no element found: line 1, column 0
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 320, in interceptRequest
self._callback(info)
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 353, in intercept
chimerax_intercept(*args, view=view, session=session)
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 455, in chimerax_intercept
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\ui\gui.py", line 438, in thread_safe
func(*args, **kw)
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 446, in defer
cxcmd(session, topic)
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 464, in cxcmd
run(session, cmd)
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 215, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 526, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 497, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\markers\\__init__.py", line 62, in open
return cmmfiles.read_cmm(session, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\markers\cmmfiles.py", line 7, in read_cmm
msets = load_markerset_xml(session, f)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\markers\cmmfiles.py", line 181, in load_markerset_xml
xml_parser.parse(input)
File "C:\Program Files\ChimeraX
1.9rc202412100036\bin\Lib\xml\sax\expatreader.py", line 111, in parse
xmlreader.IncrementalParser.parse(self, source)
File "C:\Program Files\ChimeraX
1.9rc202412100036\bin\Lib\xml\sax\xmlreader.py", line 127, in parse
self.close()
File "C:\Program Files\ChimeraX
1.9rc202412100036\bin\Lib\xml\sax\expatreader.py", line 240, in close
self.feed(b"", isFinal=True)
File "C:\Program Files\ChimeraX
1.9rc202412100036\bin\Lib\xml\sax\expatreader.py", line 221, in feed
self._err_handler.fatalError(exc)
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\xml\sax\handler.py",
line 38, in fatalError
raise exception
xml.sax._exceptions.SAXParseException:
D:\All_projects\Fousseyni-2024-2025\DENV1\Align.cmm:1:0: no element found
xml.sax._exceptions.SAXParseException:
D:\All_projects\Fousseyni-2024-2025\DENV1\Align.cmm:1:0: no element found
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\xml\sax\handler.py",
line 38, in fatalError
raise exception
See log for complete Python traceback.
> open D:\All_projects\Fousseyni-2024-2025\DENV1\Align.cmm format markers
Traceback (most recent call last):
File "C:\Program Files\ChimeraX
1.9rc202412100036\bin\Lib\xml\sax\expatreader.py", line 217, in feed
self._parser.Parse(data, isFinal)
xml.parsers.expat.ExpatError: no element found: line 1, column 0
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 320, in interceptRequest
self._callback(info)
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 353, in intercept
chimerax_intercept(*args, view=view, session=session)
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 455, in chimerax_intercept
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\ui\gui.py", line 438, in thread_safe
func(*args, **kw)
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 446, in defer
cxcmd(session, topic)
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 464, in cxcmd
run(session, cmd)
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 215, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 526, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 497, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\markers\\__init__.py", line 62, in open
return cmmfiles.read_cmm(session, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\markers\cmmfiles.py", line 7, in read_cmm
msets = load_markerset_xml(session, f)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\markers\cmmfiles.py", line 181, in load_markerset_xml
xml_parser.parse(input)
File "C:\Program Files\ChimeraX
1.9rc202412100036\bin\Lib\xml\sax\expatreader.py", line 111, in parse
xmlreader.IncrementalParser.parse(self, source)
File "C:\Program Files\ChimeraX
1.9rc202412100036\bin\Lib\xml\sax\xmlreader.py", line 127, in parse
self.close()
File "C:\Program Files\ChimeraX
1.9rc202412100036\bin\Lib\xml\sax\expatreader.py", line 240, in close
self.feed(b"", isFinal=True)
File "C:\Program Files\ChimeraX
1.9rc202412100036\bin\Lib\xml\sax\expatreader.py", line 221, in feed
self._err_handler.fatalError(exc)
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\xml\sax\handler.py",
line 38, in fatalError
raise exception
xml.sax._exceptions.SAXParseException:
D:\All_projects\Fousseyni-2024-2025\DENV1\Align.cmm:1:0: no element found
xml.sax._exceptions.SAXParseException:
D:\All_projects\Fousseyni-2024-2025\DENV1\Align.cmm:1:0: no element found
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\xml\sax\handler.py",
line 38, in fatalError
raise exception
See log for complete Python traceback.
> open D:\All_projects\Fousseyni-2024-2025\DENV1\Align.cmm format markers
Traceback (most recent call last):
File "C:\Program Files\ChimeraX
1.9rc202412100036\bin\Lib\xml\sax\expatreader.py", line 217, in feed
self._parser.Parse(data, isFinal)
xml.parsers.expat.ExpatError: no element found: line 1, column 0
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 320, in interceptRequest
self._callback(info)
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 353, in intercept
chimerax_intercept(*args, view=view, session=session)
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 455, in chimerax_intercept
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\ui\gui.py", line 438, in thread_safe
func(*args, **kw)
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 446, in defer
cxcmd(session, topic)
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 464, in cxcmd
run(session, cmd)
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 215, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 526, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 497, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\markers\\__init__.py", line 62, in open
return cmmfiles.read_cmm(session, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\markers\cmmfiles.py", line 7, in read_cmm
msets = load_markerset_xml(session, f)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\site-
packages\chimerax\markers\cmmfiles.py", line 181, in load_markerset_xml
xml_parser.parse(input)
File "C:\Program Files\ChimeraX
1.9rc202412100036\bin\Lib\xml\sax\expatreader.py", line 111, in parse
xmlreader.IncrementalParser.parse(self, source)
File "C:\Program Files\ChimeraX
1.9rc202412100036\bin\Lib\xml\sax\xmlreader.py", line 127, in parse
self.close()
File "C:\Program Files\ChimeraX
1.9rc202412100036\bin\Lib\xml\sax\expatreader.py", line 240, in close
self.feed(b"", isFinal=True)
File "C:\Program Files\ChimeraX
1.9rc202412100036\bin\Lib\xml\sax\expatreader.py", line 221, in feed
self._err_handler.fatalError(exc)
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\xml\sax\handler.py",
line 38, in fatalError
raise exception
xml.sax._exceptions.SAXParseException:
D:\All_projects\Fousseyni-2024-2025\DENV1\Align.cmm:1:0: no element found
xml.sax._exceptions.SAXParseException:
D:\All_projects\Fousseyni-2024-2025\DENV1\Align.cmm:1:0: no element found
File "C:\Program Files\ChimeraX 1.9rc202412100036\bin\Lib\xml\sax\handler.py",
line 38, in fatalError
raise exception
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 512.78
OpenGL renderer: NVIDIA GeForce GTX 1660 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows
Manufacturer: ASUSTeK COMPUTER INC.
Model: TUF Gaming FX505GU_FX95GU
OS: Microsoft Windows 11 Pro (Build 26100)
Memory: 17,022,742,528
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz
OSLanguage: en-US
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.7.1
build: 1.2.1
certifi: 2024.8.30
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9rc202412100036
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.5
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.2
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h5py: 3.12.1
html2text: 2024.2.26
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pywin32: 306
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
WMI: 1.5.1
Change History (4)
comment:1 by , 7 months ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → SAXParseException reading markers |
comment:2 by , 7 months ago
comment:3 by , 7 months ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Fixed.
Made writing a marker set file (.cmm) when no marker models are open include tags <marker_set></marker_set> to avoid an error when reading the file.
comment:4 by , 7 months ago
Actually if no marker models exist then saving markers should raise an error. I made it do that.
Note:
See TracTickets
for help on using tickets.
The user saved a file with 0 markers
then later tried to open it which produced the reported error because the file is empty. The file with no markers should probably at least write the tags <markerset> tab or the reader should handle an empty file.