Opened 6 months ago

Closed 6 months ago

Last modified 6 months ago

#17348 closed defect (fixed)

SAXParseException reading markers

Reported by: chimerax-bug-report@… 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 pett, 6 months ago

Component: Unassigned → Input/Output
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → SAXParseException reading markers

comment:2 by Tom Goddard, 6 months ago

The user saved a file with 0 markers

> save D:/All_projects/Fousseyni-2024-2025/DENV1/Align.cmm
Wrote 0 marker sets containing 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.

comment:3 by Tom Goddard, 6 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 Tom Goddard, 6 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.