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#2918 closed defect (duplicate)

Blast Protein failure + Attempted instantiation of HeaderSequence during session save

Reported by:	noemi.ruiz@…	Owned by:	Conrad Huang
Priority:	normal	Milestone:
Component:	Sequence	Version:
Keywords:		Cc:	Greg Couch
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 0.92 (2020-03-03)
Description
(Describe the actions that caused this problem to occur here)

Log:
Unknown command: refresh  

> save session C:/Users/leole/Documents/SYT1SYT3.cxs

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 796, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 556, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 255, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 288, in process  
return copy_state(data, convert=convert)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 210, in copy_state  
return _copy(data)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 195, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 195, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 195, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 195, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 204, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 204, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 195, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 195, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 204, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 204, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 204, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 204, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 205, in _copy  
return data.__class__(items)  
TypeError: __init__() missing 1 required positional argument:
'refresh_callback'  
  
TypeError: __init__() missing 1 required positional argument:
'refresh_callback'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 205, in _copy  
return data.__class__(items)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 929, in <lambda>  
save_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_save_cb(sess))  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 647, in file_save_cb  
self.save_dialog.display(self, session)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\save_dialog.py", line 139, in display  
fmt.save(session, filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 1100, in save  
run(session, cmd)  
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 2845, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 992, in save_session  
save(session, filename, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\save.py", line 64, in save  
_handle_unexpected_keyword_error(e, 5)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\save.py", line 61, in save  
fmt.export(session, filename, fmt.nicknames[0], **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 229, in export  
result = self.export_func(session, path, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 796, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 556, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 255, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 288, in process  
return copy_state(data, convert=convert)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 210, in copy_state  
return _copy(data)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 195, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 195, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 195, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 195, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 204, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 204, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 195, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 195, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 204, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 204, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 204, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 204, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 205, in _copy  
return data.__class__(items)  
TypeError: __init__() missing 1 required positional argument:
'refresh_callback'  
  
TypeError: __init__() missing 1 required positional argument:
'refresh_callback'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 205, in _copy  
return data.__class__(items)  
  
See log for complete Python traceback.  
  

> select #1:268 #2:230

16 atoms, 14 bonds, 2 models selected  
Seqview [ID: 1] region Consensus..201801_SYT3_1623pb_intensive.pdb, chain
(blank) [1-555] RMSD: 3.412  
  

> save "C:/Users/leole/Documents/05 Univ Malaga_2016_2017/20 Manuscrito
> SYT/Figuras Noemi/AlineamientoSYT1SYT3" format aln alignment 1

> toolshed show "Modeller Comparative"

No target sequence chosen for alignment 1  
Seqview [ID: 1] region Consensus..201801_SYT3_1623pb_intensive.pdb, chain
(blank) [1-555] RMSD: 3.412  
  
Seqview [ID: 1] region Consensus..201801_SYT3_1623pb_intensive.pdb, chain
(blank) [1-555] RMSD: 3.412  
  

> save "C:/Users/leole/Documents/05 Univ Malaga_2016_2017/20 Manuscrito
> SYT/Figuras Noemi/AlineamientoSYT1SYT3" format fasta alignment 1

> select #1

3819 atoms, 3915 bonds, 1 model selected  

> select #2

4367 atoms, 4470 bonds, 1 model selected  

> ~select #2

Nothing selected  

> blastprotein #1 database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 name
> bp3

Web Service: BlastProtein2 is a Python wrapper that calls blastp to search nr
or pdb for sequences similar to the given protein sequence  
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service  
Opal job id: appBlastProtein2Service15833203481191424442245  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appBlastProtein2Service15833203481191424442245  
stdout.txt = standard output  
stderr.txt = standard error  
BlastProtein finished.  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 606, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\job.py", line 96, in on_finish  
p = Parser("query", self.seq, results)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\blastp_parser.py", line 47, in __init__  
tree = ET.fromstring(output)  
File "C:\Program Files\ChimeraX\bin\lib\xml\etree\ElementTree.py", line 1316,
in XML  
return parser.close()  
File "<string>", line None  
xml.etree.ElementTree.ParseError: no element found: line 1, column 0  
  
File "", line None  
xml.etree.ElementTree.ParseError: no element found: line 1, column 0  
  
File "C:\Program Files\ChimeraX\bin\lib\xml\etree\ElementTree.py", line 1316,
in XML  
return parser.close()  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 376.54
OpenGL renderer: GeForce 920M/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Change History (2)

comment:1 by pett, 6 years ago

Cc:	Greg Couch added
Component:	Unassigned → Sequence
Owner:	set to Conrad Huang
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Blast Protein failure + Attempted instantiation of HeaderSequence during session save

This is a duplicate of both #2917 and #2789. Will be adding reporter to both of those and closing this ticket.

comment:2 by pett, 6 years ago

Reporter:	changed from chimerax-bug-report@… to noemi.ruiz@…
Resolution:	→ duplicate
Status:	assigned → closed

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