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#1361 closed defect (duplicate)

PDBio: bad format char in arg-parsing string

Reported by:	chimerax-bug-report@…	Owned by:	Eric Pettersen
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-10-10.0.17134
ChimeraX Version: 0.8 (2018-09-29)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | Updating list of available bundles failed: [Errno 11001] getaddrinfo
failed  
  
UCSF ChimeraX version: 0.8 (2018-09-29)  
How to cite UCSF ChimeraX  

open 1LDG ↵

Fetching url http://files.rcsb.org/download/1ldg.cif failed: <urlopen error
[Errno 11001] getaddrinfo failed>  

open 1LDG ↵

Summary of feedback from opening 1LDG fetched from pdb  
---  
notes | Fetching compressed mmCIF 1ldg from
http://files.rcsb.org/download/1ldg.cif  
Fetching CCD NAI from http://ligand-expo.rcsb.org/reports/N/NAI/NAI.cif  
Fetching CCD OXM from http://ligand-expo.rcsb.org/reports/O/OXM/OXM.cif  
  
1ldg title:  
Plasmodium falciparum L-lactate dehydrogenase complexed with nadh and oxamate
[more info...]  
  
Chain information for 1ldg #1  
---  
Chain | Description  
A | L-lactate dehydrogenase  
  
1ldg mmCIF Assemblies | 1| author_and_software_defined_assembly  
  

vr on

device vr true ↵

started SteamVR rendering  

vr off

device vr false ↵

close session ↵

open "C:/Users/Jacobson Lab/Desktop/capped_str.zip" ↵

Unrecognized file suffix '.zip'  

Unrecognized file suffix '.zip'  

Traceback (most recent call last):  
  File "C:\Program Files\ChimeraX-Oct-1-2018\bin\lib\site-
packages\chimerax\ui\gui.py", line 530, in _qt_safe  
    session.models.open(paths)  
  File "C:\Program Files\ChimeraX-Oct-1-2018\bin\lib\site-
packages\chimerax\core\models.py", line 575, in open  
    session, filenames, format=format, name=name, **kw)  
  File "C:\Program Files\ChimeraX-Oct-1-2018\bin\lib\site-
packages\chimerax\core\io.py", line 444, in open_multiple_data  
    models, status = open_data(session, fspec, format=format, name=name, **kw)  
  File "C:\Program Files\ChimeraX-Oct-1-2018\bin\lib\site-
packages\chimerax\core\io.py", line 404, in open_data  
    models, status = open_func(*args, **kw)  
  File "C:\Program Files\ChimeraX-Oct-1-2018\bin\lib\site-
packages\chimerax\atomic\pdb\\__init__.py", line 41, in open_file  
    coordsets=coordsets, atomic=atomic, max_models=max_models,
log_info=log_info)  
  File "C:\Program Files\ChimeraX-Oct-1-2018\bin\lib\site-
packages\chimerax\atomic\pdb\pdb.py", line 27, in open_pdb  
    pointers = _pdbio.read_pdb_file(stream, session.logger, not coordsets,
atomic)  
SystemError: argument 2 (impossible<bad format char>)  
  

SystemError: argument 2 (impossible)  
  
File "C:\Program Files\ChimeraX-Oct-1-2018\bin\lib\site-
packages\chimerax\atomic\pdb\pdb.py", line 27, in open_pdb  
pointers = _pdbio.read_pdb_file(stream, session.logger, not coordsets, atomic)  
  
See log for complete Python traceback.  
  

open "C:/Users/Jacobson
Lab/Desktop/capped_str/taspase1_Compound1_xpdocking-6.20.pdb" ↵

Traceback (most recent call last):  
  File "C:\Program Files\ChimeraX-Oct-1-2018\bin\lib\site-
packages\chimerax\ui\gui.py", line 526, in _qt_safe  
    run(session, "open " \+ quote_if_necessary(paths[0]))  
  File "C:\Program Files\ChimeraX-Oct-1-2018\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
    results = command.run(text, log=log)  
  File "C:\Program Files\ChimeraX-Oct-1-2018\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2562, in run  
    result = ci.function(session, **kw_args)  
  File "C:\Program Files\ChimeraX-Oct-1-2018\bin\lib\site-
packages\chimerax\core\commands\open.py", line 41, in open  
    from_database=from_database, ignore_cache=ignore_cache, **kw))  
  File "C:\Program Files\ChimeraX-Oct-1-2018\bin\lib\site-
packages\chimerax\core\commands\open.py", line 110, in open  
    models = handle_unknown_kw(session.models.open, paths, format=format,
name=name, **kw)  
  File "C:\Program Files\ChimeraX-Oct-1-2018\bin\lib\site-
packages\chimerax\core\commands\open.py", line 62, in handle_unknown_kw  
    return f(*args, **kw)  
  File "C:\Program Files\ChimeraX-Oct-1-2018\bin\lib\site-
packages\chimerax\core\models.py", line 575, in open  
    session, filenames, format=format, name=name, **kw)  
  File "C:\Program Files\ChimeraX-Oct-1-2018\bin\lib\site-
packages\chimerax\core\io.py", line 444, in open_multiple_data  
    models, status = open_data(session, fspec, format=format, name=name, **kw)  
  File "C:\Program Files\ChimeraX-Oct-1-2018\bin\lib\site-
packages\chimerax\core\io.py", line 404, in open_data  
    models, status = open_func(*args, **kw)  
  File "C:\Program Files\ChimeraX-Oct-1-2018\bin\lib\site-
packages\chimerax\atomic\pdb\\__init__.py", line 41, in open_file  
    coordsets=coordsets, atomic=atomic, max_models=max_models,
log_info=log_info)  
  File "C:\Program Files\ChimeraX-Oct-1-2018\bin\lib\site-
packages\chimerax\atomic\pdb\pdb.py", line 27, in open_pdb  
    pointers = _pdbio.read_pdb_file(stream, session.logger, not coordsets,
atomic)  
SystemError: argument 2 (impossible<bad format char>)  
  

SystemError: argument 2 (impossible)  
  
File "C:\Program Files\ChimeraX-Oct-1-2018\bin\lib\site-
packages\chimerax\atomic\pdb\pdb.py", line 27, in open_pdb  
pointers = _pdbio.read_pdb_file(stream, session.logger, not coordsets, atomic)  
  
See log for complete Python traceback.  
  

open "C:/Users/Jacobson Lab/Desktop/taspase1_Compound1_xpdocking-6.20.pdb" ↵

Traceback (most recent call last):  
  File "C:\Program Files\ChimeraX-Oct-1-2018\bin\lib\site-
packages\chimerax\ui\gui.py", line 526, in _qt_safe  
    run(session, "open " \+ quote_if_necessary(paths[0]))  
  File "C:\Program Files\ChimeraX-Oct-1-2018\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
    results = command.run(text, log=log)  
  File "C:\Program Files\ChimeraX-Oct-1-2018\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2562, in run  
    result = ci.function(session, **kw_args)  
  File "C:\Program Files\ChimeraX-Oct-1-2018\bin\lib\site-
packages\chimerax\core\commands\open.py", line 41, in open  
    from_database=from_database, ignore_cache=ignore_cache, **kw))  
  File "C:\Program Files\ChimeraX-Oct-1-2018\bin\lib\site-
packages\chimerax\core\commands\open.py", line 110, in open  
    models = handle_unknown_kw(session.models.open, paths, format=format,
name=name, **kw)  
  File "C:\Program Files\ChimeraX-Oct-1-2018\bin\lib\site-
packages\chimerax\core\commands\open.py", line 62, in handle_unknown_kw  
    return f(*args, **kw)  
  File "C:\Program Files\ChimeraX-Oct-1-2018\bin\lib\site-
packages\chimerax\core\models.py", line 575, in open  
    session, filenames, format=format, name=name, **kw)  
  File "C:\Program Files\ChimeraX-Oct-1-2018\bin\lib\site-
packages\chimerax\core\io.py", line 444, in open_multiple_data  
    models, status = open_data(session, fspec, format=format, name=name, **kw)  
  File "C:\Program Files\ChimeraX-Oct-1-2018\bin\lib\site-
packages\chimerax\core\io.py", line 404, in open_data  
    models, status = open_func(*args, **kw)  
  File "C:\Program Files\ChimeraX-Oct-1-2018\bin\lib\site-
packages\chimerax\atomic\pdb\\__init__.py", line 41, in open_file  
    coordsets=coordsets, atomic=atomic, max_models=max_models,
log_info=log_info)  
  File "C:\Program Files\ChimeraX-Oct-1-2018\bin\lib\site-
packages\chimerax\atomic\pdb\pdb.py", line 27, in open_pdb  
    pointers = _pdbio.read_pdb_file(stream, session.logger, not coordsets,
atomic)  
SystemError: argument 2 (impossible<bad format char>)  
  

SystemError: argument 2 (impossible)  
  
File "C:\Program Files\ChimeraX-Oct-1-2018\bin\lib\site-
packages\chimerax\atomic\pdb\pdb.py", line 27, in open_pdb  
pointers = _pdbio.read_pdb_file(stream, session.logger, not coordsets, atomic)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 391.58
OpenGL renderer: Quadro P6000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Change History (2)

comment:1 by Eric Pettersen, 7 years ago

Component:	Unassigned → Input/Output
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → PDBio: bad format char in arg-parsing string

comment:2 by Eric Pettersen, 7 years ago

Resolution:	→ duplicate
Status:	accepted → closed

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