Opened 7 years ago

Closed 7 years ago

#1399 closed defect (duplicate)

Crash reading PDB file

Reported by: chimerax-bug-report@… Owned by: pett
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:        Darwin-16.6.0-x86_64-i386-64bit
ChimeraX Version: 0.8 (2018-09-29)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.8 (2018-09-29)  
How to cite UCSF ChimeraX  

open "/Users/cusycon/Dropbox/UQ data&docs/Protein structures/4o6b.pdb" ↵

Traceback (most recent call last):  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/gui.py", line 526, in _qt_safe  
    run(session, "open " \+ quote_if_necessary(paths[0]))  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/run.py", line 31, in run  
    results = command.run(text, log=log)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2562, in run  
    result = ci.function(session, **kw_args)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/open.py", line 41, in open  
    from_database=from_database, ignore_cache=ignore_cache, **kw))  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/open.py", line 62, in handle_unknown_kw  
    return f(*args, **kw)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/models.py", line 575, in open  
    session, filenames, format=format, name=name, **kw)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/io.py", line 444, in open_multiple_data  
    models, status = open_data(session, fspec, format=format, name=name, **kw)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/io.py", line 404, in open_data  
    models, status = open_func(*args, **kw)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/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.  
  

help help:quickstart ↵

open "/Users/cusycon/Dropbox/UQ data&docs/Protein structures/4h52.pdb" ↵

Traceback (most recent call last):  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/gui.py", line 526, in _qt_safe  
    run(session, "open " \+ quote_if_necessary(paths[0]))  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/run.py", line 31, in run  
    results = command.run(text, log=log)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2562, in run  
    result = ci.function(session, **kw_args)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/open.py", line 41, in open  
    from_database=from_database, ignore_cache=ignore_cache, **kw))  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/open.py", line 62, in handle_unknown_kw  
    return f(*args, **kw)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/models.py", line 575, in open  
    session, filenames, format=format, name=name, **kw)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/io.py", line 444, in open_multiple_data  
    models, status = open_data(session, fspec, format=format, name=name, **kw)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/io.py", line 404, in open_data  
    models, status = open_func(*args, **kw)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/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: 4.1 NVIDIA-10.17.5 355.10.05.45f01
OpenGL renderer: NVIDIA GeForce GT 650M OpenGL Engine
OpenGL vendor: NVIDIA Corporation

Change History (2)

comment:1 by pett, 7 years ago

Component: Unassigned → Input/Output
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash reading PDB file

comment:2 by pett, 7 years ago

Resolution: → duplicate
Status: accepted → closed

previously fixed

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