Opened 7 years ago

Closed 7 years ago

#1340 closed defect (fixed)

PDBio: bad format char in arg-parsing string

Reported by: lize.fudan@… 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:        Darwin-17.5.0-x86_64-i386-64bit
ChimeraX Version: 0.8 (2018-09-29)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 0.8 (2018-09-29)  
How to cite UCSF ChimeraX  

open
/Users/lize/Documents/HIV_Structure/AutoSharpen/Autosharpen_4/BALenvtrimer_nogp41_sharpened_map.ccp4
↵

Opened BALenvtrimer_nogp41_sharpened_map.ccp4, grid size 160,160,160, pixel
2.2, shown at level 3.75, step 1, values float32  

close session ↵

open /Users/lize/Documents/HIV_Structure/Oct02/HIV-sharpened-6A-400-rev.mrc ↵

Opened HIV-sharpened-6A-400-rev.mrc, grid size 128,128,128, pixel 2.2, shown
at level 0.302, step 1, values float32  

open /Users/lize/Documents/HIV_Structure/Figures/mono5fuu.pdb ↵

Traceback (most recent call last):  
  File
"/Applications/ChimeraX08.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/ChimeraX08.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/ChimeraX08.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/ChimeraX08.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/ChimeraX08.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/ChimeraX08.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/ChimeraX08.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/ChimeraX08.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/ChimeraX08.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/ChimeraX08.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/ChimeraX08.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/ChimeraX08.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.  
  

open /Users/lize/Documents/HIV_Structure/Figures/mono5fuu.pdb ↵

Traceback (most recent call last):  
  File
"/Applications/ChimeraX08.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/ChimeraX08.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/ChimeraX08.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/ChimeraX08.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/ChimeraX08.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/ChimeraX08.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/ChimeraX08.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/ChimeraX08.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/ChimeraX08.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/ChimeraX08.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/ChimeraX08.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/ChimeraX08.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.  
  

open /Users/lize/Documents/HIV_Structure/Figures/BALenvmonomer.pdb ↵

Traceback (most recent call last):  
  File
"/Applications/ChimeraX08.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/ChimeraX08.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/ChimeraX08.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/ChimeraX08.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/ChimeraX08.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/ChimeraX08.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/ChimeraX08.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/ChimeraX08.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/ChimeraX08.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/ChimeraX08.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/ChimeraX08.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/ChimeraX08.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 ATI-1.66.31
OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

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: → fixed
Status: accepted → closed

Hi,

Thanks for reporting this problem. It is fixed now and the fix is in the current daily build. Sorry for the inconvenience!

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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