id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1340 PDBio: bad format char in arg-parsing string lize.fudan@… Eric Pettersen "{{{ 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) 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) 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) 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. }}} " defect closed normal Input/Output fixed all ChimeraX