id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
2511	Can't open files due to cache problem	Eric Pettersen	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-10-10)
Description
""open 3fx2"" on a new machine that had had files migrated from an old machine (using Migration Assistant)

Log:
UCSF ChimeraX version: 0.91 (2019-10-10)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 3fx2

Traceback (most recent call last):  
File
""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py"", line 254, in execute  
cmd.run(cmd_text)  
File
""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py"", line 2837, in run  
result = ci.function(session, **kw_args)  
File
""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/open.py"", line 44, in open  
db_models, status = _fetch_from_database(session, db_id, db_name, db_format,
name, ignore_cache, **kw)  
File
""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/open.py"", line 153, in _fetch_from_database  
ignore_cache=ignore_cache, **kw)  
File
""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/fetch.py"", line 434, in fetch_from_database  
models, status = df.fetch(session, id, format=format,
ignore_cache=ignore_cache, **kw)  
File
""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/fetch.py"", line 497, in fetch  
return fetch(session, database_id, ignore_cache=ignore_cache, **kw)  
File
""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py"", line 383, in fetch_cb  
return fetch_shim(session, identifier, **kw)  
File
""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py"", line 381, in fetch_shim  
return f(session, identifier, database_name=database_name,
format_name=format_name, **kw)  
File
""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/__init__.py"", line 46, in fetch_from_database  
return fetcher(session, identifier, ignore_cache=ignore_cache, **kw)  
File
""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/mmcif.py"", line 315, in fetch_mmcif  
cache, ignore_cache=ignore_cache)  
File
""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/fetch.py"", line 64, in fetch_file  
makedirs(dirname, exist_ok=True)  
File
""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/os.py"",
line 221, in makedirs  
mkdir(name, mode)  
FileNotFoundError: [Errno 2] No such file or directory:
'/Users/pett/Downloads/ChimeraX/PDB'  
  
FileNotFoundError: [Errno 2] No such file or directory:
'/Users/pett/Downloads/ChimeraX/PDB'  
  
File
""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/os.py"",
line 221, in makedirs  
mkdir(name, mode)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-2.11.20
OpenGL renderer: AMD Radeon Pro 575X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

}}}
"	defect	closed	normal		Input/Output		not a bug						all	ChimeraX