id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2499 macOS Catalina, opening file PermissionError goddard@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Darwin-19.0.0-x86_64-i386-64bit ChimeraX Version: 0.91 (2019-09-27) Description Pressing recent file thumbnail generates this error after updating macOS to Catalina. Catalina asks when an application first opens a file from a directory whether to allow the app to open files from that directory. Apparently if this is done with the Python open() function it generates a traceback because it has no way of asking. If done with the Open File dialog then it does ask and then works. After that opening files from the directory works without asking. Log: UCSF ChimeraX version: 0.91 (2019-09-27) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 3915 fromDatabase emdb Traceback (most recent call last): File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 571, in customEvent func(*args, **kw) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/htmlview.py"", line 338, in defer cxcmd(session, topic) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/htmlview.py"", line 459, in cxcmd run(session, cmd) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/Users/goddard/ucsf/chimerax/ChimeraX.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/goddard/ucsf/chimerax/ChimeraX.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/goddard/ucsf/chimerax/ChimeraX.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/goddard/ucsf/chimerax/ChimeraX.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/goddard/ucsf/chimerax/ChimeraX.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/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/emdb_fetch.py"", line 48, in fetch_emdb models, status = io.open_data(session, filename, format = 'ccp4', name = emdb_id, **kw) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py"", line 445, in open_data models, status = open_func(*args, **kw) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/volume.py"", line 3598, in open_map_format return open_map(session, path, name=name, format=format, **kw) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/volume.py"", line 3197, in open_map verbose = kw.get('verbose')) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/data/fileformats.py"", line 153, in open_file data = open_func(apath, **kw) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/data/ccp4/__init__.py"", line 18, in open return [CCP4Grid(path)] File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/data/ccp4/ccp4_grid.py"", line 21, in __init__ MRCGrid.__init__(self, path, file_type = 'ccp4') File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/data/mrc/mrc_grid.py"", line 24, in __init__ d = mrc_format.MRC_Data(path, file_type) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/data/mrc/mrc_format.py"", line 29, in __init__ file = open(path, 'rb') PermissionError: [Errno 1] Operation not permitted: '/Users/goddard/Downloads/ChimeraX/EMDB/emd_3915.map' PermissionError: [Errno 1] Operation not permitted: '/Users/goddard/Downloads/ChimeraX/EMDB/emd_3915.map' File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/data/mrc/mrc_format.py"", line 29, in __init__ file = open(path, 'rb') See log for complete Python traceback. OpenGL version: 4.1 ATI-3.0.68 OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine OpenGL vendor: ATI Technologies Inc. }}} " defect closed major Platform can't reproduce Eric Pettersen Elaine Meng Greg Couch Conrad Huang all ChimeraX