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Opened 6 years ago
Closed 5 years ago
#2565 closed defect (can't reproduce)
Problems using previously fetched files
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| 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-19.0.0-x86_64-i386-64bit ChimeraX Version: 0.9 (2019-06-06) 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: 0.9 (2019-06-06) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 4XPZ format mmCIF fromDatabase pdb Traceback (most recent call last): File "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py", line 556, in customEvent func(*args, **kw) File "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/htmlview.py", line 300, in defer cxcmd(session, topic) File "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/htmlview.py", line 421, in cxcmd run(session, cmd) File "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.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 "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2632, in run result = ci.function(session, **kw_args) File "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/open.py", line 43, in open db_models = _fetch_from_database(session, db_id, db_name, db_format, name, ignore_cache, **kw) File "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/open.py", line 144, in _fetch_from_database ignore_cache=ignore_cache, **kw) File "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.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 "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.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 "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.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 "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.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 "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/mmcif/__init__.py", line 45, in fetch_from_database return fetcher(session, identifier, ignore_cache=ignore_cache, **kw) File "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif.py", line 315, in fetch_mmcif with open(filename, 'r') as f: PermissionError: [Errno 1] Operation not permitted: '/Users/Kimiko/Downloads/ChimeraX/PDB/4xpz.cif' PermissionError: [Errno 1] Operation not permitted: '/Users/Kimiko/Downloads/ChimeraX/PDB/4xpz.cif' File "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif.py", line 315, in fetch_mmcif with open(filename, 'r') as f: See log for complete Python traceback. > open 4XPZ format mmCIF fromDatabase pdb Traceback (most recent call last): File "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py", line 556, in customEvent func(*args, **kw) File "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/htmlview.py", line 300, in defer cxcmd(session, topic) File "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/htmlview.py", line 421, in cxcmd run(session, cmd) File "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.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 "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2632, in run result = ci.function(session, **kw_args) File "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/open.py", line 43, in open db_models = _fetch_from_database(session, db_id, db_name, db_format, name, ignore_cache, **kw) File "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/open.py", line 144, in _fetch_from_database ignore_cache=ignore_cache, **kw) File "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.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 "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.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 "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.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 "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/mmcif/__init__.py", line 45, in fetch_from_database return fetcher(session, identifier, ignore_cache=ignore_cache, **kw) File "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif.py", line 315, in fetch_mmcif with open(filename, 'r') as f: PermissionError: [Errno 1] Operation not permitted: '/Users/Kimiko/Downloads/ChimeraX/PDB/4xpz.cif' PermissionError: [Errno 1] Operation not permitted: '/Users/Kimiko/Downloads/ChimeraX/PDB/4xpz.cif' File "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif.py", line 315, in fetch_mmcif with open(filename, 'r') as f: See log for complete Python traceback. > open 4XPZ format mmCIF fromDatabase pdb Traceback (most recent call last): File "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py", line 556, in customEvent func(*args, **kw) File "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/htmlview.py", line 300, in defer cxcmd(session, topic) File "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/htmlview.py", line 421, in cxcmd run(session, cmd) File "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.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 "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2632, in run result = ci.function(session, **kw_args) File "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/open.py", line 43, in open db_models = _fetch_from_database(session, db_id, db_name, db_format, name, ignore_cache, **kw) File "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/open.py", line 144, in _fetch_from_database ignore_cache=ignore_cache, **kw) File "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.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 "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.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 "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.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 "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/mmcif/__init__.py", line 45, in fetch_from_database return fetcher(session, identifier, ignore_cache=ignore_cache, **kw) File "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif.py", line 315, in fetch_mmcif with open(filename, 'r') as f: PermissionError: [Errno 1] Operation not permitted: '/Users/Kimiko/Downloads/ChimeraX/PDB/4xpz.cif' PermissionError: [Errno 1] Operation not permitted: '/Users/Kimiko/Downloads/ChimeraX/PDB/4xpz.cif' File "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif.py", line 315, in fetch_mmcif with open(filename, 'r') as f: See log for complete Python traceback. > open 4XPZ Traceback (most recent call last): File "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.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 "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2632, in run result = ci.function(session, **kw_args) File "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/open.py", line 43, in open db_models = _fetch_from_database(session, db_id, db_name, db_format, name, ignore_cache, **kw) File "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/open.py", line 144, in _fetch_from_database ignore_cache=ignore_cache, **kw) File "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.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 "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.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 "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.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 "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/mmcif/__init__.py", line 45, in fetch_from_database return fetcher(session, identifier, ignore_cache=ignore_cache, **kw) File "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif.py", line 315, in fetch_mmcif with open(filename, 'r') as f: PermissionError: [Errno 1] Operation not permitted: '/Users/Kimiko/Downloads/ChimeraX/PDB/4xpz.cif' PermissionError: [Errno 1] Operation not permitted: '/Users/Kimiko/Downloads/ChimeraX/PDB/4xpz.cif' File "/private/var/folders/sp/1n4twypx32960_kgq8bb6zrc0000gn/T/AppTranslocation/02E8D268-9106-42AF-98C6-3CC46AD9E36B/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif.py", line 315, in fetch_mmcif with open(filename, 'r') as f: See log for complete Python traceback. OpenGL version: 4.1 INTEL-14.2.16 OpenGL renderer: Intel Iris Pro OpenGL Engine OpenGL vendor: Intel Inc.
Change History (5)
comment:1 by , 6 years ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Problems using previously fetched files |
comment:2 by , 6 years ago
comment:3 by , 6 years ago
Unfortunately macOS Catalina system permissiuons Security & Privacy / Files and Folders has checkbuttons that control access to Downloads, Documents, Desktop for each app but unchecking Downloads for ChimeraX has no effect -- ChimeraX is still allowed to open files from Downloads with out granting permission. It seems these permission controls are just broken in macOS 10.15.1. I tried logging out after the change still it remembers the Downloads setting for ChimeraX but does not respect it.
So I haven't found a way to tell macOS to stop granting permission to ChimeraX on Downloads.
comment:4 by , 6 years ago
Maybe macOS allows access to files that were written by ChimeraX. I tried opening a Chimera written file in ChimeraX in Downloads and it allows it even when allowing access to Downloads is disallowed for ChimeraX in Files and Folders preferences. So the access controls in Files an Folders just seem broken.
comment:5 by , 5 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
Haven't seen this reported again. So I suspect improvements to macOS asking for permission for Downloads, Desktop and Document folder access has improved remedying the situation.
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This problem is on macOS Catalina (darwin 19) and is caused by the OS new security policy where every app must ask the user for permission to use files from Downloads, Desktop, and Documents. The app only needs to ask once and the answer is remembered for all future use of that app. The asking happens automatically when you bring up the Open File dialog. But this error happened when clicking on a file history thumbnail which shows no dialog. I have seen Catalina ask even in that case. It seems the OS catches the open system call and blocks and shows the dialog. But sometimes it doesn't bring up the dialog and simply fails. I don't understand why it sometimes works and sometimes does not.
Once you agree to allow ChimeraX to open files from Downloads (where it caches fetched files), then you should never get this error. But it may be that it forgets you granted permission when you get a new ChimeraX. I have seen it seemingly forget when I switch between using different daily builds of ChimeraX.
First step is going to be to get a reproducible case of this error. To do that I'll need to figure out how to make macOS forget that I gave permission to access Downloads.