id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2565 Problems using previously fetched files chimerax-bug-report@… Tom Goddard "{{{ 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. }}} " defect closed normal Input/Output can't reproduce all ChimeraX