id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2512 "bundle ""ChimeraX-Map""'s API forgot to override open_file()" goddard@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Darwin-19.0.0-x86_64-i386-64bit ChimeraX Version: 0.91 (2019-10-10) Description Trying to run ISOLDE tutorial. 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 Downloading bundle ChimeraX_ISOLDE-1.0b3.dev6-cp37-cp37m-macosx_10_9_x86_64.whl Successfully installed ChimeraX-Clipper-0.9.10 ChimeraX-ISOLDE-1.0b3.dev6 Installed ChimeraX-Clipper (0.9.10) Installed ChimeraX-ISOLDE (1.0b3.dev6) 'clip' is a prefix of an existing command 'clipper' > isolde tutorial > isolde demo cryo_em modelOnly true startIsolde false 6out.pdb title: Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP asymmetric unit In T=3 symmetry [more info...] Chain information for 6out.pdb #1 --- Chain | Description A B C | capsid protein VP1 Loaded cryo-EM demo: PDB ID 6out, EMDB ID 20205 > open 20205 fromDatabase emdb Summary of feedback from opening 20205 fetched from emdb --- note | Fetching compressed map 20205 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-20205/map/emd_20205.map.gz Traceback (most recent call last): File ""/Users/goddard/Desktop/ChimeraX Oct 10 2019.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/Desktop/ChimeraX Oct 10 2019.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/Desktop/ChimeraX Oct 10 2019.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/Desktop/ChimeraX Oct 10 2019.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/Desktop/ChimeraX Oct 10 2019.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/Desktop/ChimeraX Oct 10 2019.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/Desktop/ChimeraX Oct 10 2019.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/Desktop/ChimeraX Oct 10 2019.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/Desktop/ChimeraX Oct 10 2019.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/Desktop/ChimeraX Oct 10 2019.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/Desktop/ChimeraX Oct 10 2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py"", line 397, in open_data open_func = fmt.open_func File ""/Users/goddard/Desktop/ChimeraX Oct 10 2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py"", line 175, in _get_open_func self._open_func = self._boot_open_func() File ""/Users/goddard/Desktop/ChimeraX Oct 10 2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/toolshed/info.py"", line 330, in boot_open ""bundle \""%s\""'s API forgot to override open_file()"" % bi_self.name) chimerax.core.toolshed.ToolshedError: bundle ""ChimeraX-Map""'s API forgot to override open_file() chimerax.core.toolshed.ToolshedError: bundle ""ChimeraX-Map""'s API forgot to override open_file() File ""/Users/goddard/Desktop/ChimeraX Oct 10 2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/toolshed/info.py"", line 330, in boot_open ""bundle \""%s\""'s API forgot to override open_file()"" % bi_self.name) 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 normal Volume Data fixed all ChimeraX