bundle "ChimeraX-Map"'s API forgot to override open_file()

[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.

[Tom Goddard]

Fixed I think.

This did not reproduce the second time I tried it, and when I tried opening other EMDB maps. It seems to have been caused by toolshed and was primed by installing ISOLDE before opening the map. The problem it warns about is real, and I have deleted the incorrect bundle_info.xml line in the Map bundle that declares the CCP4 format.