KeyError: 'ChimeraX_ISOLDE'

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Darwin-18.2.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-01-23)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | Traceback (most recent call last):  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 338, in __init__  
  
self.init_available_from_cache(logger)  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 449, in
init_available_from_cache  
  
abc.load_from_cache()  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/available.py", line 64, in load_from_cache  
  
b = _build_bundle(d)  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/available.py", line 106, in _build_bundle  
  
bundle_d = d["bundle"][bundle_name]  
  
KeyError: 'ChimeraX_ISOLDE'  
  
  
  
  
UCSF ChimeraX version: 0.9 (2019-01-23)  
How to cite UCSF ChimeraX  

> open 2ymv format mmCIF fromDatabase pdb

Summary of feedback from opening 2ymv fetched from pdb  
---  
notes | Fetching compressed mmCIF 2ymv from
http://files.rcsb.org/download/2ymv.cif  
Fetching CCD SER from http://ligand-expo.rcsb.org/reports/S/SER/SER.cif  
Fetching CCD ASP from http://ligand-expo.rcsb.org/reports/A/ASP/ASP.cif  
Fetching CCD THR from http://ligand-expo.rcsb.org/reports/T/THR/THR.cif  
Fetching CCD ARG from http://ligand-expo.rcsb.org/reports/A/ARG/ARG.cif  
Fetching CCD LEU from http://ligand-expo.rcsb.org/reports/L/LEU/LEU.cif  
Fetching CCD VAL from http://ligand-expo.rcsb.org/reports/V/VAL/VAL.cif  
Fetching CCD ALA from http://ligand-expo.rcsb.org/reports/A/ALA/ALA.cif  
Fetching CCD ASN from http://ligand-expo.rcsb.org/reports/A/ASN/ASN.cif  
Fetching CCD GLN from http://ligand-expo.rcsb.org/reports/G/GLN/GLN.cif  
Fetching CCD PRO from http://ligand-expo.rcsb.org/reports/P/PRO/PRO.cif  
Fetching CCD HIS from http://ligand-expo.rcsb.org/reports/H/HIS/HIS.cif  
Fetching CCD TRP from http://ligand-expo.rcsb.org/reports/T/TRP/TRP.cif  
Fetching CCD ILE from http://ligand-expo.rcsb.org/reports/I/ILE/ILE.cif  
Fetching CCD GLU from http://ligand-expo.rcsb.org/reports/G/GLU/GLU.cif  
Fetching CCD GLY from http://ligand-expo.rcsb.org/reports/G/GLY/GLY.cif  
Fetching CCD LYS from http://ligand-expo.rcsb.org/reports/L/LYS/LYS.cif  
Fetching CCD PHE from http://ligand-expo.rcsb.org/reports/P/PHE/PHE.cif  
Fetching CCD MSE from http://ligand-expo.rcsb.org/reports/M/MSE/MSE.cif  
Fetching CCD CYS from http://ligand-expo.rcsb.org/reports/C/CYS/CYS.cif  
Fetching CCD TYR from http://ligand-expo.rcsb.org/reports/T/TYR/TYR.cif  
Fetching CCD FNR from http://ligand-expo.rcsb.org/reports/F/FNR/FNR.cif  
Fetching CCD FMT from http://ligand-expo.rcsb.org/reports/F/FMT/FMT.cif  
Fetching CCD IMD from http://ligand-expo.rcsb.org/reports/I/IMD/IMD.cif  
Fetching CCD ACT from http://ligand-expo.rcsb.org/reports/A/ACT/ACT.cif  
Fetching CCD PGE from http://ligand-expo.rcsb.org/reports/P/PGE/PGE.cif  
Fetching CCD HOH from http://ligand-expo.rcsb.org/reports/H/HOH/HOH.cif  
  
2ymv title:  
Structure of Reduced M Smegmatis 5246, a homologue of M.Tuberculosis Acg [more
info...]  
  
Chain information for 2ymv #1  
---  
Chain | Description  
A | acg nitroreductase  
  
Non-standard residues in 2ymv #1  
---  
ACT — acetate ion  
FMT — formic acid  
FNR —
1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydro-2H-benzo[G]pteridin-1-id-10(5H)-yl)-5-O-phosphonato-
D-ribitol (two electron reduced flavin mononucleotide)  
IMD — imidazole  
PGE — triethylene glycol  
  
  

> open
/Users/ubcg48a/Downloads/ChimeraX_ISOLDE-1.0b2-cp36-cp36m-macosx_10_9_x86_64.whl

Unrecognized file suffix '.whl'  

Unrecognized file suffix '.whl'  

Downloading bundle ChimeraX_ISOLDE-1.0b2-cp36-cp36m-macosx_10_9_x86_64.whl  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/htmlview.py", line 384, in download_finished  
session=self.session)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 605, in install_bundle  
results = self._pip_install(bundle, per_user=per_user, reinstall=reinstall)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 901, in _pip_install  
results = self._run_pip(command)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 928, in _run_pip  
raise RuntimeError(s)  
RuntimeError: ERROR:  
Traceback (most recent call last):  
File  
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-  
packages/chimerax/core/toolshed/__init__.py", line 338, in __init__  
self.init_available_from_cache(logger)  
File  
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-  
packages/chimerax/core/toolshed/__init__.py", line 449, in  
init_available_from_cache  
abc.load_from_cache()  
File  
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-  
packages/chimerax/core/toolshed/available.py", line 64, in load_from_cache  
b = _build_bundle(d)  
File  
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-  
packages/chimerax/core/toolshed/available.py", line 106, in _build_bundle  
bundle_d = d["bundle"][bundle_name]  
KeyError: 'ChimeraX_ISOLDE'  
  
  
ChimeraX_ISOLDE-1.0b2-cp36-cp36m-macosx_10_9_x86_64.whl is not a supported
wheel on this platform.  
  
  
RuntimeError: ERROR:  
Traceback (most recent call last):  
File  
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-  
packages/chimerax/core/toolshed/__init__.py", line 338, in __init__  
self.init_available_from_cache(logger)  
File  
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-  
packages/chimerax/core/toolshed/__init__.py", line 449, in  
init_available_from_cache  
abc.load_from_cache()  
File  
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-  
packages/chimerax/core/toolshed/available.py", line 64, in load_from_cache  
b = _build_bundle(d)  
File  
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-  
packages/chimerax/core/toolshed/available.py", line 106, in _build_bundle  
bundle_d = d["bundle"][bundle_name]  
KeyError: 'ChimeraX_ISOLDE'  
  
  
ChimeraX_ISOLDE-1.0b2-cp36-cp36m-macosx_10_9_x86_64.whl is not a supported
wheel on this platform.  
  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 928, in _run_pip  
raise RuntimeError(s)  
  
See log for complete Python traceback.  
  
Downloading bundle ChimeraX_ISOLDE-1.0b2-cp36-cp36m-macosx_10_9_x86_64.whl  




OpenGL version: 4.1 INTEL-12.4.7
OpenGL renderer: Intel HD Graphics 5000 OpenGL Engine
OpenGL vendor: Intel Inc.

[Greg Couch]

I'm getting the "KeyError: 'ChimeraX_ISOLDE'" error on startup in the 2018-01-23 build.

[Greg Couch]

When trying to reload cache of available bundles:

> toolshed reload all
Updating list of available bundles failed: 'ChimeraX_ISOLDE'

[Conrad Huang]

I added a fix to ignore errors where the cache is inconsistent with installed bundles.

There is no ISOLDE compatible with the daily builds now because we moved to Python 3.7. My guess is that the cache was built by 0.8 with a working ISOLDE and got picked up by 0.9 where the bundle is not available. The inconsistency caused a fatal error when it should just ignore the unusable cache information.

Greg, can you "git pull", reinstall src/core and see if the error has gone away?

[Greg Couch]

Fixed for me.

[Conrad Huang]

Fixed by same changes as #1628.