Opened 7 years ago

Closed 7 years ago

Last modified 7 years ago

#1630 closed defect (not a bug)

ChimeraX bug report submission

Reported by: n.keep@… Owned by:
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Darwin-18.2.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-01-23)
Description
Installing Isolde on Mac

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  
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.  
  




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

Change History (4)

comment:1 by Tristan Croll, 7 years ago

Platform: → all
Project: → ChimeraX

I'm afraid ISOLDE 1.0b2 is only compatible with the ChimeraX 0.8 release version, not the daily builds.

in reply to:  2 ; comment:2 by n.keep@…, 7 years ago 

Thanks worked that out

Best wishes

NIck

comment:3 by Tristan Croll, 7 years ago

Resolution: → not a bug
Status: new → closed

comment:4 by pett, 7 years ago

Component: Unassigned → Third Party
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