id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 760 ChimeraX/Isolde error: can't import clipper jjr@… Tristan Croll "{{{ Dear Sir or Madam, I have just installed ChimeraX on my MacBook Pro (running OS 10.11.6), and then installed Isolde. However, attempting to run Isolde immediately throws up an error message: ImportError: cannot import name 'clipper'. I have copied the log to the bottom of this email. Any help gratefully received, Best wishes, Dr Jonathan Ruprecht MRC Mitochondrial Biology Unit Cambridge CB2 0XY United Kingdom ________________________________________________________________ UCSF ChimeraX version: 0.1 (2017-07-19) OpenGL version: 4.1 INTEL-10.14.73 OpenGL renderer: Intel Iris Pro OpenGL Engine OpenGL vendor: Intel Inc. Downloading bundle ChimeraX_ISOLDE-0.9.13-py3-none-any.whl Successfully installed ChimeraX-ISOLDE-0.9.13 Installed ChimeraX-ISOLDE (0.9.13) open /Users/jjrlocal/laptop/m-state/datasets/M230_2/buster58/refine.pdb Summary of feedback from opening /Users/jjrlocal/laptop/m-state/datasets/M230_2/buster58/refine.pdb warnings Ignored bad PDB record found on line 1 REMARK --------------------- added by autoBUSTER ---------------------------------START Ignored bad PDB record found on line 2 REMARK run at = Tue Jul 18 19:34:40 BST 2017 Ignored bad PDB record found on line 13 REMARK Files used: Ignored bad PDB record found on line 14 REMARK PDB = ./pdbchk.pdb Ignored bad PDB record found on line 15 REMARK MTZ = /Users/jjrlocal/laptop/m-state/datasets/M230_2/Important_Files/m230_2_run8_staraniso_alldata-unique.mtz 92 messages similar to the above omitted Opened PDB data containing 2985 atoms and 3039 bonds Chain information for refine.pdb #1 Chain Description A No description available B No description available toolshed show ISOLDE Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/ui/gui.py"", line 760, in run(ses, ""toolshed show %s"" % quote_if_necessary(tool_name))) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/commands/cli.py"", line 2390, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/commands/toolshed.py"", line 307, in toolshed_show bi.start_tool(session, tool_name) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/toolshed/info.py"", line 474, in start_tool ti = f(session, tool_name, *args, **kw) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/isolde/__init__.py"", line 23, in start_tool return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/tools.py"", line 195, in get_singleton tinst = tool_class(session, tool_name, **kw) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/isolde/tool.py"", line 156, in __init__ from . import isolde File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/isolde/isolde.py"", line 18, in from chimerax import clipper ImportError: cannot import name 'clipper' ImportError: cannot import name 'clipper' File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/isolde/isolde.py"", line 18, in from chimerax import clipper See log for complete Python traceback. If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu and describe what you were doing and include a copy of the contents of the log. }}} " defect closed normal Third Party fixed all ChimeraX