ChimeraX/Isolde error: can't import clipper

[jjr@…]

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 <lambda>
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 <module>
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.

[tic20@…]

Hi Jonathan,

Yes, that's my fault. I've been meaning to make it clear that the Clipper plugin (and ISOLDE) are Linux-only for the time being - ChimeraX has the infrastructure for me to do it, but I haven't had the chance yet. I do hope to have a Mac build available in the near future, but can't say exactly when right now.

Best regards,

Tristan



Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY

[Tristan Croll]

Cleaning up old ticket - ISOLDE and Clipper have been available for all three platforms for a while now.