UnicodeDecodeError installing ISOLDE

[filip.vanpetegem@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.17134
ChimeraX Version: 0.8 (2018-12-17)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
Updating list of available bundles failed: 'list' object has no attribute
'split'  
UCSF ChimeraX version: 0.8 (2018-12-17)  
How to cite UCSF ChimeraX  

> open C:/Users/FVPetegem/Documents/WORK/PROJECTS/CaV/CaV1.1/PankajEM2.py

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 543, in _qt_safe  
run(session, "open " + quote_if_necessary(paths[0]))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2587, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 41, in open  
from_database=from_database, ignore_cache=ignore_cache, **kw))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 117, in open  
models = handle_unknown_kw(session.models.open, paths, format=format,
name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 62, in handle_unknown_kw  
return f(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 590, in open  
session, filenames, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 461, in open_multiple_data  
models, status = open_data(session, fspec, format=format, name=name, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 414, in open_data  
models, status = open_func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\scripting.py", line 75, in open_python_script  
exec(code, sandbox.__dict__)  
File "PankajEM2.py", line 1, in <module>  
ModuleNotFoundError: No module named 'cPickle'  
  
ModuleNotFoundError: No module named 'cPickle'  
  
File "PankajEM2.py", line 1, in  
  
See log for complete Python traceback.  
  

> open
C:/Users/FVPetegem/Documents/WORK/PROJECTS/CaV/CaV1.1/cryosparc_P1_J309_map_sharp-
flip.mrc

Opened cryosparc_P1_J309_map_sharp-flip.mrc, grid size 200,200,200, pixel 1.8,
shown at level 0.684, step 1, values float32  

> open C:/Users/FVPetegem/Documents/WORK/PROJECTS/CaV/CaV1.1/5gjvfitted.pdb

Summary of feedback from opening
C:/Users/FVPetegem/Documents/WORK/PROJECTS/CaV/CaV1.1/5gjvfitted.pdb  
---  
warning | Ignored bad PDB record found on line 24843  
END  
  
5gjvfitted.pdb title:  
Structure of the mammalian voltage-gated calcium channel CAV1.1 complex At
near atomic resolution [more info...]  
  
Chain information for 5gjvfitted.pdb #2  
---  
Chain | Description  
A | voltage-dependent L-type calcium channel subunit α-1S  
B | voltage-dependent L-type calcium channel subunit β-1  
C | voltage-dependent L-type calcium channel subunit β-1  
E | voltage-dependent calcium channel γ-1 subunit  
F | voltage-gated calcium channel subunit α-2/δ-1  
  

> show selAtoms ribbons

> set silhouettes true

> ui mousemode rightMode rotate and select

> ui mousemode rightMode rotate and select

> ui mousemode rightMode rotate and select

> ui mousemode rightMode rotate and select

> ui mousemode rightMode tug

> help help:user

Developer warnings in user commands index:

  * didn't expect href to be to tools/sequenceviewer.html on line 245

  

> toolshed show "Density Map Toolbar"

> volume selMaps show

> volume selMaps hide

> volume selMaps hide

> volume selMaps show

> volume selMaps style surface

> volume selMaps style mesh

> volume selMaps step 1

> volume selMaps style surface

> vop gaussian #1 sdev 5.4

> hide #!1 models

> show #!1 models

> hide #!1.1 models

> show #!1.1 models

> hide #!2.1 models

Downloading bundle ChimeraX_ISOLDE-1.0b2-cp36-cp36m-win_amd64.whl  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 386, in download_finished  
session=self.session)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 548, in install_bundle  
results = self._pip_install(bundle, per_user=per_user, reinstall=reinstall)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 845, in _pip_install  
results = self._run_pip(command)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 863, in _run_pip  
output = cp.stdout.decode("utf-8")  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xa0 in position 46:
invalid start byte  
  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xa0 in position 46:
invalid start byte  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 863, in _run_pip  
output = cp.stdout.decode("utf-8")  
  
See log for complete Python traceback.  
  
Downloading bundle ChimeraX_ISOLDE-1.0b2-cp36-cp36m-win_amd64.whl  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 386, in download_finished  
session=self.session)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 548, in install_bundle  
results = self._pip_install(bundle, per_user=per_user, reinstall=reinstall)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 845, in _pip_install  
results = self._run_pip(command)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 863, in _run_pip  
output = cp.stdout.decode("utf-8")  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xa0 in position 46:
invalid start byte  
  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xa0 in position 46:
invalid start byte  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 863, in _run_pip  
output = cp.stdout.decode("utf-8")  
  
See log for complete Python traceback.  
  
Downloading bundle ChimeraX_ISOLDE-1.0b2-cp36-cp36m-win_amd64.whl  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 386, in download_finished  
session=self.session)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 548, in install_bundle  
results = self._pip_install(bundle, per_user=per_user, reinstall=reinstall)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 845, in _pip_install  
results = self._run_pip(command)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 863, in _run_pip  
output = cp.stdout.decode("utf-8")  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xa0 in position 46:
invalid start byte  
  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xa0 in position 46:
invalid start byte  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 863, in _run_pip  
output = cp.stdout.decode("utf-8")  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 391.40
OpenGL renderer: GeForce GTX 1050/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[pett]

This is a known bug affecting ChimeraX 0.8 in Windows. Please see ​​​https://isolde.cimr.cam.ac.uk/faq/#installation for a workaround. Sorry for the hassle!