ChimeraX bug report submission

[li-ze@…]

The following bug report has been submitted:
Platform:        Darwin-17.5.0-x86_64-i386-64bit
ChimeraX Version: 0.7 (2018-08-01)
Description
When I install the ISOLDE into ChimeraX 0.7, there is also an error after I updated the pip.Please tell me how to solve this problem for this bundle. Thank you.
 
RuntimeError: Processing /Users/lize/Downloads/ChimeraX_ISOLDE-1.0b1-cp36-cp36m-macosx_10_9_x86_64.whl 
Collecting ChimeraX-Clipper>=0.2 (from ChimeraX-ISOLDE==1.0b1) Downloading https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxclipper/releases/0.2.1/ChimeraX_Clipper-0.2.1-cp36-cp36m-macosx_10_9_x86_64.whl (341kB) Collecting ChimeraX-Core==0.6 (from ChimeraX-ISOLDE==1.0b1) 
Could not find a version that satisfies the requirement ChimeraX-Core==0.6 (from ChimeraX-ISOLDE==1.0b1) (from versions: ) 
No matching distribution found for ChimeraX-Core==0.6 (from ChimeraX-ISOLDE==1.0b1) 
You are using pip version 9.0.3, however version 18.0 is available. 
You should consider upgrading via the 'pip install --upgrade pip' command. 




Log:
UCSF ChimeraX version: 0.7 (2018-08-01)  
OpenGL version: 4.1 ATI-1.66.31  
OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine  
OpenGL vendor: ATI Technologies Inc.  
How to cite UCSF ChimeraX  

help help:quickstart

Downloading bundle ChimeraX_ISOLDE-1.0b1-cp36-cp36m-macosx_10_9_x86_64.whl  
Traceback (most recent call last):  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/widgets/htmlview.py", line 366, in download_finished  
    session=self.session)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 548, in install_bundle  
    results = self._pip_install(bundle, per_user=per_user,
reinstall=reinstall)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 841, in _pip_install  
    results = self._run_pip(command)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 868, in _run_pip  
    raise RuntimeError(s)  
RuntimeError: Processing
/Users/lize/Downloads/ChimeraX_ISOLDE-1.0b1-cp36-cp36m-macosx_10_9_x86_64.whl  
Collecting ChimeraX-Clipper>=0.2 (from ChimeraX-ISOLDE==1.0b1)  
  Downloading
https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxclipper/releases/0.2.1/ChimeraX_Clipper-0.2.1-cp36-cp36m-macosx_10_9_x86_64.whl
(341kB)  
Collecting ChimeraX-Core==0.6 (from ChimeraX-ISOLDE==1.0b1)  
  Could not find a version that satisfies the requirement ChimeraX-Core==0.6
(from ChimeraX-ISOLDE==1.0b1) (from versions: )  
No matching distribution found for ChimeraX-Core==0.6 (from ChimeraX-
ISOLDE==1.0b1)  
You are using pip version 9.0.3, however version 18.0 is available.  
You should consider upgrading via the 'pip install --upgrade pip' command.  
  
  

RuntimeError: Processing
/Users/lize/Downloads/ChimeraX_ISOLDE-1.0b1-cp36-cp36m-macosx_10_9_x86_64.whl  
Collecting ChimeraX-Clipper>=0.2 (from ChimeraX-ISOLDE==1.0b1)  
Downloading
https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxclipper/releases/0.2.1/ChimeraX_Clipper-0.2.1-cp36-cp36m-macosx_10_9_x86_64.whl
(341kB)  
Collecting ChimeraX-Core==0.6 (from ChimeraX-ISOLDE==1.0b1)  
Could not find a version that satisfies the requirement ChimeraX-Core==0.6
(from ChimeraX-ISOLDE==1.0b1) (from versions: )  
No matching distribution found for ChimeraX-Core==0.6 (from ChimeraX-
ISOLDE==1.0b1)  
You are using pip version 9.0.3, however version 18.0 is available.  
You should consider upgrading via the 'pip install --upgrade pip' command.  
  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 868, in _run_pip  
raise RuntimeError(s)  
  
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.
Don't include any data you wish to remain private since a publicly viewable
bug report will be created.  

pip install --upgrade pip

Unknown command: pip install --upgrade pip  

help help:index.html

didn't expected commands hrefs to be to tools/sequenceviewer.html on line 240  




OpenGL version: 4.1 ATI-1.66.31
OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[Eric Pettersen]

Hi,

ISOLDE only currently works with Chimera 0.6, so you need to get that version from the download page in order to use ISOLDE.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab