ISOLDE run time error

[vincent.chaptal@…]

Dear Chimera developers,

I would like to install ISOLDE and run into a runtime error problem, see 
bellow.
First I installed the daily build v0.7 and then realized that it only 
works on v0.6, so I reinstalled v0.6 by overwritting on v0.7 in order to 
only keep one version on my mac.

I would gladly provide the log if you can help me locate it.

could you tell how to proceed in order to make it work?
thanks
All the best
Vincent


RuntimeError: Processing 
/Users/vchaptal/Downloads/ChimeraX_ISOLDE-1.0b1-cp36-cp36m-macosx_10_9_x86_64.whl
Requirement not upgraded as not directly required: ChimeraX-Core==0.6 in 
/Applications/ChimeraX.app/Contents/lib/python3.6/site-packages (from 
ChimeraX-ISOLDE==1.0b1)
Collecting ChimeraX-Clipper>=0.2 (from ChimeraX-ISOLDE==1.0b1)
Retrying (Retry(total=4, connect=None, read=None, redirect=None, 
status=None)) after connection broken by 'NewConnectionError(': Failed 
to establish a new connection: [Errno 65] No route to host',)': 
/simple/chimerax-clipper/
Retrying (Retry(total=3, connect=None, read=None, redirect=None, 
status=None)) after connection broken by 'NewConnectionError(': Failed 
to establish a new connection: [Errno 65] No route to host',)': 
/simple/chimerax-clipper/
Retrying (Retry(total=2, connect=None, read=None, redirect=None, 
status=None)) after connection broken by 'NewConnectionError(': Failed 
to establish a new connection: [Errno 65] No route to host',)': 
/simple/chimerax-clipper/
Retrying (Retry(total=1, connect=None, read=None, redirect=None, 
status=None)) after connection broken by 'NewConnectionError(': Failed 
to establish a new connection: [Errno 65] No route to host',)': 
/simple/chimerax-clipper/
Retrying (Retry(total=0, connect=None, read=None, redirect=None, 
status=None)) after connection broken by 'NewConnectionError(': Failed 
to establish a new connection: [Errno 65] No route to host',)': 
/simple/chimerax-clipper/
Retrying (Retry(total=4, connect=None, read=None, redirect=None, 
status=None)) after connection broken by 'ConnectTimeoutError(, 
'Connection to cxtoolshed.rbvi.ucsf.edu timed out. (connect 
timeout=15)')': /pypi/chimerax-clipper/
Retrying (Retry(total=3, connect=None, read=None, redirect=None, 
status=None)) after connection broken by 'ConnectTimeoutError(, 
'Connection to cxtoolshed.rbvi.ucsf.edu timed out. (connect 
timeout=15)')': /pypi/chimerax-clipper/
Retrying (Retry(total=2, connect=None, read=None, redirect=None, 
status=None)) after connection broken by 'ConnectTimeoutError(, 
'Connection to cxtoolshed.rbvi.ucsf.edu timed out. (connect 
timeout=15)')': /pypi/chimerax-clipper/
Retrying (Retry(total=1, connect=None, read=None, redirect=None, 
status=None)) after connection broken by 'ConnectTimeoutError(, 
'Connection to cxtoolshed.rbvi.ucsf.edu timed out. (connect 
timeout=15)')': /pypi/chimerax-clipper/
Retrying (Retry(total=0, connect=None, read=None, redirect=None, 
status=None)) after connection broken by 'ConnectTimeoutError(, 
'Connection to cxtoolshed.rbvi.ucsf.edu timed out. (connect 
timeout=15)')': /pypi/chimerax-clipper/
Could not find a version that satisfies the requirement 
ChimeraX-Clipper>=0.2 (from ChimeraX-ISOLDE==1.0b1) (from versions: )
No matching distribution found for ChimeraX-Clipper>=0.2 (from 
ChimeraX-ISOLDE==1.0b1)


File 
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/toolshed/__init__.py", 
line 730, in _run_pip
raise RuntimeError(s)

/See log for complete Python traceback./

If you wish to report this error, send mail tochimerax-bugs@cgl.ucsf.edu 
<mailto: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.


-- 

Vincent Chaptal, PhD

Institut de Biologie et Chimie des Protéines

Drug Resistance and Membrane Proteins Laboratory

7 passage du Vercors

69007 LYON

FRANCE

+33 4 37 65 29 01

http://www.ibcp.fr

[tic20@…]

Hi Vincent,

It looks like the install is failing to properly pull the Clipper-Python dependency from the PyPI. Try running the following from a command prompt:

/Applications/ChimeraX.app/contents/bin/ChimeraX -m pip install clipper-python 

If that works correctly then you should be able to repeat the ISOLDE install.

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

 

[tic20@…]

Looking at it more closely, it also looks possible that your Internet connection simply went down at a crucial moment, or was blocked by a firewall (it fails connecting to both the ChimeraX server *and* the PyPI while collecting dependencies).

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

 

[vincent.chaptal@…]

Dear All,

for your info, my IT person was able to install ISOLDE by uploading the 
plugin first on the computer, then by typing the following commands in a 
terminal:

bash2.1 amichon~: export http_proxy=http://ftprox.ibcp.fr:3128
bash2.1 amichon~:  export https_proxy=http://ftprox.ibcp.fr:3128

bash2.1 amichon~: /Applications/ChimeraX.app/Contents/bin/ChimeraX -m 
pip install 
/Users/amichon/Downloads/ChimeraX_ISOLDE-1.0b1-cp36-cp36m-macosx_10_9_x86_64.whl

I hope it can be helpful for you and other users.

All the best

Vincent


On 02/05/2018 19:29, ChimeraX wrote:

[Eric Pettersen]

Thank for the info Vincent! It will be helpful if or when others run into the same problem.

We intend to incorporate proxy-server support into ChimeraX but haven't gotten to it yet. I will open an enhancement-request ticket for it and put you on the recipient list so that you know when it happens.

--Eric