after isolde install

[kenneth.satyshur@…]

chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in bundle ChimeraX-ISOLDE:

[Errno 13] Permission denied: '/home/xray/Chimera/chimerax/lib/python3.6/site-packages/chimerax/isolde/validation/molprobity_data/rama8000-cispro.pickle'



File "/home/xray/Chimera/chimerax/lib/python3.6/site-packages/chimerax/core/toolshed/info.py", line 491, in start_tool

"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name, str(e)))


Linux owsley 3.10.0-862.3.2.el7.x86_64 #1 SMP Tue May 15 18:22:15 EDT 2018 x86_64 x86_64 x86_64 GNU/Linux
P5000, 390.48 Nvidia driver, Gnome desktop

How do I get rid of this permission error?
thanks
kas


Kenneth A. Satyshur, M.S., Ph.D.
Senior Scientist,
Depts. Bacteriology, Bio Molecular Chemistry,
Neuroscience, Oncology, Carbone Cancer Center,
and the School of Pharmacy
University of Wisconsin-Madison
Madison, Wisconsin, 53706
608-215-5207

[tic20@…]

Hi Kenneth,

Looks like you installed ISOLDE using the “for everyone” option, which puts it into a directory that requires administrator rights to write to. The short solution to your problem is that you’ll need to run ChimeraX as administrator the first time you run ISOLDE, so it can write some cache files.

Question to the ChimeraX team: do you have some pointers for using ChimeraX’s cache directory for this purpose, so I can avoid this in future builds?

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

 

[pett]

Hi Tristan,

chimerax.appdirs is an AppDirs instance (as per ​https://github.com/ActiveState/appdirs). So if what you're saving is truly a cache, then putting it in the chimerax.appdirs.user_cache_dir folder should work regardless of how ChimeraX was installed. Probably would want to have "isolde" somewhere in the name of the cache file to avoid conflicts with other tools.

--Eric

[tic20@…]

The files in question are the MolProbity rotamer/Ramachandran contours. I distribute them in their default text format, then pickle the processed data on first run for fast loading thereafter.

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

 

[pett]

I guess you might want to use user_data_dir for that. user_cache_dir will be cleared on reboot on a Mac, and probably similarly on other platforms (maybe logout, maybe never, dunno!).

--Eric

[Conrad Huang]

Eric's suggestion is correct.