[Chimera-users] Running Mole - error

Elaine Meng meng at cgl.ucsf.edu
Mon Dec 9 10:17:38 PST 2019

Hi Atanas!
I’ll have to let the others answer about this python issue, but wanted to mention for anybody interested that there is a MOLEonline web server that outputs scripts for display in Chimera:

It runs MOLE, a program for identifying and characterizing channels in macromolecular structures. Results include a profile of the channel radius and hydropathy, a list of residues lining the channel, and scripts for display in Chimera and other programs. The server is described in this paper:

Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Dec 8, 2019, at 1:35 PM, Radkov, Atanas <Atanas.Radkov at ucsf.edu> wrote:
> Hello,
> My name is Atanas Radkov, postdoc in Seemay Chou's lab at UCSF. I was wondering if you could help me set up Mole on Chimera. I installed it, as well as Mono, but I keep seeing the error below. Could you please let me know if there is a way to address this error? Thank you so much for your time and help!
> Best wishes,
> Atanas
> Traceback (most recent call last):
>   File "/Applications/Chimera.app/Contents/Resources/share/chimera/toolbar.py", line 26, in _guard
>     func()
>   File "/Users/atanasdradkov/Downloads/Mole2_plugin/MOLE2_5/MainWindow.py", line 954, in <lambda>
>     icon, lambda d=chimera.dialogs.display, n=MainWindow.name: d(n), 'MOLE 2.5', None)
>   File "/Applications/Chimera.app/Contents/Resources/share/chimera/dialogs.py", line 76, in display
>     dialog = find(name, create=1)
>   File "/Applications/Chimera.app/Contents/Resources/share/chimera/dialogs.py", line 61, in find
>     return d()
>   File "/Users/atanasdradkov/Downloads/Mole2_plugin/MOLE2_5/MainWindow.py", line 353, in __init__
>     with open(CONFIGFILE, 'w') as f:
> IOError: [Errno 13] Permission denied: '.MOLE_PluginSettings.txt'
> Error in toolbar callback:
> IOError: [Errno 13] Permission denied: '.MOLE_PluginSettings.txt'
>   File "/Users/atanasdradkov/Downloads/Mole2_plugin/MOLE2_5/MainWindow.py", line 353, in __init__
>     with open(CONFIGFILE, 'w') as f:
> See reply log for Python traceback.

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