[Chimera-users] create automatically all alternative protonation states of protein

[Thomas Evangelidis]

Hi Eric,

I don’t understand your aversion to the recursion solution.  Recursion will
> enumerate all the combinations.
>
It will not. :) I will give you an example once I set up ete3 running in
Chimera.


> Well, regardless, if you wish to use another approach that’s okay.  In
> order to install a Python package where Chimera will find it, you need to
> install it with Chimera’s Python interpreter.  How you do so is covered in
> the Programmer’s FAQ:
> https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html (actually
> tomorrow’s FAQ, since it needed a little tweak).  So namely:
>
> 3b) Installing Python packages into Chimera.
>
> To use a package from Chimera, you would need to install it with Chimera's
> Python. Chimera's Python has the Python version number appended to it, so
> it will be named python2.x (python2.7 when this was written; also on
> Windows add ".exe"). On non-Mac, it will be found in <your Chimera
> installation>/bin. On Mac it's in Chimera.app/Contents/Resources/bin —
> don't use the one in Chimera.app/Contents/MacOS!
>
> The best way to install packages is with pip, using (Chimera's) python2.x
> -m pip install *package*. If the pip module is not found, you'll need to
> install it first with (Chimera's) python2.x -m ensurepip. Then -m pip
> install will work. For packages not supported by pip, you will have to
> follow the installation instructions that come with the package.
>
Do you know how to fix this?



> $ /home/thomas/Programs/Chimera/bin/python2.7 -m pip install ete3
> pip is configured with locations that require TLS/SSL, however the ssl
> module in Python is not available.
> Requirement already satisfied: ete3 in
> /home/thomas/Programs/Chimera/lib/python2.7/site-packages/ete3-3.1.1-py2.7.egg
> (3.1.1)
> pip is configured with locations that require TLS/SSL, however the ssl
> module in Python is not available.
> Could not fetch URL https://pypi.org/simple/pip/: There was a problem
> confirming the ssl certificate: HTTPSConnectionPool(host='pypi.org',
> port=443): Max retries exceeded with url: /simple/pip/ (Caused by
> SSLError("Can't connect to HTTPS URL because the SSL module is not
> available.",)) - skipping


Thanks,
Thomas



-- 

======================================================================

Dr Thomas Evangelidis

Research Scientist

IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en>
Prague, Czech Republic
  &
CEITEC - Central European Institute of Technology <https://www.ceitec.eu/>
Brno, Czech Republic

email: tevang3 at gmail.com

website: https://sites.google.com/site/thomasevangelidishomepage/
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