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

Jaime Rodríguez-Guerra Pedregal Jaime.RodriguezGuerra at uab.cat
Fri Mar 22 05:09:35 PDT 2019

Hi Thomas,

I think there's a flag in pip so you can skip SSL validations. From pip's help:

  --trusted-host <hostname>   Mark this host as trusted, even though it does not have valid or any HTTPS.

So maybe you can just use "... -m pip --trusted-host pypi.org<http://pypi.org> install ete3". If it does not work, you can always download the package manually from PyPI and run  "... -m pip install /path/to/package/in/disk".

I faced the situation with lots of external dependencies I needed for my own projects, so in the end I wrote a wrapper to make it easier (Pychimera<https://pychimera.readthedocs.io/en/latest/>). It should help you use conda for package management and then inject the environment in Chimera. I admit that in some systems it might cause more trouble than it's worth it, but maybe you want to try. You would need to install Miniconda first, then `conda create -n ete3 -c insilichem pychimera`, followed by `conda activate ete3` and finally `pip install ete3`. To start Chimera with the injected dependencies, use `pychimera --gui` (bare `pychimera` will start the injected Python interpreter).

Let me know if you need something else.


El vie., 22 mar. 2019 a las 12:22, Thomas Evangelidis (<tevang3 at gmail.com<mailto:tevang3 at gmail.com>>) escribió:

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<http://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




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<mailto:tevang3 at gmail.com>

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

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