<div dir="ltr"><div dir="ltr"><div dir="ltr"><div class="gmail_default" style="font-size:large;color:rgb(0,0,0)"><br></div></div><div class="gmail_default" style="font-size:large;color:rgb(0,0,0)">Hi Eric,</div><div class="gmail_default" style="font-size:large;color:rgb(0,0,0)"><br></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="word-wrap:break-word"><div><span class="gmail-m_7865618084754228245Apple-tab-span" style="white-space:pre-wrap"> </span>I don’t understand your aversion to the recursion solution. Recursion will enumerate all the combinations.</div></div></blockquote><div><div class="gmail_default" style="font-size:large;color:rgb(0,0,0)"></div><div class="gmail_default" style="font-size:large;color:rgb(0,0,0)">It will not. :) I will give you an example once I set up ete3 running in Chimera.</div></div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="word-wrap:break-word"><div><span class="gmail-m_7865618084754228245Apple-tab-span" style="white-space:pre-wrap"> </span>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: <a href="https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html" target="_blank">https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html</a> (actually tomorrow’s FAQ, since it needed a little tweak). So namely:</div><div><br></div><div><h3 style="font-family:-webkit-standard"><a name="m_7865618084754228245_q3b">3b) Installing Python packages into Chimera.</a></h3><h3 style="font-family:-webkit-standard"><p style="font-weight:normal">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!</p><p style="font-weight:normal">The best way to install packages is with pip, using (Chimera's) <code>python2.x -m pip install <i>package</i></code>. If the pip module is not found, you'll need to install it first with (Chimera's) <code>python2.x -m ensurepip</code>. Then <code>-m pip install</code> will work. For packages not supported by pip, you will have to follow the installation instructions that come with the package.</p></h3></div></div></blockquote><div><div class="gmail_default" style="font-size:large;color:rgb(0,0,0)">Do you know how to fix this?</div><br></div><div> </div><div><blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex" class="gmail_quote">$ /home/thomas/Programs/Chimera/bin/python2.7 -m pip install ete3<br>pip is configured with locations that require TLS/SSL, however the ssl module in Python is not available.<br>Requirement already satisfied: ete3 in /home/thomas/Programs/Chimera/lib/python2.7/site-packages/ete3-3.1.1-py2.7.egg (3.1.1)<br>pip is configured with locations that require TLS/SSL, however the ssl module in Python is not available.<br>Could not fetch URL <a href="https://pypi.org/simple/pip/">https://pypi.org/simple/pip/</a>: There was a problem confirming the ssl certificate: HTTPSConnectionPool(host='<a href="http://pypi.org">pypi.org</a>', 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</blockquote><div class="gmail_default" style="font-size:large;color:rgb(0,0,0)"></div><br></div><div><div class="gmail_default" style="font-size:large;color:rgb(0,0,0)">Thanks,</div><div class="gmail_default" style="font-size:large;color:rgb(0,0,0)">Thomas</div><br></div><div><br></div><div> </div></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div>
<p style="margin-bottom:0cm" align="LEFT"><span style="color:rgb(0,0,0)"><span style="font-family:arial,helvetica,sans-serif"><font size="2">======================================================================</font></span></span></p>
<p style="margin-bottom:0cm" align="LEFT"><span style="color:rgb(0,0,0)"><span style="font-family:arial,helvetica,sans-serif"><font size="2">Dr Thomas Evangelidis</font></span></span></p><p style="margin-bottom:0cm" align="LEFT"><span style="color:rgb(0,0,0);font-family:arial,helvetica,sans-serif;font-size:small">Research Scientist</span></p><p style="margin-bottom:0cm" align="LEFT"><span style="color:rgb(0,0,0);font-family:arial,helvetica,sans-serif;font-size:small"><a href="https://www.uochb.cz/web/structure/31.html?lang=en" target="_blank">IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences</a></span></p><font size="2"><div><font color="#000000" face="arial, helvetica, sans-serif"><div>Prague, Czech Republic</div><div> & </div></font></div><font color="#000000" face="arial, helvetica, sans-serif"><a href="https://www.ceitec.eu/" target="_blank">CEITEC - Central European Institute of Technology</a></font><br><font color="#000000" face="arial, helvetica, sans-serif">Brno, Czech Republic </font></font></div><div><font size="2"><font color="#000000" face="arial, helvetica, sans-serif"><br></font></font></div><div dir="ltr"><p style="margin-bottom:0cm" align="LEFT"><span style="color:rgb(0,0,0)"><span style="font-family:arial,helvetica,sans-serif"><font size="2">email: </font></span></span><a href="mailto:tevang3@gmail.com" style="font-size:small;font-family:arial,helvetica,sans-serif" target="_blank">tevang3@gmail.com</a></p><p style="margin-bottom:0cm" align="LEFT"><span style="color:rgb(0,0,0)"><span style="font-family:arial,helvetica,sans-serif"><font size="2">website:
<a href="https://sites.google.com/site/thomasevangelidishomepage/" target="_blank">https://sites.google.com/site/thomasevangelidishomepage/</a></font></span></span></p><span style="color:rgb(0,0,0)"><br><br></span><p style="margin-bottom:0cm" align="LEFT">
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