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<p class="MsoNormal">Hi Tom,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks a lot for the reply, my issue is solved now.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">A pip install command would indeed be great! But for now the Command Prompt also works fine for me
<span style="font-family:"Segoe UI Emoji",sans-serif">😊</span>.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Ilse<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b><span lang="NL">Van:</span></b><span lang="NL"> Tom Goddard <goddard@sonic.net>
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<b>Verzonden:</b> 11 June 2021 06:47<br>
<b>Aan:</b> Lagerwaard, I.M. (Ilse) <i.m.lagerwaard@students.uu.nl><br>
<b>CC:</b> chimerax-users@cgl.ucsf.edu<br>
<b>Onderwerp:</b> Re: [chimerax-users] using pandas<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi Ilse,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Windows I run a Command Prompt as administrator to have permission to modify the installed ChimeraX and use<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">> cd C:\Program Files\ChimeraX-1.2.5\bin<o:p></o:p></p>
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<p class="MsoNormal">> .\python.exe -m pip install pandas<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">And then I can use "import pandas" in the ChimeraX shell (menu Tools / General / Shell) without errors.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Or in a Command Prompt that is not run as administrator I run<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">> cd C:\Program Files\ChimeraX-1.2.5\bin<o:p></o:p></p>
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<p class="MsoNormal">> .\ChimeraX-console.exe -m pip install pandas --user<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">and again pandas installs fine and imports in ChimeraX.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Definitely we should add an easy way to do this in ChimeraX without the Command Prompt rigamarole, like a ChimeraX command "pip install pandas". But we don't have that right now. Sadly the Python pip package does not have an API to do
installs using a function call -- really poor design. But probably we can work around that.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"> Tom<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Jun 9, 2021, at 10:27 AM, Tom Goddard <<a href="mailto:goddard@sonic.net">goddard@sonic.net</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hi Ilse,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"> ChimeraX distributions include Python so you just want to install pandas into the ChimeraX Python. This involves running the ChimeraX Python and using pip install. Here is how I do that on Mac. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">$ ~/Desktop/ChimeraX.app/Contents/bin/python3.8 -m pip install pandas<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Windows or Linux it would be similar. We should have a ChimeraX command to install PyPi packages but don't have that yet.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span class="apple-tab-span"> </span>Tom<o:p></o:p></p>
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<p class="MsoNormal">On Jun 9, 2021, at 3:09 AM, Lagerwaard, I.M. (Ilse) via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu">chimerax-users@cgl.ucsf.edu</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span lang="NL">Hello everyone,</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="NL"> </span><o:p></o:p></p>
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<p class="MsoNormal">Is it possible to use the pandas package in ChimeraX? I tried opening a Python script containing the line ‘import pandas’, but I get the error: ‘ModuleNotFoundError: No module named 'pandas'’.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Kind regards,<o:p></o:p></p>
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<p class="MsoNormal">Ilse<o:p></o:p></p>
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