<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Ilse,<div class=""><br class=""></div><div class="">On Windows I run a Command Prompt as administrator to have permission to modify the installed ChimeraX and use<div class=""><br class=""></div><div class="">> cd C:\Program Files\ChimeraX-1.2.5\bin</div><div class="">> .\python.exe -m pip install pandas</div><div class=""><br class=""></div><div class="">And then I can use "import pandas" in the ChimeraX shell (menu Tools / General / Shell) without errors.</div><div class=""><br class=""></div><div class="">Or in a Command Prompt that is not run as administrator I run</div><div class=""><br class=""></div><div class=""><div class="">> cd C:\Program Files\ChimeraX-1.2.5\bin</div><div class="">> .\ChimeraX-console.exe -m pip install pandas --user</div></div><div class=""><br class=""></div><div class="">and again pandas installs fine and imports in ChimeraX.</div><div class=""><br class=""></div><div class="">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.</div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""></div><div class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Jun 9, 2021, at 10:27 AM, Tom Goddard <<a href="mailto:goddard@sonic.net" class="">goddard@sonic.net</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Ilse,<div class=""><br class=""></div><div class=""> 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. <br class=""><div class=""><br class=""></div><div class=""><div class="">$ ~/Desktop/ChimeraX.app/Contents/bin/python3.8 -m pip install pandas</div><div class=""><br class=""></div><div class="">On Windows or Linux it would be similar. We should have a ChimeraX command to install PyPi packages but don't have that yet.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><blockquote type="cite" class=""><div class="">On Jun 9, 2021, at 3:09 AM, Lagerwaard, I.M. (Ilse) via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="NL" class="">Hello everyone,<o:p class=""></o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="NL" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">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 class=""></o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Kind regards,<o:p class=""></o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Ilse<o:p class=""></o:p></div></div><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">ChimeraX-users mailing list</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">ChimeraX-users@cgl.ucsf.edu</a><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Manage subscription:</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a></div></blockquote></div><br class=""></div></div></div></div></blockquote></div><br class=""></div></div></body></html>