<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<style type="text/css" style="display:none;"> P {margin-top:0;margin-bottom:0;} </style>
</head>
<body dir="ltr">
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Actually, come to think about it: the approach specified in <a href="https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-June/001216.html" id="LPlnk657993">https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-June/001216.html</a> probably won't work
for Windows, since on that platform <code>sys.executable</code> is ChimeraX.exe rather than ChimeraX-console.exe - and running "-m pip install ..." only works for the latter.</div>
<div id="appendonsend"></div>
<hr style="display:inline-block;width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Tristan Croll <tic20@cam.ac.uk><br>
<b>Sent:</b> 10 June 2021 15:53<br>
<b>To:</b> ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>; Lagerwaard, I.M. (Ilse) <i.m.lagerwaard@students.uu.nl><br>
<b>Subject:</b> Re: [chimerax-users] using pandas</font>
<div> </div>
</div>
<style type="text/css" style="display:none">
<!--
p
{margin-top:0;
margin-bottom:0}
-->
</style>
<div dir="ltr">
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
I've had this problem before. The root cause turned out to be that "/path/to/ChimeraX/python3.8 -m pip install --user" installed to the
<b>Python</b> user directory rather than the <b>ChimeraX</b> user directory. Try running:</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
"C:\Program Files\ChimeraX\bin\ChimeraX-console.exe" -m pip install --user pandas</div>
<div id="x_appendonsend"></div>
<hr tabindex="-1" style="display:inline-block; width:98%">
<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Lagerwaard, I.M. (Ilse) via ChimeraX-users <chimerax-users@cgl.ucsf.edu><br>
<b>Sent:</b> 10 June 2021 09:27<br>
<b>To:</b> ChimeraX Users Help <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [chimerax-users] using pandas</font>
<div> </div>
</div>
<style>
<!--
@font-face
{font-family:Helvetica}
@font-face
{font-family:"Cambria Math"}
@font-face
{font-family:Calibri}
p.x_x_MsoNormal, li.x_x_MsoNormal, div.x_x_MsoNormal
{margin:0cm;
font-size:11.0pt;
font-family:"Calibri",sans-serif}
a:link, span.x_x_MsoHyperlink
{color:blue;
text-decoration:underline}
span.x_x_E-mailStijl19
{font-family:"Calibri",sans-serif;
color:windowtext}
.x_x_MsoChpDefault
{font-size:10.0pt}
@page WordSection1
{margin:70.85pt 70.85pt 70.85pt 70.85pt}
-->
</style>
<div lang="EN-US" style="word-wrap:break-word">
<div class="x_x_WordSection1">
<p class="x_x_MsoNormal">Hi Eric,</p>
<p class="x_x_MsoNormal"> </p>
<p class="x_x_MsoNormal">Thank you for the reply! Unfortunately, even though I followed your instructions and do have the bz2 module (I use Windows), I still get the same error. I can ‘import pandas’ in ChimeraX’s Python, but not from within the application
itself. Do you have any idea what else might be going on?</p>
<p class="x_x_MsoNormal"> </p>
<p class="x_x_MsoNormal">Ilse</p>
<p class="x_x_MsoNormal"> </p>
<div>
<div style="border:none; border-top:solid #E1E1E1 1.0pt; padding:3.0pt 0cm 0cm 0cm">
<p class="x_x_MsoNormal"><b><span lang="NL">Van:</span></b><span lang="NL"> Eric Pettersen <pett@cgl.ucsf.edu>
<br>
<b>Verzonden:</b> 09 June 2021 19:12<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</span></p>
</div>
</div>
<p class="x_x_MsoNormal"><span lang="NL"> </span></p>
<p class="x_x_MsoNormal">Hi Ilse,</p>
<div>
<p class="x_x_MsoNormal"><span class="x_x_apple-tab-span"> </span>
You can install pandas into ChimeraX's Python using 'pip install' as described in this mailing-list message: <a href="https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-June/001216.html">https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-June/001216.html</a> .
The caveat is that though this will work on all platforms, the actual later "Import pandas" will fail on at least some Linux platforms because some of our Linux installers don't include the bz2 module in their Python, which pandas depends on. I will add
you to the cc list for the ticket we have open for this problem, in case it matters to you.</p>
</div>
<div>
<p class="x_x_MsoNormal"> </p>
</div>
<div>
<div>
<p class="x_x_MsoNormal">--Eric</p>
</div>
<div>
<p class="x_x_MsoNormal"> </p>
</div>
<div>
<p class="x_x_MsoNormal"><span class="x_x_apple-tab-span"> </span>
Eric Pettersen</p>
</div>
<div>
<p class="x_x_MsoNormal"><span class="x_x_apple-tab-span"> </span>
UCSF Computer Graphics Lab</p>
</div>
<div>
<p class="x_x_MsoNormal"> </p>
</div>
<div>
<p class="x_x_MsoNormal"><br>
<br>
</p>
<blockquote style="margin-top:5.0pt; margin-bottom:5.0pt">
<div>
<p class="x_x_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:</p>
</div>
<p class="x_x_MsoNormal"> </p>
<div>
<div>
<p class="x_x_MsoNormal">Hello everyone,</p>
</div>
<div>
<p class="x_x_MsoNormal"> </p>
</div>
<div>
<p class="x_x_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'’.</p>
</div>
<div>
<p class="x_x_MsoNormal"> </p>
</div>
<div>
<p class="x_x_MsoNormal">Kind regards,</p>
</div>
<div>
<p class="x_x_MsoNormal">Ilse</p>
</div>
<p class="x_x_MsoNormal"><span style="font-size:9.0pt; font-family:"Helvetica",sans-serif">_______________________________________________<br>
ChimeraX-users mailing list<br>
</span><a href="mailto:ChimeraX-users@cgl.ucsf.edu"><span style="font-size:9.0pt; font-family:"Helvetica",sans-serif">ChimeraX-users@cgl.ucsf.edu</span></a><span style="font-size:9.0pt; font-family:"Helvetica",sans-serif"><br>
Manage subscription:<br>
</span><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users"><span style="font-size:9.0pt; font-family:"Helvetica",sans-serif">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</span></a></p>
</div>
</blockquote>
</div>
<p class="x_x_MsoNormal"> </p>
</div>
</div>
</div>
</div>
</body>
</html>