<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">This works!<div class=""><br class=""></div><div class="">Thanks,</div><div class=""><br class=""></div><div class="">Magnus</div><div class=""><br class=""><div class=""><div><blockquote type="cite" class=""><div class="">On 06 Nov 2017, at 21:39, Billy Poon <<a href="mailto:bkpoon@lbl.gov" class="">bkpoon@lbl.gov</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Also, if you already have cctbx installed, you can install scipy into that version of python by,<div class=""><br class=""></div><div class=""><font face="monospace, monospace" class="">cctbx.python -m pip install scipy</font></div><div class=""><br class=""></div><div class="">That command places scipy in the same location as the other cctbx dependencies.</div></div><div class="gmail_extra"><br clear="all" class=""><div class=""><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div class=""><div class="">--</div><div class=""><span style="font-size:12.8000001907349px" class="">Billy K. Poon</span><br class=""></div></div><div class="">Research Scientist, Molecular Biophysics and Integrated Bioimaging</div><div class="">Lawrence Berkeley National Laboratory</div><div class="">1 Cyclotron Road, M/S 33R0345</div><div class="">Berkeley, CA 94720</div><div class="">Tel: (510) 486-5709</div><div class="">Fax: (510) 486-5909</div><div class="">Web: <a href="https://phenix-online.org/" target="_blank" class="">https://phenix-online.org</a></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br class=""><div class="gmail_quote">On Mon, Nov 6, 2017 at 12:32 PM, Peter Zwart <span dir="ltr" class=""><<a href="mailto:PHZwart@lbl.gov" target="_blank" class="">PHZwart@lbl.gov</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class="">I find the easiest way to do this is to install scipy with pip, and use the python associated with that install to be used as the python to compile the cctbx under. <div class=""><br class=""></div><div class="">P</div></div><div class="gmail_extra"><br class=""><div class="gmail_quote"><div class=""><div class="h5">On 6 November 2017 at 12:18, Magnus Andersson <span dir="ltr" class=""><<a href="mailto:magnus.andersson@scilifelab.se" target="_blank" class="">magnus.andersson@scilifelab.<wbr class="">se</a>></span> wrote:<br class=""></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class=""><div class="h5"><div style="word-wrap:break-word" class="">Hello,<div class=""><br class=""></div><div class="">I am not normally using cctbx but I’m trying to run a script that imports modules as follows:</div><div class=""><br class=""></div><div class=""><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">import sys,io,os</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">import subprocess</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">import numpy</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">import pickle</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">import math</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">import pylab</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">#import pymol</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">import time</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">import scipy</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">import iotbx.pdb</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">import cctbx</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">import mmtbx.model</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">from scipy.optimize import fmin, fmin_cg, leastsq</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">from scipy.interpolate import interp1d</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">import datetime</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">from numpy.random import random_sample</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">from cctbx.array_family import flex</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">from scitbx.math import superpose</span></div><div class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div><div class=""><span style="font-variant-ligatures:no-common-ligatures" class="">I have installed cctbx and run with cctbx.python.</span></div><div class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div><div class=""><span style="font-variant-ligatures:no-common-ligatures" class="">How can I import scipy into the cctbx python?</span></div><div class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div><div class="">Cheers,</div><div class=""><br class=""></div><div class="">Magnus</div><div class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> </span></div><div class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div><div class="">
<div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; word-wrap: break-word;" class=""><div class=""><div class="">####</div><div class="">Magnus Andersson, Docent, Ph.D.</div><div class=""><br class=""></div><div class="">Email: <a href="mailto:magnus.andersson@scilifelab.se" target="_blank" class="">magnus.andersson@scilifelab.se</a></div><div class="">Phone: 0769469872</div><div class=""><br class=""></div><div class="">Mailing address:</div><div class="">Science For Life Laboratory</div><div class="">Alpha 6</div><div class="">Box 1031</div><div class="">171 21 Solna</div><div class=""><br class=""></div><div class="">Visiting address:</div><div class="">Tomtebodavägen 23A</div><div class="">171 65 Solna</div></div></div>
</div>
<br class=""></div></div><br class=""></div></div>______________________________<wbr class="">_________________<br class="">
cctbxbb mailing list<br class="">
<a href="mailto:cctbxbb@phenix-online.org" target="_blank" class="">cctbxbb@phenix-online.org</a><br class="">
<a href="http://phenix-online.org/mailman/listinfo/cctbxbb" rel="noreferrer" target="_blank" class="">http://phenix-online.org/mailm<wbr class="">an/listinfo/cctbxbb</a><br class="">
<br class=""></blockquote></div><br class=""><br clear="all" class=""><div class=""><br class=""></div>-- <br class=""><div class="m_6335478090082045084gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div class=""><span style="font-size:small" class="">------------------------------<wbr class="">------------------------------<wbr class="">-----</span><br class=""></div><div class=""><div style="font-size:12.8px" class=""><font size="1" class="">P.H. Zwart<br class="">Staff Scientist</font></div><div style="font-size:12.8px" class=""><font size="1" class="">Molecular Biophysics and Integrated Bioimaging &</font></div><div style="font-size:12.8px" class=""><font size="1" class="">Center for Advanced Mathematics for Energy Research Applications</font></div><div style="font-size:12.8px" class=""><font size="1" class="">Lawrence Berkeley National Laboratories<br class="">1 Cyclotron Road, Berkeley, CA-94703, USA<br class="">Cell: <a href="tel:(510)%20289-9246" value="+15102899246" target="_blank" class="">510 289 9246</a></font></div><div style="font-size:12.8px" class=""><font size="1" class=""><br class=""></font></div><div style="font-size:12.8px" class=""><font size="1" class="">PHENIX: <a href="http://www.phenix-online.org/" style="color:rgb(17,85,204)" target="_blank" class="">http://www.phenix-<wbr class="">online.org</a><br class=""></font></div><div style="font-size:12.8px" class=""><font size="1" class="">CAMERA: <a href="http://camera.lbl.gov/" target="_blank" class="">http://camera.lbl.gov/</a></font></div><div style="font-size:small" class="">------------------------------<wbr class="">------------------------------<wbr class="">-----</div></div></div></div></div></div></div></div>
</div>
<br class="">______________________________<wbr class="">_________________<br class="">
cctbxbb mailing list<br class="">
<a href="mailto:cctbxbb@phenix-online.org" class="">cctbxbb@phenix-online.org</a><br class="">
<a href="http://phenix-online.org/mailman/listinfo/cctbxbb" rel="noreferrer" target="_blank" class="">http://phenix-online.org/<wbr class="">mailman/listinfo/cctbxbb</a><br class="">
<br class=""></blockquote></div><br class=""></div>
_______________________________________________<br class="">cctbxbb mailing list<br class=""><a href="mailto:cctbxbb@phenix-online.org" class="">cctbxbb@phenix-online.org</a><br class="">http://phenix-online.org/mailman/listinfo/cctbxbb<br class=""></div></blockquote></div><br class=""><div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""><div class="">####</div><div class="">Magnus Andersson, Docent, Ph.D.</div><div class=""><br class=""></div><div class="">Email: <a href="mailto:magnus.andersson@scilifelab.se" class="">magnus.andersson@scilifelab.se</a></div><div class="">Phone: 0769469872</div><div class=""><br class=""></div><div class="">Mailing address:</div><div class="">Science For Life Laboratory</div><div class="">Alpha 6</div><div class="">Box 1031</div><div class="">171 21 Solna</div><div class=""><br class=""></div><div class="">Visiting address:</div><div class="">Tomtebodavägen 23A</div><div class="">171 65 Solna</div></div></div>
</div>
<br class=""></div></div></body></html>