<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Hi again,<div><br></div><div>It seems as I'm stuck with using the wrapper cctbx.python.</div><div><br></div><div>Only one module complains now = Pymol</div><div><br></div><div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"> File "PyWAXS.py", line 8, in <module></div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"> import pymol</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">ImportError: No module named pymol</div></div><div><br></div><div>I have found a fix to the problem in the ccp4 mailing list:</div><div><br></div><div><pre style="font-family: courier, 'courier new', monospace; font-size: 14px; white-space: pre-wrap; word-wrap: break-word; margin-top: 0px; margin-bottom: 0px; line-height: 19px; background-color: rgb(255, 255, 255);">modifying the pymol startup script to source the cctbx setpaths.sh</pre><div><br></div></div><div>but I'm not sure how to implement this solution.</div><div><br></div><div>Here's what I've tried:</div><div><br></div><div>In the macports pymol startup script I've added the line:</div><div><br></div><div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">source /Users/magnus/Downloads/cctbx_build/setpaths.sh</div></div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"><br></div><div style="margin: 0px;">but I get the same error....</div><div style="margin: 0px;"><br></div><div style="margin: 0px;">Suggestions?</div><div style="margin: 0px;"><br></div><div style="margin: 0px;">Magnus</div><div> <br><div><div>On 03 Jun 2014, at 20:55, Magnus Andersson <<a href="mailto:magnus.andersson@scilifelab.se">magnus.andersson@scilifelab.se</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><meta http-equiv="Content-Type" content="text/html charset=us-ascii"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Hi Luc,<div><br></div><div>The problem is I have a macports python build that contains all the rest of the modules that I import in this script. Because cctbx is not included in macports I have a separate build for this. Hence I need to call my script as:</div><div><br></div><div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">/opt/local/bin/python2.7 script.py</div></div><div><br><div><div>I have set the PYTHONPATH in the bash shell:</div><div><br></div><div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);">export PYTHONPATH=/Users/magnus/Downloads/cctbx_sources:/opt/local</div></div><div><br></div><div>But, it's not working. Any suggestions how to deal with this?</div><div><br></div><div>Thanks,</div><div><br></div><div>Magnus</div><div><br></div><div><br></div><div>On 03 Jun 2014, at 20:47, Luc Bourhis <<a href="mailto:luc_j_bourhis@mac.com">luc_j_bourhis@mac.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><meta http-equiv="Content-Type" content="text/html charset=us-ascii"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Hi Magnus,<div><br></div><div>you need to use the wrappers cctbx.python instead of python as it sets PYTHONPATH correctly so as to add that cctbx_sources/boost.</div><div><br></div><div>Best wishes,</div><div><br></div><div>Luc</div><div><br><div><div>On 3 Jun 2014, at 20:33, Magnus Andersson <<a href="mailto:magnus.andersson@scilifelab.se">magnus.andersson@scilifelab.se</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><meta http-equiv="Content-Type" content="text/html charset=us-ascii"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div>Hi,</div><div><br></div><div>I've installed the cctbx package from the selfextracting file found in <a href="http://cci.lbl.gov/cctbx_build/">http://cci.lbl.gov/cctbx_build/</a> </div><div><br></div><div>but I run into problems when importing cctbx in my python script:</div><div><br></div><div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"> import iotbx.pdb</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"> File "/Users/magnus/Downloads/cctbx_sources/iotbx/pdb/__init__.py", line 2, in <module></div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"> from cctbx.array_family import flex</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"> File "/Users/magnus/Downloads/cctbx_sources/cctbx/array_family/flex.py", line 2, in <module></div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"> import scitbx.array_family.flex</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"> File "/Users/magnus/Downloads/cctbx_sources/scitbx/array_family/flex.py", line 2, in <module></div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"> import boost.optional # import dependency</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">ImportError: No module named boost.optional</div></div><div><br></div><div>It is flex.py that wants to import boost.optional and does not find it. </div><div><br></div><div>However, I find these three files:</div><div><br></div><div><div style="margin: 0px; font-family: Courier; color: rgb(255, 240, 165); background-color: rgb(19, 119, 62);">optional.hpp<span class="Apple-tab-span" style="white-space:pre"> </span>optional_fwd.hpp<span class="Apple-tab-span" style="white-space:pre"> </span>optional_io.hpp</div></div><div><br></div><div>in the following directory:</div><div><br></div><div><span style="color: rgb(255, 240, 165); font-family: Courier; background-color: rgb(19, 119, 62);">/Users/magnus/Downloads/cctbx_sources/boost/boost/optional</span></div><div><br></div><div>which suggests that it's present. What am I missing here? I'm using Mac OS X Version 10.9.3 and Python2.7.</div><div><br></div><div>Cheers,</div><div><br></div><div>Magnus</div><div><br></div></div>_______________________________________________<br>cctbxbb mailing list<br><a href="mailto:cctbxbb@phenix-online.org">cctbxbb@phenix-online.org</a><br><a href="http://phenix-online.org/mailman/listinfo/cctbxbb">http://phenix-online.org/mailman/listinfo/cctbxbb</a><br></blockquote></div><br></div></div>_______________________________________________<br>cctbxbb mailing list<br><a href="mailto:cctbxbb@phenix-online.org">cctbxbb@phenix-online.org</a><br><a href="http://phenix-online.org/mailman/listinfo/cctbxbb">http://phenix-online.org/mailman/listinfo/cctbxbb</a><br></blockquote></div><br></div></div></blockquote></div><br></div></body></html>