<div dir="ltr"><div><div>Hi, Billy<br><br></div>It works, after I added the flags in that file.<br></div>I also created a patch file.<br><div><div><div><div class="gmail_extra">Please check the attach file.<br></div><div class="gmail_extra">Just put it in the root folder of PHENIX, and type<br>"patch -p0 < install_base_packages.py.patch"<br><br></div><div class="gmail_extra">Thanks for your help.<br><br></div><div class="gmail_extra">By A.C.<br><br></div><div class="gmail_extra"><div class="gmail_quote">2016-02-15 16:34 GMT+08:00 Billy Poon <span dir="ltr"><<a href="mailto:bkpoon@lbl.gov" target="_blank">bkpoon@lbl.gov</a>></span>:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Hi,<div><br></div><div>Since you are installing from source, the easiest way would be to edit the Python script that installs all the base dependencies. To do so,</div><div><br></div><div>1) Open install_base_packages.py located in phenix-installer-dev-2306-source/modules/cctbx_project/libtbx/auto_build</div><div>2) Add 'configure_args.append("--enable_unicode=ucs4")' after line 644. That section just adds our flags to the configure step for installing Python. After editing, your section should look like,</div><div><br></div><div>configure_args.append("--enable-shared")</div><div>configure_args.append("--enable-unicode=ucs4")</div><div>configure_args.append("LDFLAGS=-Wl,-rpath=\$$ORIGIN/../lib")</div><div><br></div><div>3) Just run the Phenix install program (./install --prefix=<installation directory>) like normal and Python will be compiled with your new flag.</div><div><br></div><div>Let me know if you have any issues. Thanks!</div></div><div class="gmail_extra"><span class=""><br clear="all"><div><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><div>--</div><div><span style="font-size:12.8px">Billy K. Poon</span><br></div></div><div>Research Scientist, Molecular Biophysics and Integrated Bioimaging</div><div>Lawrence Berkeley National Laboratory</div><div>1 Cyclotron Road, M/S 33R0345</div><div>Berkeley, CA 94720</div><div>Tel: (510) 486-5709</div><div>Fax: (510) 486-5909</div><div>Web: <a href="https://phenix-online.org" target="_blank">https://phenix-online.org</a></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br></span><div><div class="h5"><div class="gmail_quote">On Sun, Feb 14, 2016 at 5:55 PM, acyang <span dir="ltr"><<a href="mailto:acyang0903@gmail.com" target="_blank">acyang0903@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div><div><div><div><div>Hi Billy<br><br></div>Thanks for your reply.<br></div>I installed phenix from source (phenix-installer-dev-2306-source.tar.gz).<br></div>And I used scientific linux 7.1 for my workstation.<br></div>I noticed that SCONS is adopted in the installation of phenix, and phenix will download a modified version of python (python_2.7.8_cci).<br></div>I think the problem can be solved by <span style="font-family:arial,helvetica,sans-serif">adding a flag "--enable-unicode=ucs4" in configuring Python-2.7.8_cci.</span><br><pre><span style="font-family:arial,helvetica,sans-serif">I'd appreciate if you can tell me how to modify the SCONS script file.<br></span></pre><pre><span style="font-family:arial,helvetica,sans-serif">by A.C.<br></span></pre><div><div><code><span></span></code><div><div><div><div><div><div><div class="gmail_extra"><br><div class="gmail_quote">2016-02-12 16:52 GMT+08:00 Billy Poon <span dir="ltr"><<a href="mailto:bkpoon@lbl.gov" target="_blank">bkpoon@lbl.gov</a>></span>:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Hi,<div><br></div><div>Are you installing phenix from source or from a binary distribution? And which operating system are you using? I can give you the flags (in addition to the --prefix flag for installing into the base directory) for the configure step for either OS X or Linux.</div><div><br></div><div>You can basically install Phenix normally, and then recompile our Python from scratch with our regular flags and your extra flag.</div></div><div class="gmail_extra"><br clear="all"><div><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><div>--</div><div><span style="font-size:12.8px">Billy K. Poon</span><br></div></div><div>Research Scientist, Molecular Biophysics and Integrated Bioimaging</div><div>Lawrence Berkeley National Laboratory</div><div>1 Cyclotron Road, M/S 33R0345</div><div>Berkeley, CA 94720</div><div>Tel: <a href="tel:%28510%29%20486-5709" value="+15104865709" target="_blank">(510) 486-5709</a></div><div>Fax: <a href="tel:%28510%29%20486-5909" value="+15104865909" target="_blank">(510) 486-5909</a></div><div>Web: <a href="https://phenix-online.org" target="_blank">https://phenix-online.org</a></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote"><div><div>On Wed, Feb 3, 2016 at 3:05 AM, acyang <span dir="ltr"><<a href="mailto:acyang0903@gmail.com" target="_blank">acyang0903@gmail.com</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><div><div dir="ltr"><div><div><div><div><div><div>Hi everyone<br><br></div>I've installed pymol and phenix on my scientific linux7.1 workstation.<br></div>I can launch pymol via the launching script($PYMOL_HOME/pymol) normally.<br></div>But when I launched pymol in phenix GUI, I got some error as followed:<br>*********************************************************************************************************************************<br>Traceback (most recent call last):<br> File "/opt/PyMOL/modules/pymol/__init__.py", line 71, in <module><br> import pymol<br> File "/opt/PyMOL/modules/pymol/__init__.py", line 521, in <module><br> import pymol._cmd<br>ImportError: /opt/PyMOL/modules/pymol/_cmd.so: undefined symbol: PyUnicodeUCS4_SetDefaultEncoding<br>*********************************************************************************************************************************<br></div>After <span>STFW<i>, </i>I knew the problem is about </span><span> unicode variant (UCS2, UCS4).<br></span></div><span>I also checked the configuration of two python.<br></span></div><div><span>For /bin/python (adopted by pymol)<br></span><pre><code><span>>>></span><span> </span><span>import</span><span> sys
</span><span>>>></span><span> </span><span>print</span><span> sys</span><span>.</span><span>maxunicode
</span><span>1114111<br><br></span></code><span style="font-family:arial,helvetica,sans-serif">And for $PHENIX_HOME/base/bin/python (adopted by phenix)</span><br>>>> import sys<br>>>> print sys.maxunicode<br>65535<code><span><br><br></span></code></pre><pre><span style="font-family:arial,helvetica,sans-serif">My question is : How do I add the flag --enable-unicode=ucs4 in configuring Python-2.7.8_cci</span><code><span>.<br><br></span></code><span style="font-family:arial,helvetica,sans-serif"><br>I'd appreciate if any reply on this.<span><font color="#888888"><br></font></span></span></pre><span><font color="#888888"><pre><span style="font-family:arial,helvetica,sans-serif">acyang<br></span></pre></font></span></div><span></span><div><div><span> </span></div></div></div>
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