<div dir="ltr">Hi Johan,<div><br></div><div>You should probably just download the latest Phenix source, either from our repositories or a nightly build, and compile a new copy. That should provide you with all the modules and dependencies.</div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><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:12.8000001907349px">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><div class="gmail_quote">On Wed, May 3, 2017 at 12:55 PM, Hattne, Johan <span dir="ltr"><<a href="mailto:hattnej@janelia.hhmi.org" target="_blank">hattnej@janelia.hhmi.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Not really installing. It’s an installation from 2011 that has been moved across the US and kept up-to-date (of sorts) by svn update and more recently git pull.<br>
<span class="HOEnZb"><font color="#888888"><br>
// J<br>
</font></span><div class="HOEnZb"><div class="h5"><br>
> On May 3, 2017, at 15:47, Billy Poon <<a href="mailto:bkpoon@lbl.gov">bkpoon@lbl.gov</a>> wrote:<br>
><br>
> Hi Johan,<br>
><br>
> How are you installing Phenix? The phenix builder for bootstrap.py (PhenixBuilder class) automatically includes probe and reduce.<br>
><br>
> --<br>
> Billy K. Poon<br>
> Research Scientist, Molecular Biophysics and Integrated Bioimaging<br>
> Lawrence Berkeley National Laboratory<br>
> 1 Cyclotron Road, M/S 33R0345<br>
> Berkeley, CA 94720<br>
> Tel: <a href="tel:%28510%29%20486-5709" value="+15104865709">(510) 486-5709</a><br>
> Fax: <a href="tel:%28510%29%20486-5909" value="+15104865909">(510) 486-5909</a><br>
> Web: <a href="https://phenix-online.org" rel="noreferrer" target="_blank">https://phenix-online.org</a><br>
><br>
> On Wed, May 3, 2017 at 12:21 PM, Hattne, Johan <<a href="mailto:hattnej@janelia.hhmi.org">hattnej@janelia.hhmi.org</a>> wrote:<br>
><br>
> > On May 3, 2017, at 11:40, Hattne, Johan <<a href="mailto:hattnej@janelia.hhmi.org">hattnej@janelia.hhmi.org</a>> wrote:<br>
> ><br>
> > Dear all;<br>
> ><br>
> > I appear to be missing probe in my source build. On running phenix.model_vs_data I get the traceback posted below. The error message appears to be a tad misleading, because having probe in PATH is not enough: the actual test in the code is<br>
> ><br>
> > if (not libtbx.env.has_module(name="<wbr>probe")):<br>
> ><br>
> > which leads me to believe that I’m supposed to have something probe-like in my source tree, but the duke-server I used to get these kinds of things from (quidditch?) seems unresponsive from here. This is the first time in weeks that I’m doing this, so it is very much likely that whatever happened to break my setup happened quite some time ago.<br>
> ><br>
> > Cluebat, anyone?<br>
> ><br>
> > // Cheers; Johan<br>
> ><br>
> > Traceback (most recent call last):<br>
> > File "/mnt/gonen/home/hattnej/<wbr>projects/phenix-build/../<wbr>phenix-src/phenix/phenix/<wbr>command_line/model_vs_data.py"<wbr>, line 6, in <module><br>
> > show_geometry_statistics = True)<br>
> > File "/mnt/gonen/home/hattnej/<wbr>projects/phenix-src/cctbx_<wbr>project/mmtbx/model_vs_data.<wbr>py", line 710, in run<br>
> > atom_selections = atom_selections)<br>
> > File "/mnt/gonen/home/hattnej/<wbr>projects/phenix-src/cctbx_<wbr>project/mmtbx/model_vs_data.<wbr>py", line 346, in show_geometry<br>
> > restraints_manager = restraints_manager)<br>
> > File "/mnt/gonen/home/hattnej/<wbr>projects/phenix-src/cctbx_<wbr>project/mmtbx/model_<wbr>statistics.py", line 138, in __init__<br>
> > molprobity_scores=molprobity_<wbr>scores)<br>
> > File "/mnt/gonen/home/hattnej/<wbr>projects/phenix-src/cctbx_<wbr>project/mmtbx/model_<wbr>statistics.py", line 51, in __init__<br>
> > self.clashscore = clashscore(pdb_hierarchy=pdb_<wbr>hierarchy).get_clashscore()<br>
> > File "/mnt/gonen/home/hattnej/<wbr>projects/phenix-src/cctbx_<wbr>project/mmtbx/validation/<wbr>clashscore.py", line 90, in __init__<br>
> > "<a href="http://kinemage.biochem.duke.edu/" rel="noreferrer" target="_blank">http://kinemage.biochem.duke.<wbr>edu/</a>")<br>
> > RuntimeError: Probe could not be detected on your system. Please make sure Probe is in your path.<br>
> > Probe is available at <a href="http://kinemage.biochem.duke.edu/" rel="noreferrer" target="_blank">http://kinemage.biochem.duke.<wbr>edu/</a><br>
><br>
> For the benefit of anybody else running into this: probe is at <a href="https://github.com/rlabduke/probe.git" rel="noreferrer" target="_blank">https://github.com/rlabduke/<wbr>probe.git</a>, reduce at <a href="https://github.com/rlabduke/reduce.git" rel="noreferrer" target="_blank">https://github.com/rlabduke/<wbr>reduce.git</a>.<br>
><br>
> // Johan<br>
><br>
><br>
> Research Specialist @ Gonen Lab<br>
> ______________________________<wbr>______________________<br>
> Janelia Research Campus * 19700 Helix Drive<br>
> Ashburn, VA 20147 * <a href="tel:%2B1%20%28571%29%20209-4000%20extension%203376" value="+15712094000">+1 (571) 209-4000 extension 3376</a><br>
><br>
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<br>
Research Specialist @ Gonen Lab<br>
______________________________<wbr>______________________<br>
Janelia Research Campus * 19700 Helix Drive<br>
Ashburn, VA 20147 * <a href="tel:%2B1%20%28571%29%20209-4000%20extension%203376" value="+15712094000">+1 (571) 209-4000 extension 3376</a><br>
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</div></div></blockquote></div><br></div>