<div dir="ltr">This is still much too convoluted a procedure to be practical, of course. 狢 promise I&#39;ll get around to looking at Ubuntu 12 this week but the VM setup was fiasco and we&#39;re somewhat short-handed.<div>

<br></div><div>For what it&#39;s worth, your data ran fine on our systems, although it overfit somewhat - I still need to try running phenix.refine as well to see if it actually improved anything, but it&#39;s definitely an issue with the build on your specific system. 狢&#39;ll send the results separately.</div>

<div><br></div><div style>-Nat</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Nov 5, 2013 at 5:26 AM, Jan Gebauer <span dir="ltr">&lt;<a href="mailto:jan.gebauer@uni-koeln.de" target="_blank">jan.gebauer@uni-koeln.de</a>&gt;</span> wrote:<br>

<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
  
    
  
  <div text="#000000" bgcolor="#FFFFFF">
    Hi David, hi all,<br>
    <br>
    I now managed to at least get a test refinement working. What I
    mostly changed was the Ubuntu version.<br>
    I have no idea why, but I managed to get it to work on Ubuntu 10.04.<br>
    <br>
    In principle I installed 10.04 freshly in a virtualbox and from
    their it worked rather straight-forward.<br>
    <br>
    Here is how I proceeded in detail for those of you who are
    interested:<br>
    <br>
    1) Setting up a Virtualbox 4.3.2 r90405 on Ubuntu 12.04.3.<br>
    2) Installing the 64bit version of Ubuntu 10.04 in a virtualbox (4
    processors / 90% speed cap / 4GB Ram /VT-x enabled)<br>
    3) Install VBoxAdditions<br>
    4) Update ubuntu (<tt>sudo apt-get update</tt>)<br>
    5) Installing g++ and zlib library (<tt>sudo apt-get install g++
      zlib1g-dev</tt>)<br>
    6) Installing binary version of phenix-dev-1525 to
    /usr/local/science/phenix-dev-1525 (sudo ./install
    --prefix=/usr/local/science)<br>
    7) Unpack rosetta_2013_wk42_bundle to
    /usr/local/science/rosetta_2013_wk42_bundle<br>
    8) set rossetta variables by inserting them at the start of
    /usr/local/science/pheninx-dev-1525/phenix_env.sh (just in line
    3ff):<br>
    <tt>export
      PHENIX_ROSETTA_PATH=/usr/local/science/rosetta_2013wk42_bundle</tt><tt><br>
    </tt><tt>export
      ROSETTA3_DB=/usr/local/science/rosetta_2013wk42_bundle/main/database</tt><tt><br>
    </tt><tt>export
      PATH=$PATH:/usr/local/science/rosetta_2013wk42_bundle/main/source/bin</tt><br>
    9) assign ownership to active user (<tt>sudo chown gebauer:gebauer
      /usr/local/science/ -R</tt>)<br>
    10) Compile it (phenix.build_phenix_interface nproc=4)<br>
    It should run without problems<br>
    <br>
    Testing:<br>
    1) Create a new directory (mkdir test &amp;&amp; cd test)<br>
    2) Download testset (suggested by Nat: <tt>phenix.fetch_pdb --mtz
      1yjp</tt>)<br>
    3) Run rosetta_refine (phenix.rosetta_refine 1yjp.pdb 1yjp.mtz
    nproc=4)<br>
    In my case rFree dropped from 18.21 to 14.90. It&#39;s not a low
    resolution dataset, but it show that it general works and lowRes
    would potentially take to long for a mere testing<br>
    <br>
    My real data are still being processed so I have no idea how well it
    will works... only thing I found out already:<br>
    4.5 GB RAM for 4 processes calculating ~500Aa via rosetta seems not
    to be enough. I thereby reduced my &quot;real run&quot; to only one
    processor...<br>
    <br>
    Regards,<br>
    Jan<br>
    <br>
    <br>
    <br>
    <br>
    <br>
    <br>
    <br>
    <br>
    <br>
    <br>
    <br>
    <div>Am 01.11.2013 08:39, schrieb David
      Goldstone:<br>
    </div>
    <blockquote type="cite">
      
      <div>Hi Jan,�</div>
      <div><br>
      </div>
      <div>I followed the same procedure. The only differences being
        that I have installed it to my home directory to keep it
        separate from our standard install of phenix and rosetta and I
        run the phenix_env.sh separately from the exports. I had to
        remove our default init.sh script from my .bashrc (this is our
        setup script for all programs ccp4 etc) and now manually source
        a different version to ensure it points to the correct version
        of phenix.�</div>
      <div><br>
      </div>
      <div>I originally had trouble with the python shared libraries but
        Nat has fixed this by building them into the binary installer.</div>
      <div><br>
      </div>
      <div>Sorry I can&#39;t be more help�</div>
      <div><br>
      </div>
      <div>David</div>
      <div><br>
        <br>
        <div>----</div>
        <div><span style="background-color:rgba(255,255,255,0)">Dr
            David Goldstone<br>
            Senior Lecturer<br>
            University of Auckland<br>
            New Zealand<br>
            Ph�<a href="tel:+64%209%203737599;84607" target="_blank">+64 9 3737599 x84607</a></span></div>
      </div>
      <div><br>
        On 1/11/2013, at 8:30 PM, Jan Gebauer &lt;<a href="mailto:jan.gebauer@uni-koeln.de" target="_blank">jan.gebauer@uni-koeln.de</a>&gt;
        wrote:<br>
        <br>
      </div>
      <blockquote type="cite">
        <div><span>Dear David,</span><br>
          <span></span><br>
          <span>thanks for your remark. Indeed my paths are wrong in the
            mail; however, this is due to lazy typing... I do set the
            Rosetta_DB3 path corretly...</span><br>
          <span>I&#39;m still interested to know, how you managed to install
            build it. Have you done the same procedure as described by
            me? (only with different releases?)</span><br>
          <span>Or did you do something differently?</span><br>
          <span></span><br>
          <span>Regards,</span><br>
          <span>Jan</span><br>
          <span></span><br>
          <span>Am Donnerstag, 31. Oktober 2013 23:11:42 schrieb David
            Goldstone:</span><br>
          <blockquote type="cite"><span>Dear Jan,</span><br>
          </blockquote>
          <blockquote type="cite"><span></span><br>
          </blockquote>
          <blockquote type="cite"><span>I have recently installed phenix
              with rosetta refine on Ubuntu 10.04</span><br>
          </blockquote>
          <blockquote type="cite"><span>using phenix-dev-1515 and
              rosetta_wk40_bundle.</span><br>
          </blockquote>
          <blockquote type="cite"><span></span><br>
          </blockquote>
          <blockquote type="cite"><span>This install also appears to run
              on an Ubuntu 12 install.</span><br>
          </blockquote>
          <blockquote type="cite"><span></span><br>
          </blockquote>
          <blockquote type="cite"><span>I think you export commands are
              not correct mine are as follows</span><br>
          </blockquote>
          <blockquote type="cite"><span></span><br>
          </blockquote>
          <blockquote type="cite"><span>export</span><br>
          </blockquote>
          <blockquote type="cite"><span>PHENIX_ROSETTA_PATH=/mnt/home/dgol002/programs/rosetta_2013wk40_bundle</span><br>
          </blockquote>
          <blockquote type="cite"><span>export</span><br>
          </blockquote>
          <blockquote type="cite"><span>ROSETTA3_DB=/mnt/home/dgol002/programs/rosetta_2013wk40_bundle/main/database</span><br>
          </blockquote>
          <blockquote type="cite"><span>export</span><br>
          </blockquote>
          <blockquote type="cite"><span>PATH=$PATH:/mnt/home/dgol002/programs/rosetta_2013wk40_bundle/main/source/bin</span><br>
          </blockquote>
          <blockquote type="cite"><span></span><br>
          </blockquote>
          <blockquote type="cite"><span>ie you are exporting ROSETTA_BIN
              twice rather than ROSETTA3_DB.</span><br>
          </blockquote>
          <blockquote type="cite"><span></span><br>
          </blockquote>
          <blockquote type="cite"><span>Hope this helps</span><br>
          </blockquote>
          <blockquote type="cite"><span></span><br>
          </blockquote>
          <blockquote type="cite"><span>David</span><br>
          </blockquote><div><div class="h5">
          <blockquote type="cite"><span></span><br>
          </blockquote>
          <blockquote type="cite"><span></span><br>
          </blockquote>
          <blockquote type="cite"><span></span><br>
          </blockquote>
          <blockquote type="cite"><span>On 1/11/2013 4:48 a.m., Jan
              Gebauer wrote:</span><br>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span>Dear all,</span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span></span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span>I&#39;m trying to get
                rosetta_refine working on ubuntu 12.04 LTS.</span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span></span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span>This was the (latest) way I
                tried it:</span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span></span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span>1) Downloaded phenix-dev-1523
                binary &amp; installed it via installer in</span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span>/usr/local/science/phenix4rosetta/phenix-dev-1523</span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span>2) Downloaded rosetta 2031wk42
                and extracted it in</span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span>/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle</span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span>3) Inserted into phenix_env.sh</span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span>export</span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span>ROSETTA_BIN=/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/bin</span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span>export</span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span>PHENIX_ROSETTA_PATH=/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/</span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span>export</span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span>ROSETTA_BIN=/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/database</span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span>4) sources phenix_env.sh</span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span>5) build the interface via</span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span>rosetta.build_phenix_interface
                nproc=4</span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span>6) exceute the refinement via
                phenix.rosetta_refine phasermodel.pdb</span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span>data.mtz nproc=4</span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span></span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span>The programm runs fine, up to
                the point where it should generate</span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span>models via rosetta, it then
                stops and crashes.</span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span>I have attached some logfiles</span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span></span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span>Has anyone managed to run
                rosetta_refine on Ubuntu? Which phenix and</span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span>rosetta versions did you use?
                Ist there anything wrong on my above</span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span>mentioned build protocol?</span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span></span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span>I&#39;m thankful for any help.</span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span></span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span>Regards,</span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span>Jan Gebauer</span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span></span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span></span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span></span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span>--</span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span>Dr. Jan Gebauer</span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span>AG Prof. Baumann</span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span>Institut für Biochemie /
                Uni-Köln</span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span>Otto-Fischer-Str. 12-14 /
                50674 Köln</span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span>Fon: <a href="tel:%2B49%20%28221%29%20470%203212" value="+492214703212" target="_blank">+49 (221) 470 3212</a> � �</span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span>Fax: <a href="tel:%2B49%20%28221%29%20470%205066" value="+492214705066" target="_blank">+49 (221) 470 5066</a></span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span></span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span><a href="http://px.uni-koeln.de/" target="_blank">http://px.uni-koeln.de/</a></span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span></span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span></span><br>
            </blockquote>
          </blockquote>
          </div></div><div class="im"><blockquote type="cite">
            <blockquote type="cite"><span>_______________________________________________</span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span>phenixbb mailing list</span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span><a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a></span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite">
            <blockquote type="cite"><span><a href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a></span><br>
            </blockquote>
          </blockquote>
          <blockquote type="cite"><span></span><br>
          </blockquote>
          <blockquote type="cite"><span></span><br>
          </blockquote>
          </div><blockquote type="cite"><span>--</span><br>
          </blockquote>
          <blockquote type="cite"><span>Dr David Goldstone</span><br>
          </blockquote>
          <blockquote type="cite"><span>Senior Lecturer &amp; Rutherford
              Discovery Fellow</span><br>
          </blockquote>
          <blockquote type="cite"><span>Structural Biology</span><br>
          </blockquote>
          <blockquote type="cite"><span>University of Auckland</span><br>
          </blockquote>
          <blockquote type="cite"><span>New Zealand</span><br>
          </blockquote>
          <blockquote type="cite"><span>Ph <a href="tel:%2B64%209%203737599%20x84607" value="+6493737599" target="_blank">+64 9 3737599 x84607</a></span><br>
          </blockquote>
        </div>
      </blockquote>
    </blockquote><div class="im">
    <br>
    <pre cols="72">-- 
Dr. Jan Gebauer
AG Prof. Baumann
Institut für Biochemie / Uni-Köln
Otto-Fischer-Str. 12-14 / 50674 Köln
Fon: <a href="tel:%2B49%20%28221%29%20470%203212" value="+492214703212" target="_blank">+49 (221) 470 3212</a>        
Fax: <a href="tel:%2B49%20%28221%29%20470%205066" value="+492214705066" target="_blank">+49 (221) 470 5066</a>

<a href="http://px.uni-koeln.de/" target="_blank">http://px.uni-koeln.de/</a></pre>
  </div></div>

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<br></blockquote></div><br></div>