<div dir="ltr">Have you sourced the setpaths.[c]sh file. Are you able to run any phenix programs?</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 dir="ltr">Cheers<div><br></div><div>Nigel<div><br></div><div>---</div><div>Nigel W. Moriarty<br>Building 33R0349, Molecular Biophysics and Integrated Bioimaging</div><div>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : 510-486-5709 Email : NWMoriarty@LBL.gov<br>Fax : 510-486-5909 Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Tue, Nov 29, 2016 at 12:47 PM, NISHANT SINGH <span dir="ltr"><<a href="mailto:nishantksingh11@gmail.com" target="_blank">nishantksingh11@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Everyone,<div><br></div><div>I am trying to run Phenix's rosetta refine. I seem to have downloaded and compiled the rosetta package fine, as I got the following statement after compiling was done:</div><div>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">scons: done building targets.</span></p></div><div> but I am failing at running: <span style="color:rgb(0,0,0)">rosetta.build_phenix_<wbr>interface.</span></div><div><span style="color:rgb(0,0,0)">It says that command not found. I am attaching my env page with this email. </span></div><div><span style="color:rgb(0,0,0)"><br></span></div><div>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">bmbs-imac:rosetta_bin_mac_<wbr>2016.32.58837_bundle Kumar$ env</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">ROSETTA3_DB=/Applications/<wbr>rosetta_bin_mac_2016.32.58837_<wbr>bundle/PHENIX_ROSETTA_PATH//<wbr>main/database</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">TERM_PROGRAM=Apple_Terminal</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">SHELL=/bin/bash</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">TERM=xterm-256color</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">TMPDIR=/var/folders/cb/<wbr>5v492std3d31jr42j7h3jm9h0000gp<wbr>/T/</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">Apple_PubSub_Socket_Render=/<wbr>private/tmp/com.apple.launchd.<wbr>KEC4L2Cjos/Render</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">TERM_PROGRAM_VERSION=387</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">OLDPWD=/Applications</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">TERM_SESSION_ID=A82EA51D-0920-<wbr>4F3B-BE03-92AE0C40A44B</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">USER=Kumar</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">SSH_AUTH_SOCK=/private/tmp/<wbr>com.apple.launchd.tMihawGOC7/<wbr>Listeners</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">__CF_USER_TEXT_ENCODING=0x1F6:<wbr>0x0:0x0</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">ROSETTA_BIN=/Applications/<wbr>rosetta_bin_mac_2016.32.58837_<wbr>bundle/PHENIX_ROSETTA_PATH//<wbr>main/source/bin</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">PATH=/Library/Frameworks/<wbr>Python.framework/Versions/3.5/<wbr>bin:/Library/Frameworks/<wbr>Python.framework/Versions/3.5/<wbr>bin:/Users/Kumar/miniconda2/<wbr>bin:/usr/local/bin:/usr/bin:/<wbr>bin:/usr/sbin:/sbin:/opt/X11/<wbr>bin</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">PWD=/Applications/rosetta_bin_<wbr>mac_2016.32.58837_bundle</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">LANG=en_US.UTF-8</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">XPC_FLAGS=0x0</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">XPC_SERVICE_NAME=0</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">SHLVL=1</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">HOME=/Users/Kumar</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">LOGNAME=Kumar</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">DISPLAY=/private/tmp/com.<wbr>apple.launchd.BhETYwyInl/org.<wbr>macosforge.xquartz:0</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">PHENIX_ROSETTA_PATH=/<wbr>Applications/rosetta_bin_mac_<wbr>2016.32.58837_bundle/PHENIX_<wbr>ROSETTA_PATH/</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">_=/usr/bin/env</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">bmbs-imac:rosetta_bin_mac_<wbr>2016.32.58837_bundle Kumar$ env</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">ROSETTA3_DB=/Applications/<wbr>rosetta_bin_mac_2016.32.58837_<wbr>bundle/PHENIX_ROSETTA_PATH//<wbr>main/database</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">TERM_PROGRAM=Apple_Terminal</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">SHELL=/bin/bash</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">TERM=xterm-256color</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">TMPDIR=/var/folders/cb/<wbr>5v492std3d31jr42j7h3jm9h0000gp<wbr>/T/</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">Apple_PubSub_Socket_Render=/<wbr>private/tmp/com.apple.launchd.<wbr>KEC4L2Cjos/Render</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">TERM_PROGRAM_VERSION=387</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">OLDPWD=/Applications</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">TERM_SESSION_ID=A82EA51D-0920-<wbr>4F3B-BE03-92AE0C40A44B</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">USER=Kumar</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">SSH_AUTH_SOCK=/private/tmp/<wbr>com.apple.launchd.tMihawGOC7/<wbr>Listeners</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">__CF_USER_TEXT_ENCODING=0x1F6:<wbr>0x0:0x0</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">ROSETTA_BIN=/Applications/<wbr>rosetta_bin_mac_2016.32.58837_<wbr>bundle/PHENIX_ROSETTA_PATH//<wbr>main/source/bin</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">PATH=/Library/Frameworks/<wbr>Python.framework/Versions/3.5/<wbr>bin:/Library/Frameworks/<wbr>Python.framework/Versions/3.5/<wbr>bin:/Users/Kumar/miniconda2/<wbr>bin:/usr/local/bin:/usr/bin:/<wbr>bin:/usr/sbin:/sbin:/opt/X11/<wbr>bin</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">PWD=/Applications/rosetta_bin_<wbr>mac_2016.32.58837_bundle</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">LANG=en_US.UTF-8</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">XPC_FLAGS=0x0</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">XPC_SERVICE_NAME=0</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">SHLVL=1</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">HOME=/Users/Kumar</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">LOGNAME=Kumar</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">DISPLAY=/private/tmp/com.<wbr>apple.launchd.BhETYwyInl/org.<wbr>macosforge.xquartz:0</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">PHENIX_ROSETTA_PATH=/<wbr>Applications/rosetta_bin_mac_<wbr>2016.32.58837_bundle/PHENIX_<wbr>ROSETTA_PATH/</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">_=/usr/bin/env</span></p>
<p class="m_-6258542080482777361gmail-p1"><span class="m_-6258542080482777361gmail-s1">bmbs-imac:rosetta_bin_mac_<wbr>2016.32.58837_bundle Kumar$ </span></p></div></div>
<br>______________________________<wbr>_________________<br>
phenixbb mailing list<br>
<a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
<a href="http://phenix-online.org/mailman/listinfo/phenixbb" rel="noreferrer" target="_blank">http://phenix-online.org/<wbr>mailman/listinfo/phenixbb</a><br>
Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org">phenixbb-leave@phenix-online.<wbr>org</a><br></blockquote></div><br></div>