<div dir="ltr">Hi Aaron,<div><br></div><div>Are you running rosetta.build_phenix_interface in a shell with administrative privileges (i.e. &quot;sudo -i&quot;)? Because Phenix is in /Applications and Rosetta is in /usr/local, the command needs administrative privileges to write in those directories.</div><div><br></div><div>Also, I am current testing newer versions of Rosetta since Rosetta 3.9 seems to have some problems on macOS. I&#39;ll update this thread and the documentation once we&#39;ve settled on a version.</div><div><br clear="all"><div><div dir="ltr" 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></div><br><div class="gmail_quote"><div dir="ltr">On Tue, Aug 21, 2018 at 1:45 AM Aaron Oakley &lt;<a href="mailto:aarono@uow.edu.au">aarono@uow.edu.au</a>&gt; wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">



<div style="word-wrap:break-word;line-break:after-white-space">
<div>I have repeatedly tried to install Rosetta for use in Phenix with zero success.</div>
<div><br>
</div>
<div>System:<span class="m_-7128300433066647046Apple-tab-span" style="white-space:pre-wrap"> </span>
macOS 10.13.6</div>
<div>Phenix version:<span class="m_-7128300433066647046Apple-tab-span" style="white-space:pre-wrap">
</span>phenix-1.14rc1-3177</div>
<div>Rosetta version:<span class="m_-7128300433066647046Apple-tab-span" style="white-space:pre-wrap">
</span>3.9 (rosetta_src_2018.09.60072_bundle)</div>
<div><br>
</div>
<div>Relevant environmental variables:</div>
<div><br>
</div>
<div><font face="Menlo"><b>ROSETTA3_DB=/usr/local/rosetta_src_2018.09.60072_bundle/main/database<br>
ROSETTA_TOOLS=/usr/local/rosetta_src_2018.09.60072_bundle/tools<br>
ROSETTA3=/usr/local/rosetta_src_2018.09.60072_bundle/main/source<br>
PHENIX=/Applications/phenix-1.14rc1-3177<br>
PHENIX_VERSION=1.14rc1-3177<br>
PHENIX_ROSETTA_PATH=/usr/local/rosetta_src_2018.09.60072_bundle</b><br>
</font><br>
<pre class="m_-7128300433066647046literal-block"><b>rosetta.build_phenix_interface</b> <font face="Helvetica">—seemed</font><span style="font-family:Helvetica">—</span><font face="Helvetica"> to work OK.</font></pre>
<pre class="m_-7128300433066647046literal-block"><font face="Helvetica">However...</font></pre>
<b style="font-family:Menlo">rosetta.run_tests</b> fails with</div>
<div><font face="Menlo"><br>
</font></div>
<div><font face="Menlo">DEBUG dumping error message<br>
ERROR: Rosetta exited with status 1<br>
stderr output:<br>
BACKTRACE:<br>
0   libcore.3.dylib                     0x0000000114b0e4e6 print_backtrace(char const*) + 54<br>
</font><br>
</div>
<div>…40 lines of traceback crap…</div>
<div><br>
</div>
<div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures">Traceback (most recent call last):</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures">  File &quot;/Applications/phenix-1.14rc1-3177/build/../modules/phenix/phenix/command_line/rosetta_refine.py&quot;, line 307, in &lt;module&gt;</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures">    run(sys.argv[1:], create_dir=True)</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures">  File &quot;/Applications/phenix-1.14rc1-3177/build/../modules/phenix/phenix/command_line/rosetta_refine.py&quot;, line 191, in run</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures">    debug=params.output.debug)</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures">  File &quot;/Applications/phenix-1.14rc1-3177/modules/phenix/phenix/rosetta/refine.py&quot;, line 313, in __init__</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures">    self.run_jobs()</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures">  File &quot;/Applications/phenix-1.14rc1-3177/modules/phenix/phenix/rosetta/refine.py&quot;, line 388, in run_jobs</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures">    check_result(result)</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures">  File &quot;/Applications/phenix-1.14rc1-3177/modules/phenix/phenix/rosetta/refine.py&quot;, line 379, in check_result</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures">    raise RuntimeError(&quot;Aborted due to error in job %d.&quot; % result.job_id)</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures">RuntimeError: Aborted due to error in job 1.</span></div>
</div>
<div><span style="font-variant-ligatures:no-common-ligatures"><br>
</span></div>
<div><br>
Any ideas?<br>
<div><br class="m_-7128300433066647046webkit-block-placeholder">
</div>
<div>Aaron Oakley<br>
</div>
</div>
</div>

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