<div dir="ltr">It seems that you are running the tests in a directory to which you do not have write access. Is that correct?<div><br clear="all"><div><div dir="ltr" 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></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Aug 28, 2019 at 3:06 AM Almudena Ponce Salvatierra &lt;<a href="mailto:maps.farma@gmail.com">maps.farma@gmail.com</a>&gt; wrote:<br></div><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">Dear all,<div><br></div><div>yesterday I spent quite some time trying to install Rosetta, so that I can use all it&#39;s modules within Phenix. </div><div><br></div><div>However, when I am running the tests, rosetta stops and I get the following message (see below).</div><div><br></div><div>Any help would be much appreciated.</div><div><br></div><div>Thank you</div><div><br></div><div>Almudena</div><div><br></div><div>





<p class="gmail-m_-6013431002427323907gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span class="gmail-m_-6013431002427323907gmail-s1" style="font-variant-ligatures:no-common-ligatures">======================= ROSETTA/PHENIX X-ray refinement =======================</span></p>
<p class="gmail-m_-6013431002427323907gmail-p2" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);min-height:13px"><span class="gmail-m_-6013431002427323907gmail-s1" style="font-variant-ligatures:no-common-ligatures"></span><br></p>
<p class="gmail-m_-6013431002427323907gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span class="gmail-m_-6013431002427323907gmail-s1" style="font-variant-ligatures:no-common-ligatures">Traceback (most recent call last):</span></p>
<p class="gmail-m_-6013431002427323907gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span class="gmail-m_-6013431002427323907gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="gmail-m_-6013431002427323907gmail-Apple-converted-space">  </span>File &quot;/Applications/phenix-1.14-3260/build/../modules/phenix/phenix/command_line/rosetta_refine.py&quot;, line 307, in &lt;module&gt;</span></p>
<p class="gmail-m_-6013431002427323907gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span class="gmail-m_-6013431002427323907gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="gmail-m_-6013431002427323907gmail-Apple-converted-space">    </span>run(sys.argv[1:], create_dir=True)</span></p>
<p class="gmail-m_-6013431002427323907gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span class="gmail-m_-6013431002427323907gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="gmail-m_-6013431002427323907gmail-Apple-converted-space">  </span>File &quot;/Applications/phenix-1.14-3260/build/../modules/phenix/phenix/command_line/rosetta_refine.py&quot;, line 159, in run</span></p>
<p class="gmail-m_-6013431002427323907gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span class="gmail-m_-6013431002427323907gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="gmail-m_-6013431002427323907gmail-Apple-converted-space">    </span>default_directory_number=params.output.directory_number)</span></p>
<p class="gmail-m_-6013431002427323907gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span class="gmail-m_-6013431002427323907gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="gmail-m_-6013431002427323907gmail-Apple-converted-space">  </span>File &quot;/Applications/phenix-1.14-3260/modules/cctbx_project/libtbx/utils.py&quot;, line 1925, in create_run_directory</span></p>
<p class="gmail-m_-6013431002427323907gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span class="gmail-m_-6013431002427323907gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="gmail-m_-6013431002427323907gmail-Apple-converted-space">    </span>os.makedirs(dir_name)</span></p>
<p class="gmail-m_-6013431002427323907gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span class="gmail-m_-6013431002427323907gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="gmail-m_-6013431002427323907gmail-Apple-converted-space">  </span>File &quot;/Applications/phenix-1.14-3260/base/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/../../../../../../../Python.framework/Versions/2.7/lib/python2.7/os.py&quot;, line 157, in makedirs</span></p>
<p class="gmail-m_-6013431002427323907gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span class="gmail-m_-6013431002427323907gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="gmail-m_-6013431002427323907gmail-Apple-converted-space">    </span>mkdir(name, mode)</span></p>
<p class="gmail-m_-6013431002427323907gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span class="gmail-m_-6013431002427323907gmail-s1" style="font-variant-ligatures:no-common-ligatures">OSError: [Errno 13] Permission denied: &#39;rosetta_1&#39;</span></p>
<p class="gmail-m_-6013431002427323907gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span class="gmail-m_-6013431002427323907gmail-s1" style="font-variant-ligatures:no-common-ligatures">Almudenas-MacBook-Pro:bin almudenaponce$<span class="gmail-m_-6013431002427323907gmail-Apple-converted-space"> </span></span></p></div></div>
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