<div dir="ltr">Roger<div><br></div><div>The script is trying to change the mode of a file in <span style="font-family:monospace;font-size:small;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">/opt/phenix-1.13-2998/build but you don&#39;t have that access. Can you get access or get your sys admin to run the script?</span></div><div><font face="monospace"><br clear="all"></font><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">On Fri, Jul 27, 2018 at 2:07 PM Roger Shek &lt;<a href="mailto:roger.shek@stonybrook.edu">roger.shek@stonybrook.edu</a>&gt; wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">I am trying to build the amber interface to phenix, but encounter an error. Running OpenSUSE15. Anyone have any ideas?<div><br></div><div><span style="font-family:monospace"><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">phenix.build_amber_interface                   </span><br>
<br>  Phenix modules found : /opt/phenix-1.13-2998/modules/phenix
<br>
<br>  $AMBERHOME set : /home/roger/bin/Amber/amber18
<br>
<br>  Linking AMBERHOME to Phenix modules
<br>
<br>  Not linking $AMBERHOME into Phenix modules directory because there is
<br>  already a link and it points to the same directory as $AMBERHOME.
<br>    $AMBERHOME : /home/roger/bin/Amber/amber18
<br>    Phenix link: /opt/phenix-1.13-2998/modules/amber
<br>     <br>Building amber_adaptbx
<br>
<br>  ~&gt; libtbx.configure amber
<br>
<br>Python: 2.7.14 &quot;/opt/phenix-1.13-2998/base/bin/python2.7&quot;
<br>Compiler: default
<br>Build mode: release
<br>Warning level: 0
<br>Precompiled Headers: False
<br>Static libraries: False
<br>Static exe: False
<br>Scan Boost headers: False
<br>Write full flex_fwd.h files: False
<br>Build Boost.Python extensions: True
<br>Define BOOST_PYTHON_NO_PY_SIGNATURES: False
<br>Define BOOST_PYTHON_BOOL_INT_STRICT: True
<br>Enable OpenMP if possible: False
<br>Boost threads enabled: False
<br>Enable CUDA: False
<br>Use opt_resources if available: False
<br>Use environment flags: False
<br>Enable C++11: False
<br>Python3 migration warning policy: None
<br>command_version_suffix: 1.13-2998
<br>Relocatable paths anchored at: /opt/phenix-1.13-2998/build
<br>Top-down list of all modules involved:
<br>  prime              &quot;/opt/phenix-1.13-2998/modules/cctbx_project/prime&quot;
<br>  iota               &quot;/opt/phenix-1.13-2998/modules/cctbx_project/iota&quot;
<br>  xia2               &quot;/opt/phenix-1.13-2998/modules/xia2&quot;
<br>  xfel               &quot;/opt/phenix-1.13-2998/modules/cctbx_project/xfel&quot;
<br>  dials              &quot;/opt/phenix-1.13-2998/modules/dials&quot;
<br>  simtbx             &quot;/opt/phenix-1.13-2998/modules/cctbx_project/simtbx&quot;
<br>  cma_es             &quot;/opt/phenix-1.13-2998/modules/cctbx_project/cma_es&quot;
<br>  labelit            &quot;/opt/phenix-1.13-2998/modules/labelit&quot;
<br>  rstbx              &quot;/opt/phenix-1.13-2998/modules/cctbx_project/rstbx&quot;
<br>  spotfinder         &quot;/opt/phenix-1.13-2998/modules/cctbx_project/spotfinder&quot;
<br>  annlib+adaptbx     &quot;/opt/phenix-1.13-2998/modules/annlib&quot;
<br>                     &quot;/opt/phenix-1.13-2998/modules/annlib_adaptbx&quot;
<br>  phenix             &quot;/opt/phenix-1.13-2998/modules/phenix&quot;
<br>  reel               &quot;/opt/phenix-1.13-2998/modules/reel&quot;
<br>  wxtbx              &quot;/opt/phenix-1.13-2998/modules/cctbx_project/wxtbx&quot;
<br>  phaser_regression  &quot;/opt/phenix-1.13-2998/modules/phaser_regression&quot;
<br>  phaser             &quot;/opt/phenix-1.13-2998/modules/phaser&quot;
<br>  tntbx              &quot;/opt/phenix-1.13-2998/modules/tntbx&quot;
<br>  solve_resolve      &quot;/opt/phenix-1.13-2998/modules/solve_resolve&quot;
<br>  muscle             &quot;/opt/phenix-1.13-2998/modules/muscle&quot;
<br>  ksdssp             &quot;/opt/phenix-1.13-2998/modules/ksdssp&quot;
<br>  pulchra            &quot;/opt/phenix-1.13-2998/modules/pulchra&quot;
<br>  phenix_html        &quot;/opt/phenix-1.13-2998/modules/phenix_html&quot;
<br>  phenix_regression  &quot;/opt/phenix-1.13-2998/modules/phenix_regression&quot;
<br>  elbow              &quot;/opt/phenix-1.13-2998/modules/elbow&quot;
<br>  Plex               &quot;/opt/phenix-1.13-2998/modules/Plex&quot;
<br>  PyQuante           &quot;/opt/phenix-1.13-2998/modules/PyQuante&quot;
<br>  crys3d             &quot;/opt/phenix-1.13-2998/modules/cctbx_project/crys3d&quot;
<br>  gltbx              &quot;/opt/phenix-1.13-2998/modules/cctbx_project/gltbx&quot;
<br>  amber+adaptbx      &quot;/opt/phenix-1.13-2998/modules/amber&quot;
<br>                     &quot;/opt/phenix-1.13-2998/modules/amber_adaptbx&quot;
<br>  mmtbx              &quot;/opt/phenix-1.13-2998/modules/cctbx_project/mmtbx&quot;
<br>  suitename          &quot;/opt/phenix-1.13-2998/modules/suitename&quot;
<br>  king               &quot;/opt/phenix-1.13-2998/modules/king&quot;
<br>  probe              &quot;/opt/phenix-1.13-2998/modules/probe&quot;
<br>  reduce             &quot;/opt/phenix-1.13-2998/modules/reduce&quot;
<br>  iotbx              &quot;/opt/phenix-1.13-2998/modules/cctbx_project/iotbx&quot;
<br>  ccp4io+adaptbx     &quot;/opt/phenix-1.13-2998/modules/ccp4io&quot;
<br>                     &quot;/opt/phenix-1.13-2998/modules/ccp4io_adaptbx&quot;
<br>  dxtbx              &quot;/opt/phenix-1.13-2998/modules/cctbx_project/dxtbx&quot;
<br>  cbflib+adaptbx     &quot;/opt/phenix-1.13-2998/modules/cbflib&quot;
<br>                     &quot;/opt/phenix-1.13-2998/modules/cctbx_project/cbflib_adaptbx&quot;
<br>  smtbx              &quot;/opt/phenix-1.13-2998/modules/cctbx_project/smtbx&quot;
<br>  ucif               &quot;/opt/phenix-1.13-2998/modules/cctbx_project/ucif&quot;
<br>  cctbx              &quot;/opt/phenix-1.13-2998/modules/cctbx_project/cctbx&quot;
<br>  scitbx             &quot;/opt/phenix-1.13-2998/modules/cctbx_project/scitbx&quot;
<br>  fable              &quot;/opt/phenix-1.13-2998/modules/cctbx_project/fable&quot;
<br>  omptbx             &quot;/opt/phenix-1.13-2998/modules/cctbx_project/omptbx&quot;
<br>  boost+adaptbx      &quot;/opt/phenix-1.13-2998/modules/boost&quot;
<br>                     &quot;/opt/phenix-1.13-2998/modules/cctbx_project/boost_adaptbx&quot;
<br>  tbxx               &quot;/opt/phenix-1.13-2998/modules/cctbx_project/tbxx&quot;
<br>  chiltbx            &quot;/opt/phenix-1.13-2998/modules/cctbx_project/chiltbx&quot;
<br>  libtbx             &quot;/opt/phenix-1.13-2998/modules/cctbx_project/libtbx&quot;
<br>Processing: &quot;/opt/phenix-1.13-2998/build/dispatcher_include_amber.sh&quot;
<br>Processing: &quot;/opt/phenix-1.13-2998/build/dispatcher_include_phenix.sh&quot;
<br>Creating files in build directory: &quot;/opt/phenix-1.13-2998/build&quot;
<br>    dispatcher_include_template.sh
<br>    dispatcher_head.sh
<br>Traceback (most recent call last):
<br>  File &quot;/opt/phenix-1.13-2998/modules/cctbx_project/libtbx/env_config.py&quot;, line 2462, in &lt;module&gt;
<br>    warm_start(sys.argv)
<br>  File &quot;/opt/phenix-1.13-2998/modules/cctbx_project/libtbx/env_config.py&quot;, line 2456, in warm_start
<br>    env.refresh()
<br>  File &quot;/opt/phenix-1.13-2998/modules/cctbx_project/libtbx/env_config.py&quot;, line 1615, in refresh
<br>    self.write_lib_dispatcher_head()
<br>  File &quot;/opt/phenix-1.13-2998/modules/cctbx_project/libtbx/env_config.py&quot;, line 1248, in write_lib_disp<br>atcher_head
<br>    target_file=self.under_build(target_file, return_relocatable_path=True))
<br>  File &quot;/opt/phenix-1.13-2998/modules/cctbx_project/libtbx/env_config.py&quot;, line 1146, in write_bin_sh_d<br>ispatcher
<br>    target_file.chmod(0755)
<br>  File &quot;/opt/phenix-1.13-2998/modules/cctbx_project/libtbx/path.py&quot;, line 279, in chmod
<br>    return os.chmod(abs(self), *args, **kwds)
<br>OSError: [Errno 1] Operation not permitted: &#39;/opt/phenix-1.13-2998/build/dispatcher_head.sh&#39;<br>
<br></span><br clear="all"><div><br></div>-- <br><div dir="ltr" class="m_7489999867928905873gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><span style="font-size:13px">Roger Shek</span><div style="font-size:13px"><br></div><div style="font-size:13px">Stony Brook University</div><div style="font-size:13px">Graduate Student in Biochemistry and Structural Biology (PhD)</div><div style="font-size:13px"><a href="http://sbinststrbio.com/" style="color:rgb(17,85,204);font-size:12.8px" target="_blank">Stony Brook Integrative Structural Biology Organization</a><br></div><div style="font-size:13px">Cell: (808) 386-3879<br></div><div style="font-size:13px">Website: <a href="https://www.rogershek.com" target="_blank">https://www.rogershek.com</a><br></div></div></div></div></div></div></div></div></div></div></div>
_______________________________________________<br>
phenixbb mailing list<br>
<a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
<a href="http://phenix-online.org/mailman/listinfo/phenixbb" rel="noreferrer" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org" target="_blank">phenixbb-leave@phenix-online.org</a></blockquote></div>