<div dir="ltr">Sorry guy, I was on holidays and the maintenance was a problem.<div><br></div><div>Try putting the bootstrap.py in the directory that the command is being run.</div><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 Fri, Aug 16, 2019 at 7:27 PM Christopher Williams <<a href="mailto:christopher.sci.williams@gmail.com">christopher.sci.williams@gmail.com</a>> 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"><div>Hmm. Nigel, I may need some of your expertise here. It looks like there's a consistent problem with svn checkouts.</div><div><br></div><div>"git clone" operations seem to have been successful, so it probably isn't a matter of GitHub being down. Especially since the svn checkout of geostd from Sourceforge also failed.</div><div><br></div><div>Do you know if your system has problems with svn? Our svn checkouts generally take this form: "
<span style="font-family:monospace">svn co <a href="https://github.com/rlabduke/MolProbity.git/trunk" target="_blank">https://github.com/rlabduke/MolProbity.git/trunk</a> molprobity --non-interactive --trust-server-cert</span>
" Is there perhaps a security issue with the --trust-server-cert flag?</div><div><br></div><div>I believe that the cci machines at Berkeley are under maintenance until Sunday, so there are other reasons the script won't work until then.</div><div><br></div><div>Good luck,</div><div>-Christopher Williams</div><div>---Richardson Lab, Duke University<br></div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Aug 16, 2019 at 5:45 PM Charitha Belluru Shetty <<a href="mailto:charitha-belluru.b.shetty@gsk.com" target="_blank">charitha-belluru.b.shetty@gsk.com</a>> 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 lang="EN-US">
<div class="gmail-m_-2921843659350152032gmail-m_-1134883651628135094WordSection1">
<p class="MsoNormal">Hi Christopher,<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">I ran the installer script twice and this is what I got…<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><b><span style="background:none 0% 0% repeat scroll aqua">When I ran it first time, only the modules directory was created</span></b><b><u></u><u></u></b></p>
<p class="MsoNormal">bash-4.2$ <b><span style="background:none 0% 0% repeat scroll lime">. install_via_bootstrap.sh 10</span></b><u></u><u></u></p>
<p class="MsoNormal">++++++++++ creating build directories ...<u></u><u></u></p>
<p class="MsoNormal">svn: E000110: Unable to connect to a repository at URL 'svn://<a href="http://svn.code.sf.net/p/geostd/code/trunk" target="_blank">svn.code.sf.net/p/geostd/code/trunk</a>'<u></u><u></u></p>
<p class="MsoNormal">svn: E000110: Can't read from connection: Connection timed out<u></u><u></u></p>
<p class="MsoNormal">svn: E175002: Unable to connect to a repository at URL '<a href="https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_rotamer_pct_contour_grids" target="_blank">https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_rotamer_pct_contour_grids</a>'<u></u><u></u></p>
<p class="MsoNormal">svn: E175002: OPTIONS of '<a href="https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_rotamer_pct_contour_grids" target="_blank">https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_rotamer_pct_contour_grids</a>': SSL handshake failed: SSL socket read failed (<a href="https://github.com" target="_blank">https://github.com</a>)<u></u><u></u></p>
<p class="MsoNormal">svn: E175002: Unable to connect to a repository at URL '<a href="https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_ramachandran_pct_contour_grids" target="_blank">https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_ramachandran_pct_contour_grids</a>'<u></u><u></u></p>
<p class="MsoNormal">svn: E175002: OPTIONS of '<a href="https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_ramachandran_pct_contour_grids" target="_blank">https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_ramachandran_pct_contour_grids</a>': SSL handshake failed: SSL socket read failed (<a href="https://github.com" target="_blank">https://github.com</a>)<u></u><u></u></p>
<p class="MsoNormal">svn: E175002: Unable to connect to a repository at URL '<a href="https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_cablam_pct_contour_grids" target="_blank">https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_cablam_pct_contour_grids</a>'<u></u><u></u></p>
<p class="MsoNormal">svn: E175002: OPTIONS of '<a href="https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_cablam_pct_contour_grids" target="_blank">https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_cablam_pct_contour_grids</a>': SSL handshake failed: SSL socket read failed (<a href="https://github.com" target="_blank">https://github.com</a>)<u></u><u></u></p>
<p class="MsoNormal">svn: E175002: Unable to connect to a repository at URL '<a href="https://github.com/cctbx/cctbx_project.git/trunk/libtbx/auto_build/bootstrap.py" target="_blank">https://github.com/cctbx/cctbx_project.git/trunk/libtbx/auto_build/bootstrap.py</a>'<u></u><u></u></p>
<p class="MsoNormal">svn: E175002: OPTIONS of '<a href="https://github.com/cctbx/cctbx_project.git/trunk/libtbx/auto_build/bootstrap.py" target="_blank">https://github.com/cctbx/cctbx_project.git/trunk/libtbx/auto_build/bootstrap.py</a>': SSL handshake failed: SSL socket read failed (<a href="https://github.com" target="_blank">https://github.com</a>)<u></u><u></u></p>
<p class="MsoNormal">python: can't open file 'bootstrap.py': [Errno 2] No such file or directory<u></u><u></u></p>
<p class="MsoNormal">-bash: build/setpaths.sh: No such file or directory<u></u><u></u></p>
<p class="MsoNormal">python: can't open file 'modules/chem_data/cablam_data/rebuild_cablam_cache.py': [Errno 2] No such file or directory<u></u><u></u></p>
<p class="MsoNormal">++++++++++ MolProbity configure.sh finished.<u></u><u></u></p>
<p class="MsoNormal">++++++++++ Run molprobity/setup.sh to complete installation.<u></u><u></u></p>
<p class="MsoNormal">-bash-4.2$ <u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">-bash-4.2$ pwd<u></u><u></u></p>
<p class="MsoNormal">/hpc/apps/current/molprobity/v4.4.app<u></u><u></u></p>
<p class="MsoNormal">-bash-4.2$ ls -l<u></u><u></u></p>
<p class="MsoNormal">total 31<u></u><u></u></p>
<p class="MsoNormal"><b><span style="background:none 0% 0% repeat scroll yellow">-rw-r--r-- 1 cbs72396 appmgmt 1817 Aug 14 14:03 install_via_bootstrap.sh<u></u><u></u></span></b></p>
<p class="MsoNormal"><b><span style="background:none 0% 0% repeat scroll yellow">drwxr-sr-x 3 cbs72396 appmgmt 3 Aug 15 17:58 modules</span></b><b><u></u><u></u></b></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><b><span style="background:none 0% 0% repeat scroll aqua">Second time when I ran..bootstap.py and bootstrap.pyc was crated and the modules directory…</span></b><b><u></u><u></u></b></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">-bash-4.2$ <b><span style="background:none 0% 0% repeat scroll lime">. install_via_bootstrap.sh 4</span><u></u><u></u></b></p>
<p class="MsoNormal">++++++++++ creating build directories ...<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">svn: E000110: Unable to connect to a repository at URL 'svn://<a href="http://svn.code.sf.net/p/geostd/code/trunk" target="_blank">svn.code.sf.net/p/geostd/code/trunk</a>'<u></u><u></u></p>
<p class="MsoNormal">svn: E000110: Can't read from connection: Connection timed out<u></u><u></u></p>
<p class="MsoNormal">Performing actions: hot update base build<u></u><u></u></p>
<p class="MsoNormal">Installing base packages using:<u></u><u></u></p>
<p class="MsoNormal"> python modules/cctbx_project/libtbx/auto_build/install_conda.py --builder=molprobity --install_conda<u></u><u></u></p>
<p class="MsoNormal">===== Downloading <a href="http://cci.lbl.gov/repositories/annlib.gz" target="_blank">http://cci.lbl.gov/repositories/annlib.gz</a>: 0.5 MB<u></u><u></u></p>
<p class="MsoNormal"> [0%.........20%.........40%.........60%.........80%.........100%]<u></u><u></u></p>
<p class="MsoNormal">===== Running in modules: extracting files from annlib.gz<u></u><u></u></p>
<p class="MsoNormal">===== Downloading <a href="http://cci.lbl.gov/repositories/scons.gz" target="_blank">http://cci.lbl.gov/repositories/scons.gz</a>: 0.6 MB<u></u><u></u></p>
<p class="MsoNormal"> [0%.........20%.........40%.........60%.........80%.........100%]<u></u><u></u></p>
<p class="MsoNormal">===== Running in modules: extracting files from scons.gz<u></u><u></u></p>
<p class="MsoNormal">===== Downloading <a href="http://cci.lbl.gov/repositories/ccp4io.gz" target="_blank">http://cci.lbl.gov/repositories/ccp4io.gz</a>: 1.4 MB<u></u><u></u></p>
<p class="MsoNormal"> [0%.........20%.........40%.........60%.........80%.........100%]<u></u><u></u></p>
<p class="MsoNormal">===== Running in modules: extracting files from ccp4io.gz<u></u><u></u></p>
<p class="MsoNormal">===== Running in modules: git clone --recursive <a href="https://github.com/cctbx/boost.git" target="_blank">https://github.com/cctbx/boost.git</a> boost --progress --verbose<u></u><u></u></p>
<p class="MsoNormal">Cloning into 'boost'...<u></u><u></u></p>
<p class="MsoNormal">POST git-upload-pack (942 bytes)<u></u><u></u></p>
<p class="MsoNormal">remote: Enumerating objects: 27664, done.<u></u><u></u></p>
<p class="MsoNormal">remote: Total 27664 (delta 0), reused 0 (delta 0), pack-reused 27664<u></u><u></u></p>
<p class="MsoNormal">Receiving objects: 100% (27664/27664), 20.47 MiB | 14.72 MiB/s, done.<u></u><u></u></p>
<p class="MsoNormal">Resolving deltas: 100% (15913/15913), done.<u></u><u></u></p>
<p class="MsoNormal">Checking out files: 100% (14245/14245), done.<u></u><u></u></p>
<p class="MsoNormal"> setting branch master to rebase<u></u><u></u></p>
<p class="MsoNormal">===== Running in modules/boost: git rev-parse HEAD<u></u><u></u></p>
<p class="MsoNormal">72edfa007c73dd3dd01f5530205f7ca14cda7420<u></u><u></u></p>
<p class="MsoNormal">===== Running in modules: git clone --recursive <a href="https://github.com/yayahjb/cbflib.git" target="_blank">https://github.com/yayahjb/cbflib.git</a> cbflib --progress --verbose<u></u><u></u></p>
<p class="MsoNormal">Cloning into 'cbflib'...<u></u><u></u></p>
<p class="MsoNormal">POST git-upload-pack (gzip 2442 to 1233 bytes)<u></u><u></u></p>
<p class="MsoNormal">remote: Enumerating objects: 7463, done.<u></u><u></u></p>
<p class="MsoNormal">remote: Total 7463 (delta 0), reused 0 (delta 0), pack-reused 7463<u></u><u></u></p>
<p class="MsoNormal">Receiving objects: 100% (7463/7463), 24.84 MiB | 13.21 MiB/s, done.<u></u><u></u></p>
<p class="MsoNormal">Resolving deltas: 100% (5380/5380), done.<u></u><u></u></p>
<p class="MsoNormal"> setting branch master to rebase<u></u><u></u></p>
<p class="MsoNormal">===== Running in modules/cbflib: git rev-parse HEAD<u></u><u></u></p>
<p class="MsoNormal">611f21bbef81c5104954aaab9b72e4e55ec3e70d<u></u><u></u></p>
<p class="MsoNormal">===== Running in modules: git clone --recursive <a href="https://github.com/cctbx/cctbx_project.git" target="_blank">https://github.com/cctbx/cctbx_project.git</a> cctbx_project --progress --verbose<u></u><u></u></p>
<p class="MsoNormal">Cloning into 'cctbx_project'...<u></u><u></u></p>
<p class="MsoNormal">POST git-upload-pack (gzip 1842 to 958 bytes)<u></u><u></u></p>
<p class="MsoNormal">remote: Enumerating objects: 61, done.<u></u><u></u></p>
<p class="MsoNormal">remote: Counting objects: 100% (61/61), done.<u></u><u></u></p>
<p class="MsoNormal">remote: Compressing objects: 100% (52/52), done.<u></u><u></u></p>
<p class="MsoNormal">remote: Total 243691 (delta 14), reused 22 (delta 9), pack-reused 243630<u></u><u></u></p>
<p class="MsoNormal">Receiving objects: 100% (243691/243691), 91.05 MiB | 14.77 MiB/s, done.<u></u><u></u></p>
<p class="MsoNormal">Resolving deltas: 100% (192566/192566), done.<u></u><u></u></p>
<p class="MsoNormal">Checking out files: 100% (6173/6173), done.<u></u><u></u></p>
<p class="MsoNormal"> setting branch master to rebase<u></u><u></u></p>
<p class="MsoNormal">===== Running in modules/cctbx_project: git rev-parse HEAD<u></u><u></u></p>
<p class="MsoNormal">bd3139c85312f5f43009e1eb31baa34f41734fbb<u></u><u></u></p>
<p class="MsoNormal">===== Downloading <a href="http://cci.lbl.gov/repositories/ccp4io_adaptbx.gz" target="_blank">http://cci.lbl.gov/repositories/ccp4io_adaptbx.gz</a>: 203.9 kB<u></u><u></u></p>
<p class="MsoNormal"> [0%.........20%.........40%.........60%.........80%.........100%]<u></u><u></u></p>
<p class="MsoNormal">===== Running in modules: extracting files from ccp4io_adaptbx.gz<u></u><u></u></p>
<p class="MsoNormal">===== Running in modules: git clone --recursive <a href="https://github.com/cctbx/annlib_adaptbx.git" target="_blank">https://github.com/cctbx/annlib_adaptbx.git</a> annlib_adaptbx --progress --verbose<u></u><u></u></p>
<p class="MsoNormal">Cloning into 'annlib_adaptbx'...<u></u><u></u></p>
<p class="MsoNormal">POST git-upload-pack (842 bytes)<u></u><u></u></p>
<p class="MsoNormal">remote: Enumerating objects: 175, done.<u></u><u></u></p>
<p class="MsoNormal">remote: Total 175 (delta 0), reused 0 (delta 0), pack-reused 175<u></u><u></u></p>
<p class="MsoNormal">Receiving objects: 100% (175/175), 162.09 KiB | 0 bytes/s, done.<u></u><u></u></p>
<p class="MsoNormal">Resolving deltas: 100% (77/77), done.<u></u><u></u></p>
<p class="MsoNormal"> setting branch master to rebase<u></u><u></u></p>
<p class="MsoNormal">===== Running in modules/annlib_adaptbx: git rev-parse HEAD<u></u><u></u></p>
<p class="MsoNormal">3ca66b2dd77eacd7524f915fce0705ac0764b46f<u></u><u></u></p>
<p class="MsoNormal">===== Downloading <a href="http://cci.lbl.gov/repositories/tntbx.gz" target="_blank">http://cci.lbl.gov/repositories/tntbx.gz</a>: 38.0 kB<u></u><u></u></p>
<p class="MsoNormal"> [0%.........20%.........40%.........60%.........80%.........100%]<u></u><u></u></p>
<p class="MsoNormal">===== Running in modules: extracting files from tntbx.gz<u></u><u></u></p>
<p class="MsoNormal">===== Running in .: svn co <a href="https://github.com/rlabduke/MolProbity.git/trunk" target="_blank">https://github.com/rlabduke/MolProbity.git/trunk</a> molprobity --non-interactive --trust-server-cert<u></u><u></u></p>
<p class="MsoNormal">svn: E175002: Unable to connect to a repository at URL '<a href="https://github.com/rlabduke/MolProbity.git/trunk" target="_blank">https://github.com/rlabduke/MolProbity.git/trunk</a>'<u></u><u></u></p>
<p class="MsoNormal">svn: E175002: OPTIONS of '<a href="https://github.com/rlabduke/MolProbity.git/trunk" target="_blank">https://github.com/rlabduke/MolProbity.git/trunk</a>': SSL handshake failed: SSL socket read failed (<a href="https://github.com" target="_blank">https://github.com</a>)<u></u><u></u></p>
<p class="MsoNormal">Process failed with return code 1<u></u><u></u></p>
<p class="MsoNormal">-bash: build/setpaths.sh: No such file or directory<u></u><u></u></p>
<p class="MsoNormal">Traceback (most recent call last):<u></u><u></u></p>
<p class="MsoNormal"> File "modules/chem_data/cablam_data/rebuild_cablam_cache.py", line 2, in <module><u></u><u></u></p>
<p class="MsoNormal"> import libtbx.load_env<u></u><u></u></p>
<p class="MsoNormal">ImportError: No module named libtbx.load_env<u></u><u></u></p>
<p class="MsoNormal">++++++++++ MolProbity configure.sh finished.<u></u><u></u></p>
<p class="MsoNormal">++++++++++ Run molprobity/setup.sh to complete installation.<u></u><u></u></p>
<p class="MsoNormal">-bash-4.2$ <u></u><u></u></p>
<p class="MsoNormal">-bash-4.2$ <u></u><u></u></p>
<p class="MsoNormal"><b>-bash-4.2$ ls -l<u></u><u></u></b></p>
<p class="MsoNormal"><b>total 131<u></u><u></u></b></p>
<p class="MsoNormal"><b>-rw-r--r-- 1 cbs72396 appmgmt 90799 Aug 14 18:26 bootstrap.py<u></u><u></u></b></p>
<p class="MsoNormal"><b>-rw-r--r-- 1 cbs72396 appmgmt 82015 Aug 16 13:38 bootstrap.pyc<u></u><u></u></b></p>
<p class="MsoNormal"><b>-rw-r--r-- 1 cbs72396 appmgmt 1817 Aug 14 14:03 install_via_bootstrap.sh<u></u><u></u></b></p>
<p class="MsoNormal"><b>drwxr-sr-x 12 cbs72396 appmgmt 22 Aug 16 13:38 modules<u></u><u></u></b></p>
<p class="MsoNormal"><b><u></u> <u></u></b></p>
<p class="MsoNormal"><b><u></u> <u></u></b></p>
<p class="MsoNormal">Best Regards,<u></u><u></u></p>
<p class="MsoNormal">Charitha Shetty <u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<div>
<div style="border-color:rgb(225,225,225) currentcolor currentcolor;border-style:solid none none;border-width:1pt medium medium;padding:3pt 0in 0in">
<p class="MsoNormal"><b>From:</b> Christopher Williams <<a href="mailto:christopher.sci.williams@gmail.com" target="_blank">christopher.sci.williams@gmail.com</a>>
<br>
<b>Sent:</b> Wednesday, August 14, 2019 2:23 PM<br>
<b>To:</b> Robert Nolte <<a href="mailto:robert.t.nolte@gsk.com" target="_blank">robert.t.nolte@gsk.com</a>><br>
<b>Cc:</b> Nigel Moriarty <<a href="mailto:nwmoriarty@lbl.gov" target="_blank">nwmoriarty@lbl.gov</a>>; Charitha Belluru Shetty <<a href="mailto:charitha-belluru.b.shetty@gsk.com" target="_blank">charitha-belluru.b.shetty@gsk.com</a>>; <a href="mailto:cctbxbb@phenix-online.org" target="_blank">cctbxbb@phenix-online.org</a><br>
<b>Subject:</b> Re: Molprobity / CCTBX incompatibility<u></u><u></u></p>
</div>
</div>
<p class="MsoNormal"><u></u> <u></u></p>
<p><strong><span style="font-size:10.5pt;font-family:Arial,sans-serif;color:rgb(192,0,0)">EXTERNAL</span></strong><u></u><u></u></p>
<div>
<div>
<div>
<p class="MsoNormal">Hi All,<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Okay looks like the new installer works. It uses the conda mode of the cctbx bootstrap builder for everything except chem_data, which it builds on its own.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Get the new installer from our GitHub here:<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">svn --quiet --non-interactive --trust-server-cert export <a href="https://github.com/rlabduke/MolProbity.git/trunk/install_via_bootstrap.sh" target="_blank">
https://github.com/rlabduke/MolProbity.git/trunk/install_via_bootstrap.sh</a><u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Place it in the dir where you want to install MolProbity, then run it.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">. install_via_bootstrap.sh<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">The script optionally accepts a single integer argument to set the number of processors that the bootstrap builder will use.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">. install_via_bootstrap.sh 4<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">When this is complete, cd to the molprobity dir it created and run setup.sh, as usual.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Good luck,<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">-Christopher Williams<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">---Richardson Lab, Duke University<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
</div>
<p class="MsoNormal"><u></u> <u></u></p>
<div>
<div>
<p class="MsoNormal">On Wed, Aug 14, 2019 at 1:33 PM Christopher Williams <<a href="mailto:christopher.sci.williams@gmail.com" target="_blank">christopher.sci.williams@gmail.com</a>> wrote:<u></u><u></u></p>
</div>
<blockquote style="border-color:currentcolor currentcolor currentcolor rgb(204,204,204);border-style:none none none solid;border-width:medium medium medium 1pt;padding:0in 0in 0in 6pt;margin-left:4.8pt;margin-right:0in">
<div>
<div>
<p class="MsoNormal">Hi Bob,<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">I am currently doing one more test build to make sure that the new installer works. It looks promising.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Regards,<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">-Christopher Williams<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">---Richardson Lab, Duke University<u></u><u></u></p>
</div>
</div>
<p class="MsoNormal"><u></u> <u></u></p>
<div>
<div>
<p class="MsoNormal">On Wed, Aug 14, 2019 at 11:17 AM Robert Nolte <<a href="mailto:robert.t.nolte@gsk.com" target="_blank">robert.t.nolte@gsk.com</a>> wrote:<u></u><u></u></p>
</div>
<blockquote style="border-color:currentcolor currentcolor currentcolor rgb(204,204,204);border-style:none none none solid;border-width:medium medium medium 1pt;padding:0in 0in 0in 6pt;margin-left:4.8pt;margin-right:0in">
<div>
<div>
<p class="MsoNormal">Folks,<u></u><u></u></p>
<p class="MsoNormal"> Any progress on sorting out our issue, or cleaning up the installer?<u></u><u></u></p>
<p class="MsoNormal"> Bob<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<div>
<div style="border-style:solid none none;border-width:1pt medium medium;padding:3pt 0in 0in;border-color:currentcolor">
<p class="MsoNormal"><b>From:</b> Christopher Williams <<a href="mailto:christopher.sci.williams@gmail.com" target="_blank">christopher.sci.williams@gmail.com</a>>
<br>
<b>Sent:</b> Monday, August 12, 2019 7:48 PM<br>
<b>To:</b> Nigel Moriarty <<a href="mailto:nwmoriarty@lbl.gov" target="_blank">nwmoriarty@lbl.gov</a>><br>
<b>Cc:</b> Robert Nolte <<a href="mailto:robert.t.nolte@gsk.com" target="_blank">robert.t.nolte@gsk.com</a>>; Charitha Belluru Shetty <<a href="mailto:charitha-belluru.b.shetty@gsk.com" target="_blank">charitha-belluru.b.shetty@gsk.com</a>>;
<a href="mailto:cctbxbb@phenix-online.org" target="_blank">cctbxbb@phenix-online.org</a><br>
<b>Subject:</b> Re: Molprobity / CCTBX incompatibility<u></u><u></u></p>
</div>
</div>
<p class="MsoNormal"> <u></u><u></u></p>
<p><strong><span style="font-size:10.5pt;font-family:Arial,sans-serif;color:rgb(192,0,0)">EXTERNAL</span></strong><u></u><u></u></p>
<div>
<div>
<div>
<p class="MsoNormal">The dispatcher should be using both phenix.reduce and molprobity.reduce interchangeably in all cases. Ditto for all the validations that MolProbity runs like phenix.rotalyze/molprobity.rotalyze.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">My current install of MolProbity is successfully accessing Reduce via phenix.reduce, so I don't
<i>think</i> this is the issue.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">-Christopher Williams<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">---Richardson Lab, Duke University<u></u><u></u></p>
</div>
</div>
<p class="MsoNormal"> <u></u><u></u></p>
<div>
<div>
<p class="MsoNormal">On Mon, Aug 12, 2019 at 6:07 PM Nigel Moriarty <<a href="mailto:nwmoriarty@lbl.gov" target="_blank">nwmoriarty@lbl.gov</a>> wrote:<u></u><u></u></p>
</div>
<blockquote style="border-style:none none none solid;border-width:medium medium medium 1pt;padding:0in 0in 0in 6pt;margin:5pt 0in 5pt 4.8pt;border-color:currentcolor currentcolor currentcolor rgb(204,204,204)">
<div>
<p class="MsoNormal">But maybe the installation of cctbx has molprobity.reduce and not phenix.reduce so if that is the case we can change the script to look for molprobity.reduce instead of phenix.reduce.
<u></u><u></u></p>
<div>
<p class="MsoNormal"><br clear="all">
<u></u><u></u></p>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal">Cheers
<u></u><u></u></p>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Nigel
<u></u><u></u></p>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">---<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Nigel W. Moriarty<br>
Building 33R0349, Molecular Biophysics and Integrated Bioimaging<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Lawrence Berkeley National Laboratory<br>
Berkeley, CA 94720-8235<br>
Phone : 510-486-5709 Email : <a href="mailto:NWMoriarty@LBL.gov" target="_blank">
NWMoriarty@LBL.gov</a><br>
Fax : 510-486-5909 Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a><u></u><u></u></p>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
</div>
<p class="MsoNormal"> <u></u><u></u></p>
<div>
<div>
<p class="MsoNormal">On Mon, Aug 12, 2019 at 2:58 PM Robert Nolte <<a href="mailto:robert.t.nolte@gsk.com" target="_blank">robert.t.nolte@gsk.com</a>> wrote:<u></u><u></u></p>
</div>
<blockquote style="border-style:none none none solid;border-width:medium medium medium 1pt;padding:0in 0in 0in 6pt;margin:5pt 0in 5pt 4.8pt;border-color:currentcolor currentcolor currentcolor rgb(204,204,204)">
<div>
<div>
<p class="MsoNormal">According to the log file when I just tried to run it, it is phenix.reduce that it can’t find.<u></u><u></u></p>
<p class="MsoNormal"> Bob<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<div>
<div style="border-style:solid none none;border-width:1pt medium medium;padding:3pt 0in 0in;border-color:currentcolor">
<p class="MsoNormal"><b>From:</b> Nigel Moriarty <<a href="mailto:nwmoriarty@lbl.gov" target="_blank">nwmoriarty@lbl.gov</a>>
<br>
<b>Sent:</b> Monday, August 12, 2019 5:55 PM<br>
<b>To:</b> Robert Nolte <<a href="mailto:robert.t.nolte@gsk.com" target="_blank">robert.t.nolte@gsk.com</a>><br>
<b>Cc:</b> Charitha Belluru Shetty <<a href="mailto:charitha-belluru.b.shetty@gsk.com" target="_blank">charitha-belluru.b.shetty@gsk.com</a>>; Christopher Williams <<a href="mailto:christopher.sci.williams@gmail.com" target="_blank">christopher.sci.williams@gmail.com</a>>;
<a href="mailto:cctbxbb@phenix-online.org" target="_blank">cctbxbb@phenix-online.org</a><br>
<b>Subject:</b> Re: Molprobity / CCTBX incompatibility<u></u><u></u></p>
</div>
</div>
<p class="MsoNormal"> <u></u><u></u></p>
<p><strong><span style="font-size:10.5pt;font-family:Arial,sans-serif;color:rgb(192,0,0)">EXTERNAL</span></strong><u></u><u></u></p>
<div>
<div>
<p class="MsoNormal">I'm just trying to find out if, at the command line, whether it is phenix.reduce or molprobity.reduce. Charitha just needs to type one or the other to see what happens.
<u></u><u></u></p>
<div>
<p class="MsoNormal"><br clear="all">
<u></u><u></u></p>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal">Cheers
<u></u><u></u></p>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Nigel
<u></u><u></u></p>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">---<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Nigel W. Moriarty<br>
Building 33R0349, Molecular Biophysics and Integrated Bioimaging<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Lawrence Berkeley National Laboratory<br>
Berkeley, CA 94720-8235<br>
Phone : 510-486-5709 Email : <a href="mailto:NWMoriarty@LBL.gov" target="_blank">
NWMoriarty@LBL.gov</a><br>
Fax : 510-486-5909 Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a><u></u><u></u></p>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
</div>
<p class="MsoNormal"> <u></u><u></u></p>
<div>
<div>
<p class="MsoNormal">On Mon, Aug 12, 2019 at 2:44 PM Robert Nolte <<a href="mailto:robert.t.nolte@gsk.com" target="_blank">robert.t.nolte@gsk.com</a>> wrote:<u></u><u></u></p>
</div>
<blockquote style="border-style:none none none solid;border-width:medium medium medium 1pt;padding:0in 0in 0in 6pt;margin:5pt 0in 5pt 4.8pt;border-color:currentcolor currentcolor currentcolor rgb(204,204,204)">
<div>
<div>
<p class="MsoNormal">Nigel,<u></u><u></u></p>
<p class="MsoNormal"> Currently it is not running. This was working from the scratch install last week. I am not sure what is going on now.<u></u><u></u></p>
<p class="MsoNormal"> Bob<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<div>
<div style="border-style:solid none none;border-width:1pt medium medium;padding:3pt 0in 0in;border-color:currentcolor">
<p class="MsoNormal"><b>From:</b> Nigel Moriarty <<a href="mailto:nwmoriarty@lbl.gov" target="_blank">nwmoriarty@lbl.gov</a>>
<br>
<b>Sent:</b> Monday, August 12, 2019 4:52 PM<br>
<b>To:</b> Charitha Belluru Shetty <<a href="mailto:charitha-belluru.b.shetty@gsk.com" target="_blank">charitha-belluru.b.shetty@gsk.com</a>><br>
<b>Cc:</b> Christopher Williams <<a href="mailto:christopher.sci.williams@gmail.com" target="_blank">christopher.sci.williams@gmail.com</a>>;
<a href="mailto:cctbxbb@phenix-online.org" target="_blank">cctbxbb@phenix-online.org</a>; Robert Nolte <<a href="mailto:robert.t.nolte@gsk.com" target="_blank">robert.t.nolte@gsk.com</a>><br>
<b>Subject:</b> Re: Molprobity / CCTBX incompatibility<u></u><u></u></p>
</div>
</div>
<p class="MsoNormal"> <u></u><u></u></p>
<p><strong><span style="font-size:10.5pt;font-family:Arial,sans-serif;color:rgb(192,0,0)">EXTERNAL</span></strong><u></u><u></u></p>
<div>
<div>
<p class="MsoNormal">Does molprobity.reduce run?
<u></u><u></u></p>
<div>
<p class="MsoNormal"><br clear="all">
<u></u><u></u></p>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal">Cheers
<u></u><u></u></p>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Nigel
<u></u><u></u></p>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">---<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Nigel W. Moriarty<br>
Building 33R0349, Molecular Biophysics and Integrated Bioimaging<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Lawrence Berkeley National Laboratory<br>
Berkeley, CA 94720-8235<br>
Phone : 510-486-5709 Email : <a href="mailto:NWMoriarty@LBL.gov" target="_blank">
NWMoriarty@LBL.gov</a><br>
Fax : 510-486-5909 Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a><u></u><u></u></p>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
</div>
<p class="MsoNormal"> <u></u><u></u></p>
<div>
<div>
<p class="MsoNormal">On Mon, Aug 12, 2019 at 1:14 PM Charitha Belluru Shetty <<a href="mailto:charitha-belluru.b.shetty@gsk.com" target="_blank">charitha-belluru.b.shetty@gsk.com</a>> wrote:<u></u><u></u></p>
</div>
<blockquote style="border-style:none none none solid;border-width:medium medium medium 1pt;padding:0in 0in 0in 6pt;margin:5pt 0in 5pt 4.8pt;border-color:currentcolor currentcolor currentcolor rgb(204,204,204)">
<div>
<div>
<p class="MsoNormal">Hi Nigel,<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">I hit the send button too soon..Ignore my previous email
<span style="font-family:"Segoe UI Emoji",sans-serif">😊</span><u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">-bash-4.2$ source setpaths.sh<u></u><u></u></p>
<p class="MsoNormal">-bash-4.2$<u></u><u></u></p>
<p class="MsoNormal">-bash-4.2$ env |grep -i reduce<u></u><u></u></p>
<p class="MsoNormal">-bash-4.2$<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">So the “setpath.sh” has the below contents…<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">$ cat /hpc/apps/current/molprobity/v4.4.app/MolProbity/build/setpaths.sh<u></u><u></u></p>
<p class="MsoNormal"># THIS IS AN AUTOMATICALLY GENERATED FILE.<u></u><u></u></p>
<p class="MsoNormal"># DO NOT EDIT! CHANGES WILL BE LOST.<u></u><u></u></p>
<p class="MsoNormal">ocwd="`pwd`"<u></u><u></u></p>
<p class="MsoNormal">if [ -n "$LIBTBX_BUILD_RELOCATION_HINT" ]; then<u></u><u></u></p>
<p class="MsoNormal"> cd "$LIBTBX_BUILD_RELOCATION_HINT"<u></u><u></u></p>
<p class="MsoNormal"> LIBTBX_BUILD_RELOCATION_HINT=<u></u><u></u></p>
<p class="MsoNormal"> export LIBTBX_BUILD_RELOCATION_HINT<u></u><u></u></p>
<p class="MsoNormal">elif [ -n "$BASH_SOURCE" ]; then<u></u><u></u></p>
<p class="MsoNormal"> LIBTBX_BUILD=`dirname "$BASH_SOURCE[0]"`<u></u><u></u></p>
<p class="MsoNormal"> cd "$LIBTBX_BUILD"<u></u><u></u></p>
<p class="MsoNormal">else<u></u><u></u></p>
<p class="MsoNormal"> cd "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build"<u></u><u></u></p>
<p class="MsoNormal">fi<u></u><u></u></p>
<p class="MsoNormal">LIBTBX_BUILD=`pwd -P`<u></u><u></u></p>
<p class="MsoNormal">export LIBTBX_BUILD<u></u><u></u></p>
<p class="MsoNormal">LIBTBX_OPATH="$PATH"<u></u><u></u></p>
<p class="MsoNormal">export LIBTBX_OPATH<u></u><u></u></p>
<p class="MsoNormal">PATH="$LIBTBX_BUILD/bin:$PATH"<u></u><u></u></p>
<p class="MsoNormal">export PATH<u></u><u></u></p>
<p class="MsoNormal">cd "$ocwd"<u></u><u></u></p>
<p class="MsoNormal">ocwd=<u></u><u></u></p>
<p class="MsoNormal">alias libtbx.setpaths_all=". \"$LIBTBX_BUILD/setpaths_all.sh\""<u></u><u></u></p>
<p class="MsoNormal">alias libtbx.unsetpaths=". \"$LIBTBX_BUILD/unsetpaths.sh\""<u></u><u></u></p>
<p class="MsoNormal">if [ -n "$LIBTBX_OPATH" ]; then<u></u><u></u></p>
<p class="MsoNormal"> LIBTBX_TMPVAL="$LIBTBX_OPATH"<u></u><u></u></p>
<p class="MsoNormal">else<u></u><u></u></p>
<p class="MsoNormal"> LIBTBX_TMPVAL=<u></u><u></u></p>
<p class="MsoNormal">fi<u></u><u></u></p>
<p class="MsoNormal">export LIBTBX_TMPVAL<u></u><u></u></p>
<p class="MsoNormal">PATH=`libtbx.path_utility prepend LIBTBX_TMPVAL "$LIBTBX_BUILD/bin" < /dev/null`<u></u><u></u></p>
<p class="MsoNormal">export PATH<u></u><u></u></p>
<p class="MsoNormal">if [ "$PATH" = "L_I_B_T_B_X_E_M_P_T_Y" ]; then unset PATH; fi<u></u><u></u></p>
<p class="MsoNormal">LIBTBX_TMPVAL=<u></u><u></u></p>
<p class="MsoNormal">LIBTBX_OPATH=<u></u><u></u></p>
<p class="MsoNormal">LIBTBX_BUILD=<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">Best Regards,<u></u><u></u></p>
<p class="MsoNormal">Charitha Shetty
<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<div>
<div style="border-style:solid none none;border-width:1pt medium medium;padding:3pt 0in 0in;border-color:currentcolor">
<p class="MsoNormal"><b>From:</b> Nigel Moriarty <<a href="mailto:nwmoriarty@lbl.gov" target="_blank">nwmoriarty@lbl.gov</a>>
<br>
<b>Sent:</b> Monday, August 12, 2019 4:08 PM<br>
<b>To:</b> Charitha Belluru Shetty <<a href="mailto:charitha-belluru.b.shetty@gsk.com" target="_blank">charitha-belluru.b.shetty@gsk.com</a>><br>
<b>Cc:</b> Christopher Williams <<a href="mailto:christopher.sci.williams@gmail.com" target="_blank">christopher.sci.williams@gmail.com</a>>;
<a href="mailto:cctbxbb@phenix-online.org" target="_blank">cctbxbb@phenix-online.org</a>; Robert Nolte <<a href="mailto:robert.t.nolte@gsk.com" target="_blank">robert.t.nolte@gsk.com</a>><br>
<b>Subject:</b> Re: Molprobity / CCTBX incompatibility<u></u><u></u></p>
</div>
</div>
<p class="MsoNormal"> <u></u><u></u></p>
<p><strong><span style="font-size:10.5pt;font-family:Arial,sans-serif;color:rgb(192,0,0)">EXTERNAL</span></strong><u></u><u></u></p>
<div>
<div>
<p class="MsoNormal">Once you source the setpaths.sh file in the build directory do you have phenix.reduce or molprobity.reduce?<br clear="all">
<u></u><u></u></p>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal">Cheers
<u></u><u></u></p>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Nigel
<u></u><u></u></p>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">---<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Nigel W. Moriarty<br>
Building 33R0349, Molecular Biophysics and Integrated Bioimaging<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Lawrence Berkeley National Laboratory<br>
Berkeley, CA 94720-8235<br>
Phone : 510-486-5709 Email : <a href="mailto:NWMoriarty@LBL.gov" target="_blank">
NWMoriarty@LBL.gov</a><br>
Fax : 510-486-5909 Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a><u></u><u></u></p>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
<p class="MsoNormal"> <u></u><u></u></p>
<div>
<div>
<p class="MsoNormal">On Mon, Aug 12, 2019 at 12:43 PM Charitha Belluru Shetty <<a href="mailto:charitha-belluru.b.shetty@gsk.com" target="_blank">charitha-belluru.b.shetty@gsk.com</a>> wrote:<u></u><u></u></p>
</div>
<blockquote style="border-style:none none none solid;border-width:medium medium medium 1pt;padding:0in 0in 0in 6pt;margin:5pt 0in 5pt 4.8pt;border-color:currentcolor currentcolor currentcolor rgb(204,204,204)">
<div>
<div>
<p class="MsoNormal">Hi Christopher/ Nigel,<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">Thank you for your quick reply.<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">The build process was completed without any error. Pasting few of the lines from it…<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">===== Running in build: rebuild rotarama<u></u><u></u></p>
<p class="MsoNormal">Processing data files in "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/chem_data/rotarama_data":<u></u><u></u></p>
<p class="MsoNormal"> rota8000-cys.data -> rota8000-cys.pickle: converting ... done.<u></u><u></u></p>
<p class="MsoNormal"> rota8000-asp.data -> rota8000-asp.pickle: converting ... done.<u></u><u></u></p>
<p class="MsoNormal"> rota8000-ser.data -> rota8000-ser.pickle: converting ... done.<u></u><u></u></p>
<p class="MsoNormal"> rota8000-gln.data -> rota8000-gln.pickle: converting ... done.<u></u><u></u></p>
<p class="MsoNormal"> rota8000-ile.data -> rota8000-ile.pickle: converting ... done.<u></u><u></u></p>
<p class="MsoNormal"> rota8000-pro.data -> rota8000-pro.pickle: converting ... done.<u></u><u></u></p>
<p class="MsoNormal"> rota8000-lys.data -> rota8000-lys.pickle: converting ... done.<u></u><u></u></p>
<p class="MsoNormal"> rota8000-thr.data -> rota8000-thr.pickle: converting ... done.<u></u><u></u></p>
<p class="MsoNormal"> rota8000-phetyr.data -> rota8000-phetyr.pickle: converting ... done.<u></u><u></u></p>
<p class="MsoNormal"> rota8000-glu.data -> rota8000-glu.pickle: converting ... done.<u></u><u></u></p>
<p class="MsoNormal"> rota8000-met.data -> rota8000-met.pickle: converting ... done.<u></u><u></u></p>
<p class="MsoNormal"> rota8000-his.data -> rota8000-his.pickle: converting ... done.<u></u><u></u></p>
<p class="MsoNormal"> rota8000-leu.data -> rota8000-leu.pickle: converting ... done.<u></u><u></u></p>
<p class="MsoNormal"> rota8000-arg.data -> rota8000-arg.pickle: converting ... done.<u></u><u></u></p>
<p class="MsoNormal"> rota8000-trp.data -> rota8000-trp.pickle: converting ... done.<u></u><u></u></p>
<p class="MsoNormal"> rota8000-asn.data -> rota8000-asn.pickle: converting ... done.<u></u><u></u></p>
<p class="MsoNormal"> rota8000-phetyr.data -> rota8000-phetyr.pickle: already up to date.<u></u><u></u></p>
<p class="MsoNormal"> rota8000-val.data -> rota8000-val.pickle: converting ... done.<u></u><u></u></p>
<p class="MsoNormal">Processing data files in "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/chem_data/rotarama_data":<u></u><u></u></p>
<p class="MsoNormal"> rama8000-ileval-nopreP.data -> rama8000-ileval-nopreP.pickle: converting ... done.<u></u><u></u></p>
<p class="MsoNormal"> rama8000-gly-sym.data -> rama8000-gly-sym.pickle: converting ... done.<u></u><u></u></p>
<p class="MsoNormal"> rama8000-cispro.data -> rama8000-cispro.pickle: converting ... done.<u></u><u></u></p>
<p class="MsoNormal"> rama8000-general-noGPIVpreP.data -> rama8000-general-noGPIVpreP.pickle: converting ... done.<u></u><u></u></p>
<p class="MsoNormal"> rama8000-transpro.data -> rama8000-transpro.pickle: converting ... done.<u></u><u></u></p>
<p class="MsoNormal"> rama8000-prepro-noGP.data -> rama8000-prepro-noGP.pickle: converting ... done.<u></u><u></u></p>
<p class="MsoNormal">u+s,u,s: 10.06 9.83 0.23<u></u><u></u></p>
<p class="MsoNormal">===== Running in .: libtbx.refresh<u></u><u></u></p>
<p class="MsoNormal">Python: 2.7.16 "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/bin/python2.7"<u></u><u></u></p>
<p class="MsoNormal">Compiler: default<u></u><u></u></p>
<p class="MsoNormal">Build mode: release<u></u><u></u></p>
<p class="MsoNormal">Warning level: 0<u></u><u></u></p>
<p class="MsoNormal">Precompiled Headers: False<u></u><u></u></p>
<p class="MsoNormal">Static libraries: False<u></u><u></u></p>
<p class="MsoNormal">Static exe: False<u></u><u></u></p>
<p class="MsoNormal">Scan Boost headers: False<u></u><u></u></p>
<p class="MsoNormal">Write full flex_fwd.h files: False<u></u><u></u></p>
<p class="MsoNormal">Build Boost.Python extensions: True<u></u><u></u></p>
<p class="MsoNormal">Define BOOST_PYTHON_NO_PY_SIGNATURES: False<u></u><u></u></p>
<p class="MsoNormal">Define BOOST_PYTHON_BOOL_INT_STRICT: True<u></u><u></u></p>
<p class="MsoNormal">Enable OpenMP if possible: False<u></u><u></u></p>
<p class="MsoNormal">Boost threads enabled: True<u></u><u></u></p>
<p class="MsoNormal">Enable CUDA: False<u></u><u></u></p>
<p class="MsoNormal">Use conda: False<u></u><u></u></p>
<p class="MsoNormal">Use opt_resources if available: False<u></u><u></u></p>
<p class="MsoNormal">Use environment flags: False<u></u><u></u></p>
<p class="MsoNormal">Enable C++11: False<u></u><u></u></p>
<p class="MsoNormal">Python3 migration warning policy: None<u></u><u></u></p>
<p class="MsoNormal">command_version_suffix: None<u></u><u></u></p>
<p class="MsoNormal">Relocatable paths anchored at: /hpc/apps/2018/molprobity/v4.4.app/MolProbity/build<u></u><u></u></p>
<p class="MsoNormal">Top-down list of all modules involved:<u></u><u></u></p>
<p class="MsoNormal"> mmtbx "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx"<u></u><u></u></p>
<p class="MsoNormal"> iotbx "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/iotbx"<u></u><u></u></p>
<p class="MsoNormal"> ccp4io+adaptbx "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/ccp4io"<u></u><u></u></p>
<p class="MsoNormal"> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/ccp4io_adaptbx"<u></u><u></u></p>
<p class="MsoNormal"> smtbx "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/smtbx"<u></u><u></u></p>
<p class="MsoNormal"> ucif "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/ucif"<u></u><u></u></p>
<p class="MsoNormal"> cctbx "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/cctbx"<u></u><u></u></p>
<p class="MsoNormal"> scitbx "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/scitbx"<u></u><u></u></p>
<p class="MsoNormal"> fable "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/fable"<u></u><u></u></p>
<p class="MsoNormal"> omptbx "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/omptbx"<u></u><u></u></p>
<p class="MsoNormal"> boost+adaptbx "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/boost"<u></u><u></u></p>
<p class="MsoNormal"> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/boost_adaptbx"<u></u><u></u></p>
<p class="MsoNormal"> tbxx "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/tbxx"<u></u><u></u></p>
<p class="MsoNormal"> chiltbx "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/chiltbx"<u></u><u></u></p>
<p class="MsoNormal"> libtbx "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/libtbx"<u></u><u></u></p>
<p class="MsoNormal">Creating files in build directory: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build"<u></u><u></u></p>
<p class="MsoNormal"> dispatcher_include_template.sh<u></u><u></u></p>
<p class="MsoNormal"> dispatcher_head.sh<u></u><u></u></p>
<p class="MsoNormal"> setpaths.sh<u></u><u></u></p>
<p class="MsoNormal"> setpaths.csh<u></u><u></u></p>
<p class="MsoNormal"> setpaths_all.sh<u></u><u></u></p>
<p class="MsoNormal"> setpaths_all.csh<u></u><u></u></p>
<p class="MsoNormal"> setpaths_debug.sh<u></u><u></u></p>
<p class="MsoNormal"> unsetpaths.sh<u></u><u></u></p>
<p class="MsoNormal"> setpaths_debug.csh<u></u><u></u></p>
<p class="MsoNormal"> unsetpaths.csh<u></u><u></u></p>
<p class="MsoNormal"> SConstruct<u></u><u></u></p>
<p class="MsoNormal"> Makefile<u></u><u></u></p>
<p class="MsoNormal"> run_tests.csh<u></u><u></u></p>
<p class="MsoNormal">Processing: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/libtbx/command_line"<u></u><u></u></p>
<p class="MsoNormal">Processing: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/boost_adaptbx/command_line"<u></u><u></u></p>
<p class="MsoNormal">Processing: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/fable/command_line"<u></u><u></u></p>
<p class="MsoNormal">Processing: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/scitbx/command_line"<u></u><u></u></p>
<p class="MsoNormal">Processing: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/cctbx/command_line"<u></u><u></u></p>
<p class="MsoNormal">Processing: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/smtbx/command_line"<u></u><u></u></p>
<p class="MsoNormal">Processing: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/iotbx/command_line"<u></u><u></u></p>
<p class="MsoNormal">Processing: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx/command_line"<u></u><u></u></p>
<p class="MsoNormal">Processing: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/boost_adaptbx/libtbx_refresh.py"<u></u><u></u></p>
<p class="MsoNormal">Processing: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/scitbx/libtbx_refresh.py"<u></u><u></u></p>
<p class="MsoNormal"> Generating C++ header files in:<u></u><u></u></p>
<p class="MsoNormal"> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/scitbx/array_family"<u></u><u></u></p>
<p class="MsoNormal"> Generating C++ files in:<u></u><u></u></p>
<p class="MsoNormal"> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/scitbx/array_family/boost_python"<u></u><u></u></p>
<p class="MsoNormal"> Using fable to convert scitbx/lbfgs.f<u></u><u></u></p>
<p class="MsoNormal">Processing: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/cctbx/libtbx_refresh.py"<u></u><u></u></p>
<p class="MsoNormal"> Generating C++ files in:<u></u><u></u></p>
<p class="MsoNormal"> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/cctbx/eltbx"<u></u><u></u></p>
<p class="MsoNormal"> Generating C++ files in:<u></u><u></u></p>
<p class="MsoNormal"> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/cctbx/boost_python"<u></u><u></u></p>
<p class="MsoNormal">Processing: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/smtbx/libtbx_refresh.py"<u></u><u></u></p>
<p class="MsoNormal"> Generating C++ files in:<u></u><u></u></p>
<p class="MsoNormal"> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/smtbx/boost_python"<u></u><u></u></p>
<p class="MsoNormal">Processing: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/iotbx/libtbx_refresh.py"<u></u><u></u></p>
<p class="MsoNormal"> Using fable to convert iotbx/pdb/hybrid_36_f.f<u></u><u></u></p>
<p class="MsoNormal"> Writing: iotbx/pdb/hybrid_36_fem.cpp<u></u><u></u></p>
<p class="MsoNormal">Processing: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx/libtbx_refresh.py"<u></u><u></u></p>
<p class="MsoNormal">Processing: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/exe_dev"<u></u><u></u></p>
<p class="MsoNormal">Regenerating module files in /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base<u></u><u></u></p>
<p class="MsoNormal">/hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/etc/pango not present, could not regenerate pango files<u></u><u></u></p>
<p class="MsoNormal">/hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/etc/gtk-2.0 not present, could not regenerate gdk-pixbuf.loaders<u></u><u></u></p>
<p class="MsoNormal">/hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/etc/fonts not present, could not rebuild fonts<u></u><u></u></p>
<p class="MsoNormal">generating index.theme file<u></u><u></u></p>
<p class="MsoNormal">Done.<u></u><u></u></p>
<p class="MsoNormal"><b> </b><u></u><u></u></p>
<p class="MsoNormal"><b><span style="background:none 0% 0% repeat scroll yellow">Bootstrap success: build</span></b><u></u><u></u></p>
<p class="MsoNormal"><b><span style="background:none 0% 0% repeat scroll yellow">++++++++++ MolProbity configure.sh finished.</span></b><u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">[tm375568@uptus060-3 MolProbity]$ ./setup.sh
<u></u><u></u></p>
<p class="MsoNormal">++++++++++ creating directories ...<u></u><u></u></p>
<p class="MsoNormal">++++++++++ setting permisions ...<u></u><u></u></p>
<p class="MsoNormal"><b><span style="background:none 0% 0% repeat scroll yellow">Couldn't get a file descriptor referring to the console
</span></b><b><span style="font-family:Wingdings;background:none 0% 0% repeat scroll yellow">à</span><span style="color:red;background:none 0% 0% repeat scroll yellow"> I assume this can be ignored.</span><span style="color:red">
</span></b><u></u><u></u></p>
<p class="MsoNormal">[tm375568@uptus060-3 MolProbity]$<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">Best Regards,<u></u><u></u></p>
<p class="MsoNormal">Charitha Shetty
<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<div>
<div style="border-style:solid none none;border-width:1pt medium medium;padding:3pt 0in 0in;border-color:currentcolor">
<p class="MsoNormal"><b>From:</b> Christopher Williams <<a href="mailto:christopher.sci.williams@gmail.com" target="_blank">christopher.sci.williams@gmail.com</a>>
<br>
<b>Sent:</b> Monday, August 12, 2019 3:34 PM<br>
<b>To:</b> Charitha Belluru Shetty <<a href="mailto:charitha-belluru.b.shetty@gsk.com" target="_blank">charitha-belluru.b.shetty@gsk.com</a>><br>
<b>Cc:</b> Nigel Moriarty (<a href="mailto:nwmoriarty@lbl.gov" target="_blank">nwmoriarty@lbl.gov</a>) <<a href="mailto:nwmoriarty@lbl.gov" target="_blank">nwmoriarty@lbl.gov</a>>;
<a href="mailto:cctbxbb@phenix-online.org" target="_blank">cctbxbb@phenix-online.org</a>; Robert Nolte <<a href="mailto:robert.t.nolte@gsk.com" target="_blank">robert.t.nolte@gsk.com</a>><br>
<b>Subject:</b> Re: Molprobity / CCTBX incompatibility<u></u><u></u></p>
</div>
</div>
<p class="MsoNormal"> <u></u><u></u></p>
<p><strong><span style="font-size:10.5pt;font-family:Arial,sans-serif;color:rgb(192,0,0)">EXTERNAL</span></strong><u></u><u></u></p>
<div>
<div>
<div>
<p class="MsoNormal">Hmm. It looks like Reduce and/or Probe has failed to install correctly. Most likely an early call to Reduce has resulted in an empty file, which is then passed into other programs,
resulting in error messages.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">The configure script ran a build process. Do you know if that process finished successfully or if it ended with errors? If the build exited early, it may have never reached the
part where Reduce gets compiled. Some dependencies have changed, and I have been having trouble with my own builds lately.
<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">It is also possible that there was just a network hiccup that prevented something from downloading correctly, and a second attempt will work.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">I am working on a new configure/install script for more consistent handling of dependencies. Hopefully it will be ready in about a day.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Good luck,<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">-Christopher Williams<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">---Richardson Lab, Duke University<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
</div>
</div>
</div>
<p><strong><span style="font-family:Calibri,sans-serif;color:black">GSK monitors email communications sent to and from GSK in order to protect GSK, our employees, customers, suppliers and business partners, from cyber threats and loss of GSK Information.
GSK monitoring is conducted with appropriate confidentiality controls and in accordance with local laws and after appropriate consultation.</span></strong><u></u><u></u></p>
</div>
</blockquote>
</div>
</div>
</div>
<p><strong><span style="font-family:Calibri,sans-serif;color:black">GSK monitors email communications sent to and from GSK in order to protect GSK, our employees, customers, suppliers and business partners, from cyber threats and loss of GSK Information.
GSK monitoring is conducted with appropriate confidentiality controls and in accordance with local laws and after appropriate consultation.</span></strong><u></u><u></u></p>
</div>
</blockquote>
</div>
</div>
</div>
<p><strong><span style="font-family:Calibri,sans-serif;color:black">GSK monitors email communications sent to and from GSK in order to protect GSK, our employees, customers, suppliers and business partners, from cyber threats and loss of GSK Information.
GSK monitoring is conducted with appropriate confidentiality controls and in accordance with local laws and after appropriate consultation.</span></strong><u></u><u></u></p>
</div>
</blockquote>
</div>
</div>
</div>
<p><strong><span style="font-family:Calibri,sans-serif;color:black">GSK monitors email communications sent to and from GSK in order to protect GSK, our employees, customers, suppliers and business partners, from cyber threats and loss of GSK Information.
GSK monitoring is conducted with appropriate confidentiality controls and in accordance with local laws and after appropriate consultation.</span></strong><u></u><u></u></p>
</div>
</blockquote>
</div>
</blockquote>
</div>
</div>
</div>
<p><strong><span style="font-family:Calibri,sans-serif;color:black">GSK monitors email communications sent to and from GSK in order to protect GSK, our employees, customers, suppliers and business partners, from cyber threats and loss of GSK Information.
GSK monitoring is conducted with appropriate confidentiality controls and in accordance with local laws and after appropriate consultation.</span></strong><u></u><u></u></p>
</div>
</blockquote>
</div>
</blockquote>
</div>
</div>
</div>
<p><span style="color:rgb(0,0,0)"><strong>GSK monitors email communications sent to and from GSK in order to protect GSK, our employees, customers, suppliers and business partners, from cyber threats and loss of GSK Information. GSK monitoring is conducted with
appropriate confidentiality controls and in accordance with local laws and after appropriate consultation.</strong></span></p>
</div>
</blockquote></div>
</blockquote></div>