- cctbxbb - phenix-online.org

Booststrap fails: zlib.h missing on Mojave with Xcode 10.3
by Luc Bourhis 13 Aug '19

13 Aug '19

Hi, I am trying to setup a Python 3 cctbx. I did python bootstrap.py --git-ssh --python3 --builder cctbxlite But it fails at the installation of OpenSSL. Clang version is "Apple LLVM version 10.0.1 (clang-1001.0.46.4)”. I attached the OpenSSL install log but I don’t see any error in it. And the advice to run xcode-select is bogus: I have it already setup. Best wishes, Luc Installing OpenSSL... log file is /Users/luc/Developer/cctbx/base_tmp/OpenSSL_install_log getting package openssl-1.0.2r.tar.gz... downloading from https://gitcdn.link/repo/dials/dependencies/master/openssl-1.0.2r.tar.gz : 5223 kB installing openssl-1.0.2r.tar.gz... package openssl took 219.5s to install -------------------------------------------------------------------------------- zlib.h missing -- try running 'xcode-select --install' first Process failed with return code 1

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Clipper updates for C++11
by Billy Poon 12 Aug '19

12 Aug '19

Hi everyone, As part of making CCTBX-based software compile with C++11, it looks like we need to update our checkout of clipper to the latest version. http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper.html As a side note, is this a feature that is widely used? If not, we can disable the downloading of the clipper source files. Also, in addition to this post on the bulletin board, I have started an issue on Github (https://github.com/cctbx/cctbx_project/issues/379). Feel free to comment on any of these forums. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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Re: [cctbxbb] Molprobity / CCTBX incompatibility
by Nigel Moriarty 12 Aug '19

12 Aug '19

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. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov On Mon, Aug 12, 2019 at 2:58 PM Robert Nolte <robert.t.nolte(a)gsk.com> wrote: > According to the log file when I just tried to run it, it is phenix.reduce > that it can’t find. > > Bob > > > > > > *From:* Nigel Moriarty <nwmoriarty(a)lbl.gov> > *Sent:* Monday, August 12, 2019 5:55 PM > *To:* Robert Nolte <robert.t.nolte(a)gsk.com> > *Cc:* Charitha Belluru Shetty <charitha-belluru.b.shetty(a)gsk.com>; > Christopher Williams <christopher.sci.williams(a)gmail.com>; > cctbxbb(a)phenix-online.org > *Subject:* Re: Molprobity / CCTBX incompatibility > > > > *EXTERNAL* > > 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. > > > Cheers > > > > Nigel > > > > --- > > Nigel W. Moriarty > Building 33R0349, Molecular Biophysics and Integrated Bioimaging > > Lawrence Berkeley National Laboratory > Berkeley, CA 94720-8235 > Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov > Fax : 510-486-5909 Web : CCI.LBL.gov > > > > > > On Mon, Aug 12, 2019 at 2:44 PM Robert Nolte <robert.t.nolte(a)gsk.com> > wrote: > > Nigel, > > Currently it is not running. This was working from the scratch > install last week. I am not sure what is going on now. > > Bob > > > > > > *From:* Nigel Moriarty <nwmoriarty(a)lbl.gov> > *Sent:* Monday, August 12, 2019 4:52 PM > *To:* Charitha Belluru Shetty <charitha-belluru.b.shetty(a)gsk.com> > *Cc:* Christopher Williams <christopher.sci.williams(a)gmail.com>; > cctbxbb(a)phenix-online.org; Robert Nolte <robert.t.nolte(a)gsk.com> > *Subject:* Re: Molprobity / CCTBX incompatibility > > > > *EXTERNAL* > > Does molprobity.reduce run? > > > Cheers > > > > Nigel > > > > --- > > Nigel W. Moriarty > Building 33R0349, Molecular Biophysics and Integrated Bioimaging > > Lawrence Berkeley National Laboratory > Berkeley, CA 94720-8235 > Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov > Fax : 510-486-5909 Web : CCI.LBL.gov > > > > > > On Mon, Aug 12, 2019 at 1:14 PM Charitha Belluru Shetty < > charitha-belluru.b.shetty(a)gsk.com> wrote: > > Hi Nigel, > > > > I hit the send button too soon..Ignore my previous email 😊 > > > > -bash-4.2$ source setpaths.sh > > -bash-4.2$ > > -bash-4.2$ env |grep -i reduce > > -bash-4.2$ > > > > So the “setpath.sh” has the below contents… > > > > $ cat /hpc/apps/current/molprobity/v4.4.app/MolProbity/build/setpaths.sh > > # THIS IS AN AUTOMATICALLY GENERATED FILE. > > # DO NOT EDIT! CHANGES WILL BE LOST. > > ocwd="`pwd`" > > if [ -n "$LIBTBX_BUILD_RELOCATION_HINT" ]; then > > cd "$LIBTBX_BUILD_RELOCATION_HINT" > > LIBTBX_BUILD_RELOCATION_HINT= > > export LIBTBX_BUILD_RELOCATION_HINT > > elif [ -n "$BASH_SOURCE" ]; then > > LIBTBX_BUILD=`dirname "$BASH_SOURCE[0]"` > > cd "$LIBTBX_BUILD" > > else > > cd "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build" > > fi > > LIBTBX_BUILD=`pwd -P` > > export LIBTBX_BUILD > > LIBTBX_OPATH="$PATH" > > export LIBTBX_OPATH > > PATH="$LIBTBX_BUILD/bin:$PATH" > > export PATH > > cd "$ocwd" > > ocwd= > > alias libtbx.setpaths_all=". \"$LIBTBX_BUILD/setpaths_all.sh\"" > > alias libtbx.unsetpaths=". \"$LIBTBX_BUILD/unsetpaths.sh\"" > > if [ -n "$LIBTBX_OPATH" ]; then > > LIBTBX_TMPVAL="$LIBTBX_OPATH" > > else > > LIBTBX_TMPVAL= > > fi > > export LIBTBX_TMPVAL > > PATH=`libtbx.path_utility prepend LIBTBX_TMPVAL "$LIBTBX_BUILD/bin" < > /dev/null` > > export PATH > > if [ "$PATH" = "L_I_B_T_B_X_E_M_P_T_Y" ]; then unset PATH; fi > > LIBTBX_TMPVAL= > > LIBTBX_OPATH= > > LIBTBX_BUILD= > > > > > > Best Regards, > > Charitha Shetty > > > > *From:* Nigel Moriarty <nwmoriarty(a)lbl.gov> > *Sent:* Monday, August 12, 2019 4:08 PM > *To:* Charitha Belluru Shetty <charitha-belluru.b.shetty(a)gsk.com> > *Cc:* Christopher Williams <christopher.sci.williams(a)gmail.com>; > cctbxbb(a)phenix-online.org; Robert Nolte <robert.t.nolte(a)gsk.com> > *Subject:* Re: Molprobity / CCTBX incompatibility > > > > *EXTERNAL* > > Once you source the setpaths.sh file in the build directory do you have > phenix.reduce or molprobity.reduce? > > Cheers > > > > Nigel > > > > --- > > Nigel W. Moriarty > Building 33R0349, Molecular Biophysics and Integrated Bioimaging > > Lawrence Berkeley National Laboratory > Berkeley, CA 94720-8235 > Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov > Fax : 510-486-5909 Web : CCI.LBL.gov > > > > > > On Mon, Aug 12, 2019 at 12:43 PM Charitha Belluru Shetty < > charitha-belluru.b.shetty(a)gsk.com> wrote: > > Hi Christopher/ Nigel, > > > > Thank you for your quick reply. > > > > The build process was completed without any error. Pasting few of the > lines from it… > > > > > > ===== Running in build: rebuild rotarama > > Processing data files in > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/chem_data/rotarama_data": > > rota8000-cys.data -> rota8000-cys.pickle: converting ... done. > > rota8000-asp.data -> rota8000-asp.pickle: converting ... done. > > rota8000-ser.data -> rota8000-ser.pickle: converting ... done. > > rota8000-gln.data -> rota8000-gln.pickle: converting ... done. > > rota8000-ile.data -> rota8000-ile.pickle: converting ... done. > > rota8000-pro.data -> rota8000-pro.pickle: converting ... done. > > rota8000-lys.data -> rota8000-lys.pickle: converting ... done. > > rota8000-thr.data -> rota8000-thr.pickle: converting ... done. > > rota8000-phetyr.data -> rota8000-phetyr.pickle: converting ... done. > > rota8000-glu.data -> rota8000-glu.pickle: converting ... done. > > rota8000-met.data -> rota8000-met.pickle: converting ... done. > > rota8000-his.data -> rota8000-his.pickle: converting ... done. > > rota8000-leu.data -> rota8000-leu.pickle: converting ... done. > > rota8000-arg.data -> rota8000-arg.pickle: converting ... done. > > rota8000-trp.data -> rota8000-trp.pickle: converting ... done. > > rota8000-asn.data -> rota8000-asn.pickle: converting ... done. > > rota8000-phetyr.data -> rota8000-phetyr.pickle: already up to date. > > rota8000-val.data -> rota8000-val.pickle: converting ... done. > > Processing data files in > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/chem_data/rotarama_data": > > rama8000-ileval-nopreP.data -> rama8000-ileval-nopreP.pickle: converting > ... done. > > rama8000-gly-sym.data -> rama8000-gly-sym.pickle: converting ... done. > > rama8000-cispro.data -> rama8000-cispro.pickle: converting ... done. > > rama8000-general-noGPIVpreP.data -> rama8000-general-noGPIVpreP.pickle: > converting ... done. > > rama8000-transpro.data -> rama8000-transpro.pickle: converting ... done. > > rama8000-prepro-noGP.data -> rama8000-prepro-noGP.pickle: converting ... > done. > > u+s,u,s: 10.06 9.83 0.23 > > ===== Running in .: libtbx.refresh > > Python: 2.7.16 > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/bin/python2.7" > > Compiler: default > > Build mode: release > > Warning level: 0 > > Precompiled Headers: False > > Static libraries: False > > Static exe: False > > Scan Boost headers: False > > Write full flex_fwd.h files: False > > Build Boost.Python extensions: True > > Define BOOST_PYTHON_NO_PY_SIGNATURES: False > > Define BOOST_PYTHON_BOOL_INT_STRICT: True > > Enable OpenMP if possible: False > > Boost threads enabled: True > > Enable CUDA: False > > Use conda: False > > Use opt_resources if available: False > > Use environment flags: False > > Enable C++11: False > > Python3 migration warning policy: None > > command_version_suffix: None > > Relocatable paths anchored at: > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/build > > Top-down list of all modules involved: > > mmtbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx" > > iotbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/iotbx" > > ccp4io+adaptbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/ccp4io" > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/ccp4io_adaptbx" > > smtbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/smtbx" > > ucif > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/ucif" > > cctbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/cctbx" > > scitbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/scitbx" > > fable > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/fable" > > omptbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/omptbx" > > boost+adaptbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/boost" > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/boost_adaptbx" > > tbxx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/tbxx" > > chiltbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/chiltbx" > > libtbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/libtbx" > > Creating files in build directory: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build" > > dispatcher_include_template.sh > > dispatcher_head.sh > > setpaths.sh > > setpaths.csh > > setpaths_all.sh > > setpaths_all.csh > > setpaths_debug.sh > > unsetpaths.sh > > setpaths_debug.csh > > unsetpaths.csh > > SConstruct > > Makefile > > run_tests.csh > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/libtbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/boost_adaptbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/fable/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/scitbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/cctbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/smtbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/iotbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/boost_adaptbx/libtbx_refresh.py" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/scitbx/libtbx_refresh.py" > > Generating C++ header files in: > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/scitbx/array_family" > > Generating C++ files in: > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/scitbx/array_family/boost_python" > > Using fable to convert scitbx/lbfgs.f > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/cctbx/libtbx_refresh.py" > > Generating C++ files in: > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/cctbx/eltbx" > > Generating C++ files in: > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/cctbx/boost_python" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/smtbx/libtbx_refresh.py" > > Generating C++ files in: > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/smtbx/boost_python" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/iotbx/libtbx_refresh.py" > > Using fable to convert iotbx/pdb/hybrid_36_f.f > > Writing: iotbx/pdb/hybrid_36_fem.cpp > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx/libtbx_refresh.py" > > Processing: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/exe_dev" > > Regenerating module files in > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base > > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/etc/pango not present, > could not regenerate pango files > > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/etc/gtk-2.0 not > present, could not regenerate gdk-pixbuf.loaders > > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/etc/fonts not present, > could not rebuild fonts > > generating index.theme file > > Done. > > > > *Bootstrap success: build* > > *++++++++++ MolProbity configure.sh finished.* > > > > > > > > [tm375568@uptus060-3 MolProbity]$ ./setup.sh > > ++++++++++ creating directories ... > > ++++++++++ setting permisions ... > > *Couldn't get a file descriptor referring to the console **à I assume > this can be ignored. * > > [tm375568@uptus060-3 MolProbity]$ > > > > Best Regards, > > Charitha Shetty > > > > *From:* Christopher Williams <christopher.sci.williams(a)gmail.com> > *Sent:* Monday, August 12, 2019 3:34 PM > *To:* Charitha Belluru Shetty <charitha-belluru.b.shetty(a)gsk.com> > *Cc:* Nigel Moriarty (nwmoriarty(a)lbl.gov) <nwmoriarty(a)lbl.gov>; > cctbxbb(a)phenix-online.org; Robert Nolte <robert.t.nolte(a)gsk.com> > *Subject:* Re: Molprobity / CCTBX incompatibility > > > > *EXTERNAL* > > 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. > > > > 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. > > > > It is also possible that there was just a network hiccup that prevented > something from downloading correctly, and a second attempt will work. > > > > I am working on a new configure/install script for more consistent > handling of dependencies. Hopefully it will be ready in about a day. > > > > Good luck, > > -Christopher Williams > > ---Richardson Lab, Duke University > > > > > > > > > > > > *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.* > > *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.* > > *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.* > > *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.* >

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Re: [cctbxbb] Molprobity / CCTBX incompatibility
by Nigel Moriarty 12 Aug '19

12 Aug '19

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. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov On Mon, Aug 12, 2019 at 2:44 PM Robert Nolte <robert.t.nolte(a)gsk.com> wrote: > Nigel, > > Currently it is not running. This was working from the scratch > install last week. I am not sure what is going on now. > > Bob > > > > > > *From:* Nigel Moriarty <nwmoriarty(a)lbl.gov> > *Sent:* Monday, August 12, 2019 4:52 PM > *To:* Charitha Belluru Shetty <charitha-belluru.b.shetty(a)gsk.com> > *Cc:* Christopher Williams <christopher.sci.williams(a)gmail.com>; > cctbxbb(a)phenix-online.org; Robert Nolte <robert.t.nolte(a)gsk.com> > *Subject:* Re: Molprobity / CCTBX incompatibility > > > > *EXTERNAL* > > Does molprobity.reduce run? > > > Cheers > > > > Nigel > > > > --- > > Nigel W. Moriarty > Building 33R0349, Molecular Biophysics and Integrated Bioimaging > > Lawrence Berkeley National Laboratory > Berkeley, CA 94720-8235 > Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov > Fax : 510-486-5909 Web : CCI.LBL.gov > > > > > > On Mon, Aug 12, 2019 at 1:14 PM Charitha Belluru Shetty < > charitha-belluru.b.shetty(a)gsk.com> wrote: > > Hi Nigel, > > > > I hit the send button too soon..Ignore my previous email 😊 > > > > -bash-4.2$ source setpaths.sh > > -bash-4.2$ > > -bash-4.2$ env |grep -i reduce > > -bash-4.2$ > > > > So the “setpath.sh” has the below contents… > > > > $ cat /hpc/apps/current/molprobity/v4.4.app/MolProbity/build/setpaths.sh > > # THIS IS AN AUTOMATICALLY GENERATED FILE. > > # DO NOT EDIT! CHANGES WILL BE LOST. > > ocwd="`pwd`" > > if [ -n "$LIBTBX_BUILD_RELOCATION_HINT" ]; then > > cd "$LIBTBX_BUILD_RELOCATION_HINT" > > LIBTBX_BUILD_RELOCATION_HINT= > > export LIBTBX_BUILD_RELOCATION_HINT > > elif [ -n "$BASH_SOURCE" ]; then > > LIBTBX_BUILD=`dirname "$BASH_SOURCE[0]"` > > cd "$LIBTBX_BUILD" > > else > > cd "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build" > > fi > > LIBTBX_BUILD=`pwd -P` > > export LIBTBX_BUILD > > LIBTBX_OPATH="$PATH" > > export LIBTBX_OPATH > > PATH="$LIBTBX_BUILD/bin:$PATH" > > export PATH > > cd "$ocwd" > > ocwd= > > alias libtbx.setpaths_all=". \"$LIBTBX_BUILD/setpaths_all.sh\"" > > alias libtbx.unsetpaths=". \"$LIBTBX_BUILD/unsetpaths.sh\"" > > if [ -n "$LIBTBX_OPATH" ]; then > > LIBTBX_TMPVAL="$LIBTBX_OPATH" > > else > > LIBTBX_TMPVAL= > > fi > > export LIBTBX_TMPVAL > > PATH=`libtbx.path_utility prepend LIBTBX_TMPVAL "$LIBTBX_BUILD/bin" < > /dev/null` > > export PATH > > if [ "$PATH" = "L_I_B_T_B_X_E_M_P_T_Y" ]; then unset PATH; fi > > LIBTBX_TMPVAL= > > LIBTBX_OPATH= > > LIBTBX_BUILD= > > > > > > Best Regards, > > Charitha Shetty > > > > *From:* Nigel Moriarty <nwmoriarty(a)lbl.gov> > *Sent:* Monday, August 12, 2019 4:08 PM > *To:* Charitha Belluru Shetty <charitha-belluru.b.shetty(a)gsk.com> > *Cc:* Christopher Williams <christopher.sci.williams(a)gmail.com>; > cctbxbb(a)phenix-online.org; Robert Nolte <robert.t.nolte(a)gsk.com> > *Subject:* Re: Molprobity / CCTBX incompatibility > > > > *EXTERNAL* > > Once you source the setpaths.sh file in the build directory do you have > phenix.reduce or molprobity.reduce? > > Cheers > > > > Nigel > > > > --- > > Nigel W. Moriarty > Building 33R0349, Molecular Biophysics and Integrated Bioimaging > > Lawrence Berkeley National Laboratory > Berkeley, CA 94720-8235 > Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov > Fax : 510-486-5909 Web : CCI.LBL.gov > > > > > > On Mon, Aug 12, 2019 at 12:43 PM Charitha Belluru Shetty < > charitha-belluru.b.shetty(a)gsk.com> wrote: > > Hi Christopher/ Nigel, > > > > Thank you for your quick reply. > > > > The build process was completed without any error. Pasting few of the > lines from it… > > > > > > ===== Running in build: rebuild rotarama > > Processing data files in > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/chem_data/rotarama_data": > > rota8000-cys.data -> rota8000-cys.pickle: converting ... done. > > rota8000-asp.data -> rota8000-asp.pickle: converting ... done. > > rota8000-ser.data -> rota8000-ser.pickle: converting ... done. > > rota8000-gln.data -> rota8000-gln.pickle: converting ... done. > > rota8000-ile.data -> rota8000-ile.pickle: converting ... done. > > rota8000-pro.data -> rota8000-pro.pickle: converting ... done. > > rota8000-lys.data -> rota8000-lys.pickle: converting ... done. > > rota8000-thr.data -> rota8000-thr.pickle: converting ... done. > > rota8000-phetyr.data -> rota8000-phetyr.pickle: converting ... done. > > rota8000-glu.data -> rota8000-glu.pickle: converting ... done. > > rota8000-met.data -> rota8000-met.pickle: converting ... done. > > rota8000-his.data -> rota8000-his.pickle: converting ... done. > > rota8000-leu.data -> rota8000-leu.pickle: converting ... done. > > rota8000-arg.data -> rota8000-arg.pickle: converting ... done. > > rota8000-trp.data -> rota8000-trp.pickle: converting ... done. > > rota8000-asn.data -> rota8000-asn.pickle: converting ... done. > > rota8000-phetyr.data -> rota8000-phetyr.pickle: already up to date. > > rota8000-val.data -> rota8000-val.pickle: converting ... done. > > Processing data files in > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/chem_data/rotarama_data": > > rama8000-ileval-nopreP.data -> rama8000-ileval-nopreP.pickle: converting > ... done. > > rama8000-gly-sym.data -> rama8000-gly-sym.pickle: converting ... done. > > rama8000-cispro.data -> rama8000-cispro.pickle: converting ... done. > > rama8000-general-noGPIVpreP.data -> rama8000-general-noGPIVpreP.pickle: > converting ... done. > > rama8000-transpro.data -> rama8000-transpro.pickle: converting ... done. > > rama8000-prepro-noGP.data -> rama8000-prepro-noGP.pickle: converting ... > done. > > u+s,u,s: 10.06 9.83 0.23 > > ===== Running in .: libtbx.refresh > > Python: 2.7.16 > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/bin/python2.7" > > Compiler: default > > Build mode: release > > Warning level: 0 > > Precompiled Headers: False > > Static libraries: False > > Static exe: False > > Scan Boost headers: False > > Write full flex_fwd.h files: False > > Build Boost.Python extensions: True > > Define BOOST_PYTHON_NO_PY_SIGNATURES: False > > Define BOOST_PYTHON_BOOL_INT_STRICT: True > > Enable OpenMP if possible: False > > Boost threads enabled: True > > Enable CUDA: False > > Use conda: False > > Use opt_resources if available: False > > Use environment flags: False > > Enable C++11: False > > Python3 migration warning policy: None > > command_version_suffix: None > > Relocatable paths anchored at: > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/build > > Top-down list of all modules involved: > > mmtbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx" > > iotbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/iotbx" > > ccp4io+adaptbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/ccp4io" > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/ccp4io_adaptbx" > > smtbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/smtbx" > > ucif > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/ucif" > > cctbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/cctbx" > > scitbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/scitbx" > > fable > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/fable" > > omptbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/omptbx" > > boost+adaptbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/boost" > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/boost_adaptbx" > > tbxx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/tbxx" > > chiltbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/chiltbx" > > libtbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/libtbx" > > Creating files in build directory: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build" > > dispatcher_include_template.sh > > dispatcher_head.sh > > setpaths.sh > > setpaths.csh > > setpaths_all.sh > > setpaths_all.csh > > setpaths_debug.sh > > unsetpaths.sh > > setpaths_debug.csh > > unsetpaths.csh > > SConstruct > > Makefile > > run_tests.csh > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/libtbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/boost_adaptbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/fable/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/scitbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/cctbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/smtbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/iotbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/boost_adaptbx/libtbx_refresh.py" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/scitbx/libtbx_refresh.py" > > Generating C++ header files in: > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/scitbx/array_family" > > Generating C++ files in: > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/scitbx/array_family/boost_python" > > Using fable to convert scitbx/lbfgs.f > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/cctbx/libtbx_refresh.py" > > Generating C++ files in: > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/cctbx/eltbx" > > Generating C++ files in: > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/cctbx/boost_python" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/smtbx/libtbx_refresh.py" > > Generating C++ files in: > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/smtbx/boost_python" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/iotbx/libtbx_refresh.py" > > Using fable to convert iotbx/pdb/hybrid_36_f.f > > Writing: iotbx/pdb/hybrid_36_fem.cpp > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx/libtbx_refresh.py" > > Processing: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/exe_dev" > > Regenerating module files in > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base > > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/etc/pango not present, > could not regenerate pango files > > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/etc/gtk-2.0 not > present, could not regenerate gdk-pixbuf.loaders > > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/etc/fonts not present, > could not rebuild fonts > > generating index.theme file > > Done. > > > > *Bootstrap success: build* > > *++++++++++ MolProbity configure.sh finished.* > > > > > > > > [tm375568@uptus060-3 MolProbity]$ ./setup.sh > > ++++++++++ creating directories ... > > ++++++++++ setting permisions ... > > *Couldn't get a file descriptor referring to the console **à I assume > this can be ignored. * > > [tm375568@uptus060-3 MolProbity]$ > > > > Best Regards, > > Charitha Shetty > > > > *From:* Christopher Williams <christopher.sci.williams(a)gmail.com> > *Sent:* Monday, August 12, 2019 3:34 PM > *To:* Charitha Belluru Shetty <charitha-belluru.b.shetty(a)gsk.com> > *Cc:* Nigel Moriarty (nwmoriarty(a)lbl.gov) <nwmoriarty(a)lbl.gov>; > cctbxbb(a)phenix-online.org; Robert Nolte <robert.t.nolte(a)gsk.com> > *Subject:* Re: Molprobity / CCTBX incompatibility > > > > *EXTERNAL* > > 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. > > > > 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. > > > > It is also possible that there was just a network hiccup that prevented > something from downloading correctly, and a second attempt will work. > > > > I am working on a new configure/install script for more consistent > handling of dependencies. Hopefully it will be ready in about a day. > > > > Good luck, > > -Christopher Williams > > ---Richardson Lab, Duke University > > > > > > > > > > > > *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.* > > *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.* > > *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.* >

1 0

Re: [cctbxbb] Molprobity / CCTBX incompatibility
by Nigel Moriarty 12 Aug '19

12 Aug '19

Does molprobity.reduce run? Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov On Mon, Aug 12, 2019 at 1:14 PM Charitha Belluru Shetty < charitha-belluru.b.shetty(a)gsk.com> wrote: > Hi Nigel, > > > > I hit the send button too soon..Ignore my previous email 😊 > > > > -bash-4.2$ source setpaths.sh > > -bash-4.2$ > > -bash-4.2$ env |grep -i reduce > > -bash-4.2$ > > > > So the “setpath.sh” has the below contents… > > > > $ cat /hpc/apps/current/molprobity/v4.4.app/MolProbity/build/setpaths.sh > > # THIS IS AN AUTOMATICALLY GENERATED FILE. > > # DO NOT EDIT! CHANGES WILL BE LOST. > > ocwd="`pwd`" > > if [ -n "$LIBTBX_BUILD_RELOCATION_HINT" ]; then > > cd "$LIBTBX_BUILD_RELOCATION_HINT" > > LIBTBX_BUILD_RELOCATION_HINT= > > export LIBTBX_BUILD_RELOCATION_HINT > > elif [ -n "$BASH_SOURCE" ]; then > > LIBTBX_BUILD=`dirname "$BASH_SOURCE[0]"` > > cd "$LIBTBX_BUILD" > > else > > cd "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build" > > fi > > LIBTBX_BUILD=`pwd -P` > > export LIBTBX_BUILD > > LIBTBX_OPATH="$PATH" > > export LIBTBX_OPATH > > PATH="$LIBTBX_BUILD/bin:$PATH" > > export PATH > > cd "$ocwd" > > ocwd= > > alias libtbx.setpaths_all=". \"$LIBTBX_BUILD/setpaths_all.sh\"" > > alias libtbx.unsetpaths=". \"$LIBTBX_BUILD/unsetpaths.sh\"" > > if [ -n "$LIBTBX_OPATH" ]; then > > LIBTBX_TMPVAL="$LIBTBX_OPATH" > > else > > LIBTBX_TMPVAL= > > fi > > export LIBTBX_TMPVAL > > PATH=`libtbx.path_utility prepend LIBTBX_TMPVAL "$LIBTBX_BUILD/bin" < > /dev/null` > > export PATH > > if [ "$PATH" = "L_I_B_T_B_X_E_M_P_T_Y" ]; then unset PATH; fi > > LIBTBX_TMPVAL= > > LIBTBX_OPATH= > > LIBTBX_BUILD= > > > > > > Best Regards, > > Charitha Shetty > > > > *From:* Nigel Moriarty <nwmoriarty(a)lbl.gov> > *Sent:* Monday, August 12, 2019 4:08 PM > *To:* Charitha Belluru Shetty <charitha-belluru.b.shetty(a)gsk.com> > *Cc:* Christopher Williams <christopher.sci.williams(a)gmail.com>; > cctbxbb(a)phenix-online.org; Robert Nolte <robert.t.nolte(a)gsk.com> > *Subject:* Re: Molprobity / CCTBX incompatibility > > > > *EXTERNAL* > > Once you source the setpaths.sh file in the build directory do you have > phenix.reduce or molprobity.reduce? > > Cheers > > > > Nigel > > > > --- > > Nigel W. Moriarty > Building 33R0349, Molecular Biophysics and Integrated Bioimaging > > Lawrence Berkeley National Laboratory > Berkeley, CA 94720-8235 > Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov > Fax : 510-486-5909 Web : CCI.LBL.gov > > > > > > On Mon, Aug 12, 2019 at 12:43 PM Charitha Belluru Shetty < > charitha-belluru.b.shetty(a)gsk.com> wrote: > > Hi Christopher/ Nigel, > > > > Thank you for your quick reply. > > > > The build process was completed without any error. Pasting few of the > lines from it… > > > > > > ===== Running in build: rebuild rotarama > > Processing data files in > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/chem_data/rotarama_data": > > rota8000-cys.data -> rota8000-cys.pickle: converting ... done. > > rota8000-asp.data -> rota8000-asp.pickle: converting ... done. > > rota8000-ser.data -> rota8000-ser.pickle: converting ... done. > > rota8000-gln.data -> rota8000-gln.pickle: converting ... done. > > rota8000-ile.data -> rota8000-ile.pickle: converting ... done. > > rota8000-pro.data -> rota8000-pro.pickle: converting ... done. > > rota8000-lys.data -> rota8000-lys.pickle: converting ... done. > > rota8000-thr.data -> rota8000-thr.pickle: converting ... done. > > rota8000-phetyr.data -> rota8000-phetyr.pickle: converting ... done. > > rota8000-glu.data -> rota8000-glu.pickle: converting ... done. > > rota8000-met.data -> rota8000-met.pickle: converting ... done. > > rota8000-his.data -> rota8000-his.pickle: converting ... done. > > rota8000-leu.data -> rota8000-leu.pickle: converting ... done. > > rota8000-arg.data -> rota8000-arg.pickle: converting ... done. > > rota8000-trp.data -> rota8000-trp.pickle: converting ... done. > > rota8000-asn.data -> rota8000-asn.pickle: converting ... done. > > rota8000-phetyr.data -> rota8000-phetyr.pickle: already up to date. > > rota8000-val.data -> rota8000-val.pickle: converting ... done. > > Processing data files in > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/chem_data/rotarama_data": > > rama8000-ileval-nopreP.data -> rama8000-ileval-nopreP.pickle: converting > ... done. > > rama8000-gly-sym.data -> rama8000-gly-sym.pickle: converting ... done. > > rama8000-cispro.data -> rama8000-cispro.pickle: converting ... done. > > rama8000-general-noGPIVpreP.data -> rama8000-general-noGPIVpreP.pickle: > converting ... done. > > rama8000-transpro.data -> rama8000-transpro.pickle: converting ... done. > > rama8000-prepro-noGP.data -> rama8000-prepro-noGP.pickle: converting ... > done. > > u+s,u,s: 10.06 9.83 0.23 > > ===== Running in .: libtbx.refresh > > Python: 2.7.16 > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/bin/python2.7" > > Compiler: default > > Build mode: release > > Warning level: 0 > > Precompiled Headers: False > > Static libraries: False > > Static exe: False > > Scan Boost headers: False > > Write full flex_fwd.h files: False > > Build Boost.Python extensions: True > > Define BOOST_PYTHON_NO_PY_SIGNATURES: False > > Define BOOST_PYTHON_BOOL_INT_STRICT: True > > Enable OpenMP if possible: False > > Boost threads enabled: True > > Enable CUDA: False > > Use conda: False > > Use opt_resources if available: False > > Use environment flags: False > > Enable C++11: False > > Python3 migration warning policy: None > > command_version_suffix: None > > Relocatable paths anchored at: > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/build > > Top-down list of all modules involved: > > mmtbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx" > > iotbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/iotbx" > > ccp4io+adaptbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/ccp4io" > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/ccp4io_adaptbx" > > smtbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/smtbx" > > ucif > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/ucif" > > cctbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/cctbx" > > scitbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/scitbx" > > fable > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/fable" > > omptbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/omptbx" > > boost+adaptbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/boost" > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/boost_adaptbx" > > tbxx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/tbxx" > > chiltbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/chiltbx" > > libtbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/libtbx" > > Creating files in build directory: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build" > > dispatcher_include_template.sh > > dispatcher_head.sh > > setpaths.sh > > setpaths.csh > > setpaths_all.sh > > setpaths_all.csh > > setpaths_debug.sh > > unsetpaths.sh > > setpaths_debug.csh > > unsetpaths.csh > > SConstruct > > Makefile > > run_tests.csh > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/libtbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/boost_adaptbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/fable/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/scitbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/cctbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/smtbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/iotbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/boost_adaptbx/libtbx_refresh.py" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/scitbx/libtbx_refresh.py" > > Generating C++ header files in: > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/scitbx/array_family" > > Generating C++ files in: > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/scitbx/array_family/boost_python" > > Using fable to convert scitbx/lbfgs.f > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/cctbx/libtbx_refresh.py" > > Generating C++ files in: > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/cctbx/eltbx" > > Generating C++ files in: > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/cctbx/boost_python" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/smtbx/libtbx_refresh.py" > > Generating C++ files in: > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/smtbx/boost_python" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/iotbx/libtbx_refresh.py" > > Using fable to convert iotbx/pdb/hybrid_36_f.f > > Writing: iotbx/pdb/hybrid_36_fem.cpp > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx/libtbx_refresh.py" > > Processing: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/exe_dev" > > Regenerating module files in > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base > > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/etc/pango not present, > could not regenerate pango files > > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/etc/gtk-2.0 not > present, could not regenerate gdk-pixbuf.loaders > > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/etc/fonts not present, > could not rebuild fonts > > generating index.theme file > > Done. > > > > *Bootstrap success: build* > > *++++++++++ MolProbity configure.sh finished.* > > > > > > > > [tm375568@uptus060-3 MolProbity]$ ./setup.sh > > ++++++++++ creating directories ... > > ++++++++++ setting permisions ... > > *Couldn't get a file descriptor referring to the console **à I assume > this can be ignored. * > > [tm375568@uptus060-3 MolProbity]$ > > > > Best Regards, > > Charitha Shetty > > > > *From:* Christopher Williams <christopher.sci.williams(a)gmail.com> > *Sent:* Monday, August 12, 2019 3:34 PM > *To:* Charitha Belluru Shetty <charitha-belluru.b.shetty(a)gsk.com> > *Cc:* Nigel Moriarty (nwmoriarty(a)lbl.gov) <nwmoriarty(a)lbl.gov>; > cctbxbb(a)phenix-online.org; Robert Nolte <robert.t.nolte(a)gsk.com> > *Subject:* Re: Molprobity / CCTBX incompatibility > > > > *EXTERNAL* > > 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. > > > > 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. > > > > It is also possible that there was just a network hiccup that prevented > something from downloading correctly, and a second attempt will work. > > > > I am working on a new configure/install script for more consistent > handling of dependencies. Hopefully it will be ready in about a day. > > > > Good luck, > > -Christopher Williams > > ---Richardson Lab, Duke University > > > > > > > > > > > > *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.* > > *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.* >

1 0

Re: [cctbxbb] Molprobity / CCTBX incompatibility
by Nigel Moriarty 12 Aug '19

12 Aug '19

Once you source the setpaths.sh file in the build directory do you have phenix.reduce or molprobity.reduce? Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov On Mon, Aug 12, 2019 at 12:43 PM Charitha Belluru Shetty < charitha-belluru.b.shetty(a)gsk.com> wrote: > Hi Christopher/ Nigel, > > > > Thank you for your quick reply. > > > > The build process was completed without any error. Pasting few of the > lines from it… > > > > > > ===== Running in build: rebuild rotarama > > Processing data files in > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/chem_data/rotarama_data": > > rota8000-cys.data -> rota8000-cys.pickle: converting ... done. > > rota8000-asp.data -> rota8000-asp.pickle: converting ... done. > > rota8000-ser.data -> rota8000-ser.pickle: converting ... done. > > rota8000-gln.data -> rota8000-gln.pickle: converting ... done. > > rota8000-ile.data -> rota8000-ile.pickle: converting ... done. > > rota8000-pro.data -> rota8000-pro.pickle: converting ... done. > > rota8000-lys.data -> rota8000-lys.pickle: converting ... done. > > rota8000-thr.data -> rota8000-thr.pickle: converting ... done. > > rota8000-phetyr.data -> rota8000-phetyr.pickle: converting ... done. > > rota8000-glu.data -> rota8000-glu.pickle: converting ... done. > > rota8000-met.data -> rota8000-met.pickle: converting ... done. > > rota8000-his.data -> rota8000-his.pickle: converting ... done. > > rota8000-leu.data -> rota8000-leu.pickle: converting ... done. > > rota8000-arg.data -> rota8000-arg.pickle: converting ... done. > > rota8000-trp.data -> rota8000-trp.pickle: converting ... done. > > rota8000-asn.data -> rota8000-asn.pickle: converting ... done. > > rota8000-phetyr.data -> rota8000-phetyr.pickle: already up to date. > > rota8000-val.data -> rota8000-val.pickle: converting ... done. > > Processing data files in > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/chem_data/rotarama_data": > > rama8000-ileval-nopreP.data -> rama8000-ileval-nopreP.pickle: converting > ... done. > > rama8000-gly-sym.data -> rama8000-gly-sym.pickle: converting ... done. > > rama8000-cispro.data -> rama8000-cispro.pickle: converting ... done. > > rama8000-general-noGPIVpreP.data -> rama8000-general-noGPIVpreP.pickle: > converting ... done. > > rama8000-transpro.data -> rama8000-transpro.pickle: converting ... done. > > rama8000-prepro-noGP.data -> rama8000-prepro-noGP.pickle: converting ... > done. > > u+s,u,s: 10.06 9.83 0.23 > > ===== Running in .: libtbx.refresh > > Python: 2.7.16 > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/bin/python2.7" > > Compiler: default > > Build mode: release > > Warning level: 0 > > Precompiled Headers: False > > Static libraries: False > > Static exe: False > > Scan Boost headers: False > > Write full flex_fwd.h files: False > > Build Boost.Python extensions: True > > Define BOOST_PYTHON_NO_PY_SIGNATURES: False > > Define BOOST_PYTHON_BOOL_INT_STRICT: True > > Enable OpenMP if possible: False > > Boost threads enabled: True > > Enable CUDA: False > > Use conda: False > > Use opt_resources if available: False > > Use environment flags: False > > Enable C++11: False > > Python3 migration warning policy: None > > command_version_suffix: None > > Relocatable paths anchored at: > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/build > > Top-down list of all modules involved: > > mmtbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx" > > iotbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/iotbx" > > ccp4io+adaptbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/ccp4io" > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/ccp4io_adaptbx" > > smtbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/smtbx" > > ucif > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/ucif" > > cctbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/cctbx" > > scitbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/scitbx" > > fable > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/fable" > > omptbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/omptbx" > > boost+adaptbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/boost" > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/boost_adaptbx" > > tbxx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/tbxx" > > chiltbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/chiltbx" > > libtbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/libtbx" > > Creating files in build directory: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build" > > dispatcher_include_template.sh > > dispatcher_head.sh > > setpaths.sh > > setpaths.csh > > setpaths_all.sh > > setpaths_all.csh > > setpaths_debug.sh > > unsetpaths.sh > > setpaths_debug.csh > > unsetpaths.csh > > SConstruct > > Makefile > > run_tests.csh > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/libtbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/boost_adaptbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/fable/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/scitbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/cctbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/smtbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/iotbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/boost_adaptbx/libtbx_refresh.py" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/scitbx/libtbx_refresh.py" > > Generating C++ header files in: > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/scitbx/array_family" > > Generating C++ files in: > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/scitbx/array_family/boost_python" > > Using fable to convert scitbx/lbfgs.f > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/cctbx/libtbx_refresh.py" > > Generating C++ files in: > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/cctbx/eltbx" > > Generating C++ files in: > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/cctbx/boost_python" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/smtbx/libtbx_refresh.py" > > Generating C++ files in: > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/smtbx/boost_python" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/iotbx/libtbx_refresh.py" > > Using fable to convert iotbx/pdb/hybrid_36_f.f > > Writing: iotbx/pdb/hybrid_36_fem.cpp > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx/libtbx_refresh.py" > > Processing: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/exe_dev" > > Regenerating module files in > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base > > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/etc/pango not present, > could not regenerate pango files > > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/etc/gtk-2.0 not > present, could not regenerate gdk-pixbuf.loaders > > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/etc/fonts not present, > could not rebuild fonts > > generating index.theme file > > Done. > > > > *Bootstrap success: build* > > *++++++++++ MolProbity configure.sh finished.* > > > > > > > > [tm375568@uptus060-3 MolProbity]$ ./setup.sh > > ++++++++++ creating directories ... > > ++++++++++ setting permisions ... > > *Couldn't get a file descriptor referring to the console **à** I assume > this can be ignored.* > > [tm375568@uptus060-3 MolProbity]$ > > > > Best Regards, > > Charitha Shetty > > > > *From:* Christopher Williams <christopher.sci.williams(a)gmail.com> > *Sent:* Monday, August 12, 2019 3:34 PM > *To:* Charitha Belluru Shetty <charitha-belluru.b.shetty(a)gsk.com> > *Cc:* Nigel Moriarty (nwmoriarty(a)lbl.gov) <nwmoriarty(a)lbl.gov>; > cctbxbb(a)phenix-online.org; Robert Nolte <robert.t.nolte(a)gsk.com> > *Subject:* Re: Molprobity / CCTBX incompatibility > > > > *EXTERNAL* > > 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. > > > > 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. > > > > It is also possible that there was just a network hiccup that prevented > something from downloading correctly, and a second attempt will work. > > > > I am working on a new configure/install script for more consistent > handling of dependencies. Hopefully it will be ready in about a day. > > > > Good luck, > > -Christopher Williams > > ---Richardson Lab, Duke University > > > > > > > > > > > > *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.* >

1 0

Re: [cctbxbb] Molprobity / CCTBX incompatibility
by Nigel Moriarty 12 Aug '19

12 Aug '19

Not sure about the selection problem but the missing commands are likely molprobity.reduce and molprobity.probe. Chris, you should be able to change that. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov On Mon, Aug 12, 2019 at 11:43 AM Charitha Belluru Shetty < charitha-belluru.b.shetty(a)gsk.com> wrote: > Hi Christopher/Nigel, > > > > We downloaded the molprobity after the patch and ran the configure.sh and > setup scripts. Now things got worst. > > > > Can you please help us on this. > > > > Here is the output we are getting. > > > > > > > > > > > > > > When we press the *“Click here”* button, below log file is generated. > > > > [PLACE YOUR COMMENTS HERE] > > > > ================================================== > > USER / SERVER INFORMATION > > ================================================== > > User IP : 11.27.95.128 > > User browser : Mozilla/5.0 (Windows NT 10.0; Win64; x64) > AppleWebKit/537.36 (KHTML, like Gecko) Chrome/76.0.3809.100 Safari/537.36 > > Session ID : c2h8n399dagb0ggfn8kpla6fu4 > > Session URL : > http://uptus002vm.corpnet2.com/molprobity/index.php?MolProbSID=c2h8n399dagb… > > > > MolProb. ver. : 4.4 > > Server name : uptus002vm.corpnet2.com > > Server time : 2019 Aug 12 18:24:41 > > > > ================================================== > > ERRORS FROM THIS SESSION > > ================================================== > > > > > > sh: phenix.reduce: command not found > > sh: phenix.reduce: command not found > > sh: phenix.reduce: command not found > > sh: phenix.probe: command not found > > sh: phenix.probe: command not found > > sh: phenix.reduce: command not found > > sh: phenix.reduce: command not found > > sh: phenix.probe: command not found > > sh: phenix.probe: command not found > > > > Starting phenix.clashscore > > on Mon Aug 12 13:50:31 2019 by appmgmt > > > =============================================================================== > > > > Processing files: > > > ------------------------------------------------------------------------------- > > > > Files not used by program: > > -------------------------- > > > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/public_html/data/c2h8n399dagb0ggfn8kpla6fu4/coordinates/1irkFH.pdb > > > > Processing PHIL parameters: > > > ------------------------------------------------------------------------------- > > > > Adding command-line PHIL: > > ------------------------- > > b_factor_cutoff=40 > > clash_cutoff=-0.4 > > > > Final processed PHIL parameters: > > > ------------------------------------------------------------------------------- > > data_manager { > > default_output_filename = "cctbx_program" > > } > > b_factor_cutoff = 40 > > > > > > Starting job > > > =============================================================================== > > Sorry: 0 model(s) found. Expected at least 1. > > chartClashlist ran for 5 seconds > > do Charts ran for 0 seconds > > sh: phenix.probe: command not found > > do Kinemage ran for 0 seconds > > > > Traceback (most recent call last): > > File > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/../modules/cctbx_project/mmtbx/command_line/mp_geo.py", > line 7, in <module> > > mp_geo.run(sys.argv[1:]) > > File > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx/validation/molprobity/mp_geo.py", > line 132, in run > > pdb_hierarchy.models()[0].chains(): > > IndexError: list index out of range > > > > > > > > > > sh: phenix.reduce: command not found > > > > sh: phenix.reduce: command not found > > > > sh: phenix.reduce: command not found > > > > sh: phenix.probe: command not found > > > > sh: phenix.probe: command not found > > > > sh: phenix.reduce: command not found > > > > sh: phenix.reduce: command not found > > > > sh: phenix.probe: command not found > > > > sh: phenix.probe: command not found > > > > > > > > Starting phenix.clashscore > > > > on Mon Aug 12 13:50:31 2019 by appmgmt > > > > > =============================================================================== > > > > > > > > Processing files: > > > > > ------------------------------------------------------------------------------- > > > > > > > > Files not used by program: > > > > -------------------------- > > > > > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/public_html/data/c2h8n399dagb0ggfn8kpla6fu4/coordinates/1irkFH.pdb > > > > > > > > Processing PHIL parameters: > > > > > ------------------------------------------------------------------------------- > > > > > > > > Adding command-line PHIL: > > > > ------------------------- > > > > b_factor_cutoff=40 > > > > clash_cutoff=-0.4 > > > > > > > > Final processed PHIL parameters: > > > > > ------------------------------------------------------------------------------- > > > > data_manager { > > > > default_output_filename = "cctbx_program" > > > > } > > > > b_factor_cutoff = 40 > > > > > > > > > > > > Starting job > > > > > =============================================================================== > > > > Sorry: 0 model(s) found. Expected at least 1. > > > > chartClashlist ran for 5 seconds > > > > do Charts ran for 0 seconds > > > > sh: phenix.probe: command not found > > > > do Kinemage ran for 0 seconds > > > > > > > > Traceback (most recent call last): > > > > File > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/../modules/cctbx_project/mmtbx/command_line/mp_geo.py", > line 7, in <module> > > > > mp_geo.run(sys.argv[1:]) > > > > File > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx/validation/molprobity/mp_geo.py", > line 132, in run > > > > pdb_hierarchy.models()[0].chains(): > > > > IndexError: list index out of range > > > > > > > > > > > > sh: phenix.reduce: command not found > > > > sh: phenix.reduce: command not found > > > > sh: phenix.reduce: command not found > > > > sh: phenix.probe: command not found > > > > sh: phenix.probe: command not found > > > > sh: phenix.reduce: command not found > > > > sh: phenix.reduce: command not found > > > > sh: phenix.probe: command not found > > > > sh: phenix.probe: command not found > > > > > > > > Starting phenix.clashscore > > > > on Mon Aug 12 13:50:31 2019 by appmgmt > > > > > =============================================================================== > > > > > > > > Processing files: > > > > > ------------------------------------------------------------------------------- > > > > > > > > Files not used by program: > > > > -------------------------- > > > > > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/public_html/data/c2h8n399dagb0ggfn8kpla6fu4/coordinates/1irkFH.pdb > > > > > > > > Processing PHIL parameters: > > > > > ------------------------------------------------------------------------------- > > > > > > > > Adding command-line PHIL: > > > > ------------------------- > > > > b_factor_cutoff=40 > > > > clash_cutoff=-0.4 > > > > > > > > Final processed PHIL parameters: > > > > > ------------------------------------------------------------------------------- > > > > data_manager { > > > > default_output_filename = "cctbx_program" > > > > } > > > > b_factor_cutoff = 40 > > > > > > > > > > > > Starting job > > > > > =============================================================================== > > > > Sorry: 0 model(s) found. Expected at least 1. > > > > chartClashlist ran for 5 seconds > > > > do Charts ran for 0 seconds > > > > sh: phenix.probe: command not found > > > > do Kinemage ran for 0 seconds > > > > > > > > Traceback (most recent call last): > > > > File > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/../modules/cctbx_project/mmtbx/command_line/mp_geo.py", > line 7, in <module> > > > > mp_geo.run(sys.argv[1:]) > > > > File > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx/validation/molprobity/mp_geo.py", > line 132, in run > > > > pdb_hierarchy.models()[0].chains(): > > > > IndexError: list index out of range > > > > > > > > > > > > > > > > > > > > sh: phenix.reduce: command not found > > > > > > > > sh: phenix.reduce: command not found > > > > > > > > sh: phenix.reduce: command not found > > > > > > > > sh: phenix.probe: command not found > > > > > > > > sh: phenix.probe: command not found > > > > > > > > sh: phenix.reduce: command not found > > > > > > > > sh: phenix.reduce: command not found > > > > > > > > sh: phenix.probe: command not found > > > > > > > > sh: phenix.probe: command not found > > > > > > > > > > > > > > > > Starting phenix.clashscore > > > > > > > > on Mon Aug 12 13:50:31 2019 by appmgmt > > > > > > > > > =============================================================================== > > > > > > > > > > > > > > > > Processing files: > > > > > > > > > ------------------------------------------------------------------------------- > > > > > > > > > > > > > > > > Files not used by program: > > > > > > > > -------------------------- > > > > > > > > > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/public_html/data/c2h8n399dagb0ggfn8kpla6fu4/coordinates/1irkFH.pdb > > > > > > > > > > > > > > > > Processing PHIL parameters: > > > > > > > > > ------------------------------------------------------------------------------- > > > > > > > > > > > > > > > > Adding command-line PHIL: > > > > > > > > ------------------------- > > > > > > > > b_factor_cutoff=40 > > > > > > > > clash_cutoff=-0.4 > > > > > > > > > > > > > > > > Final processed PHIL parameters: > > > > > > > > > ------------------------------------------------------------------------------- > > > > > > > > data_manager { > > > > > > > > default_output_filename = "cctbx_program" > > > > > > > > } > > > > > > > > b_factor_cutoff = 40 > > > > > > > > > > > > > > > > > > > > > > > > Starting job > > > > > > > > > =============================================================================== > > > > > > > > Sorry: 0 model(s) found. Expected at least 1. > > > > > > > > chartClashlist ran for 5 seconds > > > > > > > > do Charts ran for 0 seconds > > > > > > > > sh: phenix.probe: command not found > > > > > > > > do Kinemage ran for 0 seconds > > > > > > > > > > > > > > > > Traceback (most recent call last): > > > > > > > > File > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/../modules/cctbx_project/mmtbx/command_line/mp_geo.py", > line 7, in <module> > > > > > > > > mp_geo.run(sys.argv[1:]) > > > > > > > > File > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx/validation/molprobity/mp_geo.py", > line 132, in run > > > > > > > > pdb_hierarchy.models()[0].chains(): > > > > > > > > IndexError: list index out of range > > > > > > Best Regards, > > Charitha Shetty > > > > *From:* Robert Nolte > *Sent:* Sunday, August 11, 2019 12:39 PM > *To:* Nigel Moriarty (nwmoriarty(a)lbl.gov) <nwmoriarty(a)lbl.gov>; > cctbxbb(a)phenix-online.org > *Cc:* Charitha Belluru Shetty <charitha-belluru.b.shetty(a)gsk.com> > *Subject:* Molprobity / CCTBX incompatibility > > > > We are trying to reinstall our internal molprobity server, and have hit an > issue with the github version where it appears to be a version conflict > with the version of cctbx that is currently being downloaded by > configuration script in the master branch of molprobity. We are getting > errors when we run the validation routine such as > > > > Unrecogized PHIL parameter: data_version=8000 > > > > or > > > > Unrecognized PHIL parameter: clash_cutoff=-0.4 > > > > The analysis for clashscore, rotalyze, are failing to run and we get a > number of divide by zero errors for several of the other ‘visualize’ and > ‘eff_resolution’ routines. > > > > Can you help get this working. > > Thanks, > > Bob Nolte > > > > > > > > *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.* >

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Molprobity / CCTBX incompatibility
by Robert Nolte 11 Aug '19

11 Aug '19

We are trying to reinstall our internal molprobity server, and have hit an issue with the github version where it appears to be a version conflict with the version of cctbx that is currently being downloaded by configuration script in the master branch of molprobity. We are getting errors when we run the validation routine such as Unrecogized PHIL parameter: data_version=8000 or Unrecognized PHIL parameter: clash_cutoff=-0.4 The analysis for clashscore, rotalyze, are failing to run and we get a number of divide by zero errors for several of the other 'visualize' and 'eff_resolution' routines. Can you help get this working. Thanks, Bob Nolte 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.

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Azure pipelines Linux builds failing with segmentation fault
by richard.gildea＠diamond.ac.uk 01 Aug '19

01 Aug '19

Recent Azure builds are failing for the Linux builds with the following error: ##[section]Starting: Test ============================================================================== Task : Command line Description : Run a command line script using Bash on Linux and macOS and cmd.exe on Windows Version : 2.151.2 Author : Microsoft Corporation Help : https://docs.microsoft.com/azure/devops/pipelines/tasks/utility/command-line ============================================================================== Generating script. ========================== Starting Command Output =========================== [command]/bin/bash --noprofile --norc /__w/_temp/823d09b8-e953-4f93-a9a8-0d863a25f1ce.sh /__w/_temp/823d09b8-e953-4f93-a9a8-0d863a25f1ce.sh: line 11: 6307 Segmentation fault (core dumped) libtbx.run_tests_parallel module=boost_adaptbx module=cctbx module=cma_es module=fable module=gltbx module=iotbx module=libtbx module=rstbx module=scitbx module=simtbx module=smtbx module=spotfinder module=annlib_adaptbx module=cbflib_adaptbx nproc=4 ##[error]Bash exited with code '139'. ##[section]Finishing: Test https://dev.azure.com/cctbx/cctbx_project/_build/results?buildId=256 The last successful Linux Python 2.7 master build was https://dev.azure.com/cctbx/cctbx_project/_build/results?buildId=240 The first failing Linux Python 2.7 master build was https://dev.azure.com/cctbx/cctbx_project/_build/results?buildId=245 Mac builds appear to be fine. Does anyone have any idea what is the issue? Cheers, Richard Dr Richard Gildea Data Analysis Scientist Tel: +441235 77 8078 Diamond Light Source Ltd. Diamond House Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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Failing tests on python3 builds
by richard.gildea＠diamond.ac.uk 30 Jul '19

30 Jul '19

Hi, Whilst looking into test failures reported against a pull request I currently have open, I noticed that there are several (9) failing tests on the Python 3 build. It appears that Markus reported these 3 weeks ago - is anyone looking into these failures? Having builds permanently reporting failure isn't particularly helpful as it discourages people from looking at the results, and will likely lead to further Python 3 regressions being introduced into the codebase. https://dev.azure.com/cctbx/cctbx_project/_build/results?buildId=240 https://github.com/cctbx/cctbx_project/issues Cheers, Richard Dr Richard Gildea Data Analysis Scientist Tel: +441235 77 8078 Diamond Light Source Ltd. Diamond House Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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