- cctbxbb - phenix-online.org

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.* >

1 0

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.

1 0

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

2 2

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

3 4

"duplicate" cif categories
by wtempel 06 Jul '19

06 Jul '19

Hi, wwpdb onedep recently rejected a file that I had manipulated (but not validated, I admit) in IOTBX. The error was "duplicate categories", or a similar complaint. I had added _reflns.* items related to data processing to a phenix.refine cif file that already included a _reflns.B_iso_Wilson_estimate. Merely running sort() on the relevant block made the error go away, but who knows what side effects there may have been. Does the CCTBX ecosystem provide some higher-level management of cif categories? Thanks. Wolfram

1 0

align density maps
by Peter Schmidtke 02 Jul '19

02 Jul '19

2 3

pickling nan values
by Robert Oeffner 13 Jun '19

13 Jun '19

Hi all, It seems that a flex.double array containing "nan" values doesn't survive pickling as in: oeffner@grove:~$ cctbx.python Python 2.7.15 (default, Sep 11 2018, 23:48:45) [GCC 4.4.7 20120313 (Red Hat 4.4.7-18)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> >>> from cctbx.array_family import flex >>> import pickle >>> flex_nans = flex.double(3, float('nan')) >>> list(flex_nans) [nan, nan, nan] >>> list(pickle.loads( pickle.dumps(flex_nans))) [0.0, 0.0, 0.0] >>> >>> If the flex double is cast into a python list then it does survive pickling as in: >>> >>> list(pickle.loads( pickle.dumps(list( flex_nans )))) [nan, nan, nan] >>> I would like to use nan values to indicate missing or invalid data values. Would anyone have a suggestion how to go about this? Many thanks, Rob -- Robert Oeffner, Ph.D. Research Associate, The Read Group Department of Haematology, Cambridge Institute for Medical Research University of Cambridge Cambridge Biomedical Campus The Keith Peters Building Hills Road Cambridge CB2 0XY www.cimr.cam.ac.uk/investigators/read/index.html tel: +44(0)1223 763234

2 1

Fwd: Conda/DIALS 1.14.5 source build with --use-conda does not work
by Nicholas Devenish 28 May '19

28 May '19

(Forwarding this manually as apparently my Diamond address isn't on cctbxbb) Hi All, On 24 May 2019, at 14:12, David Waterman - UKRI STFC < david.waterman(a)stfc.ac.uk<mailto:[email protected]>> wrote: > In the process, I discovered that the source builds we point to from > https://dials.github.io/installation.html don't work with --use-conda > because the paths to various packages are out of date. This seems to be to be a fundamental problem with the conda implementation? Let’s try to reproduce an old build from, say, 1st march: the point in cctbx_project at which dials 1.14 split off. This is https://github.com/cctbx/cctbx_project/commit/35652e06564da7ff989500a6d929b… . Try reproducing this point: git clone git(a)github.com<mailto:[email protected]>:cctbx/cctbx_project.git modules/cctbx_project ( cd modules/cctbx_project/ && git checkout 35652e06564da7ff989500a6d929bc595f69040f ) ln -s modules/cctbx_project/libtbx/auto_build/bootstrap.py . ./bootstrap.py base --use-conda —> many "An HTTP error occurred when trying to retrieve this URL.” This means that with the current conda implementation it’s impossible to guarantee reproducibility for any build beyond the past few days, without lots and lots of manual work reconstructing the versioning out of the file list dump. Because the version constraints aren’t kept with the repository, this means that a source distribution is not nearly enough to recreate any given release. This seems like a problem? Nick

3 2

Python3 / scons / non-conda builds
by Graeme.Winter＠Diamond.ac.uk 13 May '19

13 May '19

Dear All, Back in the mists of time, one could build cctbx modules without bootstrap or conda by having the right modules available yourself - a so-called baseless install which I think is still important in X-fel land? Anyhow, trying this with Python3 suggests that we have some special constraints which are perhaps too tight regarding module locations - for example scons - Grey-Area p3_compile :( $ pip3 install scons Collecting scons Downloading https://files.pythonhosted.org/packages/65/41/ac58638421414acc64e26fc120c81… (831kB) 100% |████████████████████████████████| 839kB 14.3MB/s Installing collected packages: scons Successfully installed scons-3.0.5 You are using pip version 19.0.1, however version 19.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. Grey-Area p3_compile :) $ make ./bin/libtbx.scons -j "`./bin/libtbx.show_number_of_processors`" ModuleNotFoundError: No module named 'SCons' During handling of the above exception, another exception occurred: Sorry: SCons is not available. A possible solution is to unpack a SCons distribution in one of these directories: "/Users/graeme/svn/scr" "/Users/graeme/svn/scr/cctbx_project" SCons distributions are available at this location: http://www.scons.org/ It may be necessary to rename the unpacked distribution, e.g.: mv scons-0.96.1 scons make: *** [default] Error 1 Grey-Area p3_compile :( $ which scons /Library/Frameworks/Python.framework/Versions/3.7/bin/scons Should we require that scons is installed as part of cctbx when it is already installed on the system? If we *do* have to have this constraint, maybe that should be checked at configure time (where it complains about six and future) Thoughts? In other news - the syntax changing branch referenced in https://github.com/cctbx/cctbx_project/pull/325 now compiles correctly on Python3 (note: not run, just compile but this means that it’s purpose is done) for the modules which it intends to touch and has no conflicts right now… Best wishes Graeme -- 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

2 2

Overloading Python builtin names with local variables
by Graeme.Winter＠Diamond.ac.uk 03 May '19

03 May '19

Morning all, As a side-effect of looking at some of the Python3 refactoring I stumbled across a few places where e.g. range is used as a variable name. While this is fine and legal, when moving the code to Python3 xrange => range and from builtins import range is a back-port of Python3 range to Python2 which allows the existing behaviour of xrange generator to be maintained This is fine except for where range is a variable name and we then get a “variable referenced before assignment” type error As a general statement I would say overloading Python reserved names with local variables is untidy at best, and can easily cause confusion (as well as real problems as identified above) - I have therefore taken the liberty of adding a tool to libtbx which can be used to find such variables to give people a chance to avoid them: Grey-Area dxtbx :) [master] $ libtbx.find_reserved_names format/ Checking format/ format/FormatSMVRigakuSaturn.py:239 "format" format = self._scan_factory.format("SMV") format/FormatTIFFRayonixESRF.py:36 "format" format = {LITTLE_ENDIAN: "<", BIG_ENDIAN: ">"}[order] format/FormatTIFFRayonixESRF.py:29 "bytes" width, height, depth, order, bytes = FormatTIFFRayonix.get_tiff_header( format/FormatCBFMini.py:231 "format" format = self._scan_factory.format("CBF") format/FormatTIFFRayonix.py:176 "format" format = self._scan_factory.format("TIFF") format/FormatTIFFRayonix.py:31 "bytes" width, height, depth, order, bytes = FormatTIFF.get_tiff_header(image_file) format/FormatTIFFRayonix.py:74 "bytes" width, height, depth, order, bytes = FormatTIFF.get_tiff_header(image_file) format/FormatSMVRigakuEiger.py:243 "format" format = self._scan_factory.format("SMV") format/FormatSMVADSC.py:212 "format" format = self._scan_factory.format("SMV") format/Registry.py:88 "format" for format in sorted(self._formats, key=lambda x: x.__name__): format/FormatSMVJHSim.py:141 "format" format = self._scan_factory.format("SMV") format/FormatSMVRigakuPilatus.py:188 "format" format = self._scan_factory.format("SMV") format/FormatSMVADSCSN928.py:47 "format" format = self._scan_factory.format("SMV") format/FormatRAXISIVSpring8.py:134 "format" format = self._scan_factory.format("RAXIS") format/FormatTIFFRayonixSPring8.py:31 "bytes" width, height, depth, order, bytes = FormatTIFFRayonix.get_tiff_header( format/FormatSMVADSCmlfsom.py:37 "format" format = self._scan_factory.format("SMV") format/FormatTIFFBruker.py:174 "format" format = self._scan_factory.format("TIFF") format/FormatTIFFBruker.py:31 "bytes" width, height, depth, order, bytes = FormatTIFF.get_tiff_header(image_file) format/FormatTIFFBruker.py:71 "bytes" width, height, depth, order, bytes = FormatTIFF.get_tiff_header(image_file) format/FormatCBFMiniADSCHF4M.py:26 "format" for format in ["%a_%b_%d_%H:%M:%S_%Y"]: format/FormatCBFMiniADSCHF4M.py:169 "format" format = self._scan_factory.format("CBF") format/FormatSMVADSCNoDateStamp.py:54 "format" format = self._scan_factory.format("SMV") format/FormatSMVRigakuSaturnNoTS.py:228 "format" format = self._scan_factory.format("SMV") format/FormatPYunspecified.py:152 "format" format = "" format/FormatSMVRigakuA200.py:234 "format" format = self._scan_factory.format("SMV") format/FormatCBFMiniEigerPhotonFactory.py:131 "format" format = self._scan_factory.format("CBF") format/FormatSMVTimePix_SU.py:97 "format" format = self._scan_factory.format("SMV") format/FormatCBFMiniPilatus.py:83 "format" format = self._scan_factory.format("CBF") format/FormatCBFMiniPilatusHelpers.py:22 "format" for format in ["%Y-%b-%dT%H:%M:%S", "%Y-%m-%dT%H:%M:%S", "%Y/%b/%d %H:%M:%S"]: format/FormatSMVADSCSNAPSID19.py:91 "format" format = self._scan_factory.format("SMV") format/FormatCBFMiniEiger.py:216 "format" format = self._scan_factory.format("CBF") format/FormatSMVNOIR.py:218 "format" format = self._scan_factory.format("SMV") format/FormatSMVCMOS1.py:197 "format" format = self._scan_factory.format("SMV") format/FormatRAXIS.py:238 "format" format = self._scan_factory.format("RAXIS") is an example where “format” is scattered all over the place but is also a useful function - replacing with fmt will mean the same and avoid this overloading, as an example. This uses AST parsing to work through the code and find variable assignments - doing this for dials found lots of examples of “file” and “type” being used. How much people care about this is a local issue, but I thought the tool would be useful All the best Graeme -- 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

1 0

modulo operation on flex.double
by Robert Oeffner 11 Apr '19

11 Apr '19

Hi, I have a flex.double array of phase values between -360 and 360 degrees I would like to cast them all in one go to lie within 0 to 360. Does anybody know if there is a nice way of doing this with flex arrays? The modulo operator doesn't seem to be supported for flex arrays unlike the +, -, * and the / operators. This would otherwise be handy as I could then convert the array in one line of code like phases = phases % 360.0 If not I guess I'll have to numpy the problem :-) Many thanks, Rob

5 5

Re: [cctbxbb] cannot compile Phenix
by R. D. Oeffner 06 Apr '19

06 Apr '19

>From the messages on the cctbx github mailing list it seems that Dials people have been extricating dxtbx from cctbx_project. Rob -----Original Message----- From: Pavel Afonine Sent: Saturday, April 6, 2019 7:07 PM To: phenixdev Subject: cannot compile Phenix Hi, anyone knows why current Phenix code is broken: python bootstrap.py --builder=phenix --sfuser=afonine --cciuser=afonine update python bootstrap.py --builder=phenix --sfuser=afonine --cciuser=afonine build --nproc=12 leads to (...) AttributeError: 'empty' object has no attribute 'dxtbx_include': File "/Users/pafonine/phenix/build/SConstruct", line 31: SConscript("spotfinder/SConscript") File "/Users/pafonine/phenix/modules/scons/engine/SCons/Script/SConscript.py", line 607: return method(*args, **kw) File "/Users/pafonine/phenix/modules/scons/engine/SCons/Script/SConscript.py", line 544: return _SConscript(self.fs, *files, **subst_kw) File "/Users/pafonine/phenix/modules/scons/engine/SCons/Script/SConscript.py", line 253: call_stack[-1].globals) File "/Users/pafonine/phenix/modules/cctbx_project/spotfinder/SConscript", line 22: env_etc.dxtbx_include, usr+sys time: 1.94 seconds wall clock time: 4.51 seconds Process failed with return code 2 Any idea for a workaround? Pavel --- This email has been checked for viruses by AVG. https://www.avg.com

2 3

jupyter notebook
by wtempel 02 Apr '19

02 Apr '19

Hi all, how does one configure, and run inside a jupyter notebook, a cctbx-enabled kernel, beginning with a downloaded [cctbx build]( http://cci.lbl.gov/cctbx_build/)? [This page]( https://medium.com/@sljack1992/making-a-custom-ipython-notebook-kernel-c59e…) seems to describe the first part, but may no longer apply to more recent cctbx builds. Thanks. Wolfram Tempel

2 1

mtz2map gridding
by Elliot Nelson 21 Feb '19

21 Feb '19

Hi All, I've been trying to use Phenix.mtz2map to sample maps to a particular array size with the "gridding" option, but found that this seems to have no effect on the output of the program. I was wondering whether there were some restrictions to the integers that are permitted or otherwise what might be the cause of this behaviour. Having hunted through the code it seems to just set n_real in the crystal gridding, which is then fed into an fft - possibly the latter ignores n_reals that aren't sensible? Any idea? Thanks, Conor on behalf of Conor Wild: conor.wild(a)oriel.ox.ac.uk Elliot DPhil Student, Systems Approaches to Biomedical Science<http://www.sabsidc.ox.ac.uk/> Protein Crystallography<http://www.thesgc.org/groupprofile/9489>, Structural Genomics Consortium, NDM, University of Oxford Oxford Protein Informatics Group<http://opig.stats.ox.ac.uk/>, Department of Statistics, University of Oxford

2 1

OpenMP in fftpack
by Keitaro Yamashita 31 Jan '19

31 Jan '19

Dear CCTBX/PHENIX developers, According to PHENIX FAQ: https://www.phenix-online.org/documentation/faqs/index.html#general > In addition to these options, it is also possible to compile phenix.refine and Phaser with the OpenMP library, which automatically parallelizes specific instructions such as the FFT. This requires using the source installer for Phenix, and adding the argument "--openmp" to the install command. Because of threading conflicts, OpenMP is not compatible with the Phenix GUI. FFT in phenix.refine can be parallelized if OpenMP is enabled. However, it seems incorrect since 2017 due to this change: https://github.com/cctbx/cctbx_project/commit/3e932248e0491847a04ddeee429f8… The FAQ may need updating, but I am curious to know why it is disabled now. Best regards, Keitaro

1 0

This is a test
by Billy Poon 28 Jan '19

28 Jan '19

The Phenix website was down for a few hours, so this is a test to see if the bulletin board is working. -- 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

1 0

Re: [cctbxbb] [git/cctbx] master: Fix typo geobox (1ad3fe055)
by Pavel Afonine 22 Dec '18

22 Dec '18

Bad idea to hard-wire package name into lowest level code. Now imagine we need the same for afit, amber, quantumbio, rosetta, etc.. Are we going to have a page-long block of "if" statements. Please re-think and remove. For example, whether you want to shift it or not can be a parameter that you cast way level up in the context specific code. Pavel On 12/20/18 09:53, CCTBX commit wrote: > Repository : ssh://g18-sc-serv-04.diamond.ac.uk/cctbx > On branch : master > > ------------------------------------------------------------------------ > > > commit 1ad3fe05571162839e770c35ed032a7fc38a33b7 > Author: Gydo van Zundert <gydo.vanzundert(a)schrodinger.com> > Date: Wed Dec 19 14:58:36 2018 -0500 > > Fix typo geobox > > > ------------------------------------------------------------------------ > > > 1ad3fe05571162839e770c35ed032a7fc38a33b7 > mmtbx/refinement/real_space/individual_sites.py | 4 ++-- > 1 file changed, 2 insertions(+), 2 deletions(-) > > diff --git a/mmtbx/refinement/real_space/individual_sites.py > b/mmtbx/refinement/real_space/individual_sites.py > index c61e88b01..20f38a6b0 100644 > --- a/mmtbx/refinement/real_space/individual_sites.py > +++ b/mmtbx/refinement/real_space/individual_sites.py > @@ -350,7 +350,7 @@ class box_refinement_manager(object): > > # When using the Schrodinger force field, move the whole > structure as the > # selected atoms are environment aware. > - if geobox.get_source() == 'SCHRODINGER': > + if geo_box.get_source() == 'SCHRODINGER': > geo_box.shift_cart(box.shift_cart) > > rsr_simple_refiner = simple( > @@ -377,7 +377,7 @@ class box_refinement_manager(object): > iselection, sites_cart_refined) > self.xray_structure.set_sites_cart(sites_cart_moving) > self.sites_cart = self.xray_structure.sites_cart() > - if geobox.get_source() == 'SCHRODINGER': > + if geo_box.get_source() == 'SCHRODINGER': > geo_box.shift_cart(shift_back) > else: # NCS constraints are present > # select on xrs, grm, ncs_groups > > ------------------------------------------------------------------------ > > To unsubscribe from the CCTBX-COMMIT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCTBX-COMMIT&A=1 >

4 6

Broken iotbx/pdb/cif test
by richard.gildea＠diamond.ac.uk 19 Dec '18

19 Dec '18

According to Jenkins these two tests have been broken for several days - does anyone know what the issue is and could a fix be applied? Both look like the same error. iotbx/regression/tst_pdb_as_cif.py iotbx/regression/tst_data_manager.py These have been failing since this commit: https://github.com/cctbx/cctbx_project/commit/2c119fcf012ca4cc60dfce231902c… The tests also fail locally for me (not just on Jenkins). Cheers, Richard Traceback (most recent call last): File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/iotbx/regression/tst_pdb_as_cif.py", line 106, in <module> exercise_01() File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/iotbx/regression/tst_pdb_as_cif.py", line 37, in exercise_01 logger=null_out(), File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/iotbx/cli_parser.py", line 71, in run_program task.run() File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/programs/pdb_as_cif.py", line 37, in run txt = model.model_as_mmcif() File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py", line 879, in model_as_mmcif if self.get_restraints_manager() is not None: File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py", line 622, in get_restraints_manager self.setup_restraints_manager() File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py", line 1042, in setup_restraints_manager self._process_input_model() File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py", line 959, in _process_input_model use_neutron_distances = self._pdb_interpretation_params.pdb_interpretation.use_neutron_distances) File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/utils/__init__.py", line 998, in __init__ use_neutron_distances=use_neutron_distances, File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/server.py", line 675, in __init__ use_neutron_distances=use_neutron_distances, File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/server.py", line 689, in convert_all use_neutron_distances=use_neutron_distances, File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/server.py", line 700, in convert_lib_atom entry = cif_types.energy_lib_atom(**dict(row)) File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/cif_types.py", line 49, in __init__ raise_value_error("Floating-point") File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/cif_types.py", line 39, in raise_value_error expected_type, looped_id.split(":",1)[0], val)) ValueError: Floating-point value expected in CIF file: _lib_atom.ion_radius 1,7 Traceback (most recent call last): File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/iotbx/regression/tst_data_manager.py", line 532, in <module> test_model_datatype() File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/iotbx/regression/tst_data_manager.py", line 233, in test_model_datatype dm.get_model().model_as_mmcif(), overwrite=True) File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py", line 879, in model_as_mmcif if self.get_restraints_manager() is not None: File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py", line 622, in get_restraints_manager self.setup_restraints_manager() File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py", line 1042, in setup_restraints_manager self._process_input_model() File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py", line 959, in _process_input_model use_neutron_distances = self._pdb_interpretation_params.pdb_interpretation.use_neutron_distances) File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/utils/__init__.py", line 998, in __init__ use_neutron_distances=use_neutron_distances, File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/server.py", line 675, in __init__ use_neutron_distances=use_neutron_distances, File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/server.py", line 689, in convert_all use_neutron_distances=use_neutron_distances, File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/server.py", line 700, in convert_lib_atom entry = cif_types.energy_lib_atom(**dict(row)) File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/cif_types.py", line 49, in __init__ raise_value_error("Floating-point") File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/cif_types.py", line 39, in raise_value_error expected_type, looped_id.split(":",1)[0], val)) ValueError: Floating-point value expected in CIF file: _lib_atom.ion_radius 1,7 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

3 7

forcing building boost_python early in SConscript
by Robert Oeffner 17 Nov '18

17 Nov '18

We are working on a newer version of Phaser. The new SConscript file for Phaser imports features from boost_python. Therefore it is currently not straightforward to build it since an empty build directory does not yet contain the boost_python module to be imported by SConscript (or python). So SCons crashes when it reads the new Phaser SCsonscript stating that boost_python cannot be imported. Currently our workaround is to first build CCTBX alone and then subsequently to build Phaser. My question is if it is possible to specify dependencies in cctbx_project/boost_adaptbx/SConscript to force building boost_python early on. On Windows boost_thread and a few other libraries are built before other SConscript files are read. So I have put some Depends(boost_thread, boost_python) andDepends(boost_thread, boost_python_meta_ext) statements into cctbx_project/boost_adaptbx/SConscript. These do seem to force building the boost_python.lib and .dll files. But building the boost_python_meta_ext python module fails with the error: boost_adaptbx\meta_ext.cpp(14): fatal error C1083: Cannot open include file: 'boost_adaptbx/type_id_eq.h' It's possible that I'm not using SCons as it's supposed to be used. Let me know if anyone has a suggestion on how to force building boost_python before other SConscript are read. Many thanks, Rob -- Robert Oeffner, Ph.D. Research Associate, The Read Group Department of Haematology, Cambridge Institute for Medical Research University of Cambridge Cambridge Biomedical Campus Wellcome Trust/MRC Building Hills Road Cambridge CB2 0XY www.cimr.cam.ac.uk/investigators/read/index.html tel: +44(0)1223 763234

5 5

Fwd: Re: indexing diffraction pattern
by Pavel Afonine 14 Nov '18

14 Nov '18

Perhaps someone can reply Wen.. Pavel -------- Forwarded Message -------- Subject: Re: indexing diffraction pattern Date: Sat, 10 Nov 2018 09:30:53 -0500 From: Wen Jiang <jiang12(a)purdue.edu> To: Pavel Afonine <pafonine(a)lbl.gov> Pavel, Sorry for insufficient details. The scenario is that I have a numpy 2D array of float values that represents an image of "diffraction pattern" (generated by an image processing operation, not actual X-ray diffraction). I need to determine the peak positions and then find a 2D lattice (two 2D vectors) going through these peaks. I have my own simple functions that can detect the peaks and find a 2-D lattice to cross the peaks but it often fails when the "diffraction pattern" is not very clean. Thus, I want to find a more robust method that works well when the peaks are relatively weak, not very sharp, and when there are some spurious peaks off the lattice. I think these tasks are exactly what cctbx has solved for indexing X-ray diffraction images. Hope that these explanations help clarify the problem. Thanks, Wen Prof. Wen Jiang Department of Biological Sciences Department of Chemistry (Courtesy) Scientific Director, Purdue Cryo-EM Facility Purdue University Hockmeyer Hall of Structural Biology 240 S. Martin Jischke Drive West Lafayette, IN 47907 http://jiang.bio.purdue.edu On Sat, Nov 10, 2018 at 8:03 AM Pavel Afonine <pafonine(a)lbl.gov <mailto:[email protected]>> wrote: Hi Wen, I'm not sure I fully understand your question... You say a function that takes a numpy array.. Array of what? Then, "a list of diffraction spots" -- these are measured in diffraction experiment. If you could provide more details as to what you are trying to do as well as what exactly the inputs are then I will do my best to see how to do this in CCTBX or forward your questions to CCTBX mailing list so that others can comment. All the best, Pavel On 11/10/18 03:56, Wen Jiang wrote: > Hi Pavel, > I am looking for a function that takes a numpy array and returns a > list of diffraction spots and lattice vectors. I think > cctbx should have such a function but I am not familiar with it. > Can you point me in the right direction? > Thanks, > > Wen > > Prof. Wen Jiang > Department of Biological Sciences > Department of Chemistry (Courtesy) > Scientific Director, Purdue Cryo-EM Facility > Purdue University > Hockmeyer Hall of Structural Biology > 240 S. Martin Jischke Drive > West Lafayette, IN 47907 > http://jiang.bio.purdue.edu >

2 1

Windows woes
by Luc Bourhis 09 Nov '18

09 Nov '18

Hi, Trying to install cctbx on Windows 10, 1. install latest python 2 from Python.org 2. python2 bootstrap.py —builder=cctbxlite —with-python=\path-to-python-from-step-1 It fails because of missing module “builtins”. So I installed pip, then used it to install “future”. Then I had to install “six” with pip. Am I being stupid or cctbx does not install out of the box anymore? Best wishes, Luc J Bourhis

3 3

Python 3 and CCP4
by David Waterman 02 Nov '18

02 Nov '18

Hi folks, It's great to see the momentum building behind the project to migrate to Python 3. From the roadmap <https://github.com/cctbx/cctbx_project/wiki/Python-3-roadmap>, there is clearly still some way to go, but current activity makes me wonder if the proposed deadline of complete migration by 2020 might be beaten easily. What is not clear from the roadmap is whether there are any plans for a post-transition grace period, in which we have switched from writing forwards compatible Python 2 code to writing backwards compatible Python 3 code. Has this been thought about? Or will it be the case that the first commit of Py3-only code seals the deal? I ask because CCP4 has to support a large number of Python projects and these have not all considered the Python 3 switch nearly as seriously as cctbx yet. What I would like to request is a reasonable period of backwards compatibility is ensured to allow other CCP4 projects to catch up, and that this protected period is enshrined within the roadmap or developer guidelines. What do you think? Best wishes -- David

3 2

construct hkl arrays from number of reflections and resolution
by Robert Oeffner 29 Oct '18

29 Oct '18

I would like a function that spits out an HKL array as a function of number of reflections, dmin and dmax. It's quite likely this has already been done somewhere in the CCTBX. Would anyone know if this is the case rather than me having to reinvent the wheel? Many thanks, Rob -- Robert Oeffner, Ph.D. Research Associate, The Read Group Department of Haematology, Cambridge Institute for Medical Research University of Cambridge Cambridge Biomedical Campus Wellcome Trust/MRC Building Hills Road Cambridge CB2 0XY www.cimr.cam.ac.uk/investigators/read/index.html tel: +44(0)1223 763234

2 1

Bootstrap on macOS Mojave
by Graeme.Winter＠Diamond.ac.uk 17 Oct '18

17 Oct '18

Folks, For info: https://github.com/cctbx/cctbx_project/issues/240 wxPython appears to not build on macOS Mojave - possibly updated C++ standards or something who knows? But I guess because we are fixed on an old (4 years, just about [1]) version of wxPython this should not be a surprise. We should probably have some kind of answer for this though - thoughts? Many thanks Graeme ——— [1] https://wxpython.org/news/wxpython-3.0.2.0-release/index.html -- 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

1 2

Fwd: cctbx conventions
by Graeme.Winter＠Diamond.ac.uk 08 Oct '18

08 Oct '18

HI Folks, Question from a colleague - any ideas? Many thanks Graeme Begin forwarded message: From: "Bombardi, Alessandro (DLSLtd,RAL,SCI)" <alessandro.bombardi(a)diamond.ac.uk<mailto:[email protected]>> Subject: cctbx conventions Date: 8 October 2018 at 14:54:10 BST To: "Winter, Graeme (DLSLtd,RAL,LSCI)" <Graeme.Winter(a)Diamond.ac.uk<mailto:[email protected]>> Hi Graeme, I am trying to understand the convention used by cctbx, for the anomalous part of the atomic scattering factor. Do you know if it is written as f+f'+if'' with f'' >0 or with f+f'-if'' with f'' >0 can you help me? All the best, Alessandro -- 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

3 3

non-standard test naming in mmtbx
by Pearce, N.M. (Nick) 03 Oct '18

03 Oct '18

Hi, I’m trying to use the automatic pytest discovery in mmtbx and I notice that there are a few “libtbx-style” tests, namely "$D/conformation_dependent_library/test_cdl.py", "$D/conformation_dependent_library/test_cdl_esd.py", “$D/conformation_dependent_library/test_rdl.py", "$D/conformation_dependent_library/test_hpdl.py”, that follow the “pytest” naming convention, and are thus picked up by the pytest.discover() function. They then error because pytest cannot run them. There are — as far as I can tell — normal libtbx tests (they are registered in run_tests.py). Is there any reason they do not follow the typical naming convention? Changing their filenames and modifying run_tests.py accordingly seems to lead to the same behaviour when running tests. Is there any reason they should not be renamed from “test_*.py” to “tst_*.py”? Thanks, Nick

3 3

Allocators
by Graeme.Winter＠Diamond.ac.uk 25 Sep '18

25 Sep '18

Hello All, In keeping with the spirit of https://github.com/cctbx/cctbx_project/wiki/cctbx-contributors-guide we would like to revisit the allocator work now Phenix 1.14 is out in the wild - however since we now know that this needs to be done we are interested in other points of view people have on ways to do this, and options people would like to have. It is important to note that we have no intention of changing the default behaviour, but we do want to be able to use customised allocators with flex arrays e.g. for handing out memory of well known and repeatedly used sizes (say, 16 M pixel double arrays) or allocate in specific areas for NUMA systems such as xeon phi. We prototyped this a while back and stepped the changes back out again to enable the phenix release to proceed smoothly, so we have a pretty good idea of the sorts of things we would expect to do however will welcome input if you would like additional features. As a baseline, we are talking as a parameter that PHENIX are no longer supporting CENTOS 5 32 bit (since ISTR this was a constraint before) Any thoughts? Appreciate a number of folks will be travelling back after the PHENIX workshop. Many thanks Graeme -- 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

2 2

Conda
by Graeme.Winter＠Diamond.ac.uk 24 Sep '18

24 Sep '18

Hello again, Trying to keep threads from getting warped :-) We’re interested in what the plans and timescales are for the move to Conda for a base to cctbx-related projects, and in particular - - what is planned? - when i.e. timescales (rough) - will bootstrap go away? I know from talking to Billy on Wednesday that this is back on the cards again now the PHENIX release is out, but I didn’t ask at the time fo the details… oops! Many thanks Graeme -- 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

2 2

Fwd: [git/cctbx] master: Python 3 syntax changes (790d9e315)
by Graeme.Winter＠Diamond.ac.uk 21 Sep '18

21 Sep '18

Folks, I expressed some surprise at this & friends however - - this is necessary to make the bootstrap process Python 3 compatible - the timetable for which said this should have been finished 9 months ago (https://github.com/cctbx/cctbx_project/wiki/Python-3-roadmap) - these changes were discussed and agreed (https://github.com/cctbx/cctbx_project/pull/199) The only part of this which was not approved was reverted before the request was merged (I felt that this annotation was helpful as the changes themselves go back ~6 months so people have possibly forgotten the context) Best wishes Graeme Begin forwarded message: From: CCTBX commit <diamondlightsource.jenkins(a)GMAIL.COM<mailto:[email protected]>> Subject: [git/cctbx] master: Python 3 syntax changes (790d9e315) Date: 21 September 2018 at 14:25:29 BST To: <CCTBX-COMMIT(a)JISCMAIL.AC.UK<mailto:[email protected]>> Reply-To: <cctbxbb(a)PHENIX-ONLINE.ORG<mailto:[email protected]>> Repository : ssh://ws133.diamond.ac.uk/cctbx On branch : master ________________________________ commit 790d9e315a2a6ae5a875ba86b461ed570c77280d Author: Markus Gerstel <markus.gerstel(a)diamond.ac.uk<mailto:[email protected]>> Date: Thu May 24 12:16:38 2018 +0100 Python 3 syntax changes Replace the reduce(add, ...) function by sum(). reduce() is no longer in the global namespace in python 3. ________________________________ 790d9e315a2a6ae5a875ba86b461ed570c77280d scitbx/math/__init__.py | 34 ++++++++++++++++------------------ 1 file changed, 16 insertions(+), 18 deletions(-) diff --git a/scitbx/math/__init__.py b/scitbx/math/__init__.py index a13405f92..49e295eb0 100644 --- a/scitbx/math/__init__.py +++ b/scitbx/math/__init__.py @@ -1,11 +1,13 @@ -from __future__ import division, absolute_import +from __future__ import absolute_import, division, print_function + +import math + from scitbx.math.ext import * import scitbx.linalg.eigensystem import scitbx.math.gaussian # implicit import from scitbx import matrix from scitbx.array_family import flex from boost import rational # implicit import -import math gaussian_fit_1d_analytical.__doc__ = """ Fits a gaussian function to a list of points. @@ -88,16 +90,14 @@ def r3_rotation_average_rotation_matrix_from_matrices(*matrices): """ if not matrices: - raise TypeError, "Average of empty sequence" + raise TypeError("Average of empty sequence") - import operator import scitbx.matrix - average = reduce( - operator.add, - [ scitbx.matrix.col( r3_rotation_matrix_as_unit_quaternion( e ) ) - for e in matrices ] - ) + average = sum( + scitbx.matrix.col( r3_rotation_matrix_as_unit_quaternion( e ) ) + for e in matrices + ) return r3_rotation_unit_quaternion_as_matrix( average.normalize() ) @@ -111,13 +111,12 @@ def r3_rotation_average_rotation_via_lie_algebra(matrices, maxiter = 100, conver """ if not matrices: - raise TypeError, "Average of empty sequence" + raise TypeError("Average of empty sequence") if maxiter < 0 or convergence <= 0: - raise ValueError, "Invalid iteration parameters" + raise ValueError("Invalid iteration parameters") from scitbx.math import so3_lie_algebra - import operator conv_sq = convergence * convergence norm = 1.0 / len( matrices ) @@ -125,10 +124,9 @@ def r3_rotation_average_rotation_via_lie_algebra(matrices, maxiter = 100, conver for i in range( maxiter ): inverse = current.inverse() - log_diff = norm * reduce( - operator.add, - [ so3_lie_algebra.element.from_rotation_matrix( matrix = inverse * m ) - for m in matrices ] + log_diff = norm * sum( + so3_lie_algebra.element.from_rotation_matrix( matrix = inverse * m ) + for m in matrices ) if log_diff.norm_sq() < conv_sq: @@ -136,7 +134,7 @@ def r3_rotation_average_rotation_via_lie_algebra(matrices, maxiter = 100, conver current *= log_diff.exponential() - raise RuntimeError, "Iteration limit exceeded" + raise RuntimeError("Iteration limit exceeded") def euler_angles_as_matrix(angles, deg=False): if (deg): @@ -174,7 +172,7 @@ class erf_verification(object): if (self.max_delta < delta): self.max_delta = delta if (delta > self.tolerance): - print x, expected_result, result, delta + print(x, expected_result, result, delta) class minimum_covering_sphere_nd(object): ________________________________ To unsubscribe from the CCTBX-COMMIT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCTBX-COMMIT&A=1 -- 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

1 0

Re: [cctbxbb] [git/cctbx] master: Python 3 syntax changes (790d9e315)
by Graeme Winter 21 Sep '18

21 Sep '18

Folks, I expressed some surprise at this & friends however - - this is necessary to make the bootstrap process Python 3 compatible - the timetable for which said this should have been finished 9 months ago (https://github.com/cctbx/cctbx_project/wiki/Python-3-roadmap <https://github.com/cctbx/cctbx_project/wiki/Python-3-roadmap>) - these changes were discussed and agreed (https://github.com/cctbx/cctbx_project/pull/199 <https://github.com/cctbx/cctbx_project/pull/199>) The only part of this which was not approved was reverted before the request was merged (I felt that this annotation was helpful as the changes themselves go back ~6 months so people have possibly forgotten the context) Best wishes Graeme > On 21 Sep 2018, at 14:25, CCTBX commit <diamondlightsource.jenkins(a)GMAIL.COM> wrote: > > Repository : ssh://ws133.diamond.ac.uk/cctbx > On branch : master > > > > commit 790d9e315a2a6ae5a875ba86b461ed570c77280d > Author: Markus Gerstel <markus.gerstel(a)diamond.ac.uk> > Date: Thu May 24 12:16:38 2018 +0100 > > Python 3 syntax changes > > Replace the reduce(add, ...) function by sum(). > reduce() is no longer in the global namespace in python 3. > > > > > 790d9e315a2a6ae5a875ba86b461ed570c77280d > scitbx/math/__init__.py | 34 ++++++++++++++++------------------ > 1 file changed, 16 insertions(+), 18 deletions(-) > > diff --git a/scitbx/math/__init__.py b/scitbx/math/__init__.py > index a13405f92..49e295eb0 100644 > --- a/scitbx/math/__init__.py > +++ b/scitbx/math/__init__.py > @@ -1,11 +1,13 @@ > -from __future__ import division, absolute_import > +from __future__ import absolute_import, division, print_function > + > +import math > + > from scitbx.math.ext import * > import scitbx.linalg.eigensystem > import scitbx.math.gaussian # implicit import > from scitbx import matrix > from scitbx.array_family import flex > from boost import rational # implicit import > -import math > > gaussian_fit_1d_analytical.__doc__ = """ > Fits a gaussian function to a list of points. > @@ -88,16 +90,14 @@ def r3_rotation_average_rotation_matrix_from_matrices(*matrices): > """ > > if not matrices: > - raise TypeError, "Average of empty sequence" > + raise TypeError("Average of empty sequence") > > - import operator > import scitbx.matrix > > - average = reduce( > - operator.add, > - [ scitbx.matrix.col( r3_rotation_matrix_as_unit_quaternion( e ) ) > - for e in matrices ] > - ) > + average = sum( > + scitbx.matrix.col( r3_rotation_matrix_as_unit_quaternion( e ) ) > + for e in matrices > + ) > > return r3_rotation_unit_quaternion_as_matrix( average.normalize() ) > > @@ -111,13 +111,12 @@ def r3_rotation_average_rotation_via_lie_algebra(matrices, maxiter = 100, conver > """ > > if not matrices: > - raise TypeError, "Average of empty sequence" > + raise TypeError("Average of empty sequence") > > if maxiter < 0 or convergence <= 0: > - raise ValueError, "Invalid iteration parameters" > + raise ValueError("Invalid iteration parameters") > > from scitbx.math import so3_lie_algebra > - import operator > > conv_sq = convergence * convergence > norm = 1.0 / len( matrices ) > @@ -125,10 +124,9 @@ def r3_rotation_average_rotation_via_lie_algebra(matrices, maxiter = 100, conver > > for i in range( maxiter ): > inverse = current.inverse() > - log_diff = norm * reduce( > - operator.add, > - [ so3_lie_algebra.element.from_rotation_matrix( matrix = inverse * m ) > - for m in matrices ] > + log_diff = norm * sum( > + so3_lie_algebra.element.from_rotation_matrix( matrix = inverse * m ) > + for m in matrices > ) > > if log_diff.norm_sq() < conv_sq: > @@ -136,7 +134,7 @@ def r3_rotation_average_rotation_via_lie_algebra(matrices, maxiter = 100, conver > > current *= log_diff.exponential() > > - raise RuntimeError, "Iteration limit exceeded" > + raise RuntimeError("Iteration limit exceeded") > > def euler_angles_as_matrix(angles, deg=False): > if (deg): > @@ -174,7 +172,7 @@ class erf_verification(object): > if (self.max_delta < delta): > self.max_delta = delta > if (delta > self.tolerance): > - print x, expected_result, result, delta > + print(x, expected_result, result, delta) > > class minimum_covering_sphere_nd(object): > > > To unsubscribe from the CCTBX-COMMIT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCTBX-COMMIT&A=1 <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCTBX-COMMIT&A=1>

1 0

Post-PHENIX changes
by Graeme.Winter＠Diamond.ac.uk 21 Sep '18

21 Sep '18

Morning All, I see from http://phenix-online.org/ That PHENIX 1.14 has been released Now, I see at https://github.com/cctbx/cctbx_project/pulls we have a few fairly hefty pull requests parked as “hold for phenix release” - I would certainly not suggest merging all these in one go however probably we should give some thought to stepping through some of them, deciding which ones we should look at first and starting to merge things? I for one would like Nick’s allocator code to come back into play (so we can make use of it for DIALS) Thoughts / opinions? For info: PHENIX folks did you tag the version which was released in PHENIX 1.14 to allow a release branch for .1 etc. releases? Many thanks Graeme -- 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

1 1

repr for flex arrays
by Graeme.Winter＠Diamond.ac.uk 14 Sep '18

14 Sep '18

Hi Folks, Is there a reason for not having a helpful __repr__ for flex arrays i.e. Grey-Area:002-decide-when graeme$ dials.python Python 2.7.14 (default, Apr 17 2018, 15:02:10) [GCC 4.2.1 Compatible Apple LLVM 9.1.0 (clang-902.0.39.1)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> from dials.array_family import flex >>> a = flex.double([1, 2, 3]) >>> print a <scitbx_array_family_flex_ext.double object at 0x1095673c0> (I have a feeling I asked this before but cannot find reference) For example >>> print a.as_numpy_array() [ 1. 2. 3.] is more useful… but annoying to type I appreciate a could be “big” but numpy seems to handle this OK even - could __repr__ be punned to as_numpy_array(),__repr__()? Currently it prints the type of the array and its location in ram, which are adequately served by >>> type(a) <class 'scitbx_array_family_flex_ext.double'> >>> print id(a) 4451627968 If I print an array I more often want to see the content and less often the storage class and location (I humbly assert) Thoughts? I know this tends to confuse and annoy people who are new to flex arrays (and veterans who are busy debugging stuff…) Many thanks Graeme -- 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

4 9

Python 3 status
by Graeme.Winter＠Diamond.ac.uk 06 Sep '18

06 Sep '18

Hi Folks, Are there any updates on the progress to Python 3 compatibility? I know there is a project here https://github.com/cctbx/cctbx_project/projects/2 but I have lost the thread of activities since I have been out of the office much of the summer. At the very least I know no progress has been made from this side of the pond as we’ve put this work down for now. i would guess that a lot is on hold while the PHENIX release is done - however I thought I should check in case I have missed anything? Part of why I ask is that there is a PHENIX meeting in Cambridge real soon now (mid September) and I wonder if it is worth folks from DIALS and PHENIX getting together at that time to discuss this? Any thoughts? Thanks & best wishes Graeme -- 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

7 12

Re: [cctbxbb] [git/cctbx] master: re-defining the shift/est convergence limit in terms of crystallographic rather than independent parameters to make it easier to relate to the convergence reported in the CIF; also caching the shifts for further analysis and reporting; (9339fd5f7)
by Nicholas Sauter 05 Sep '18

05 Sep '18

I'm worried about making changes like this to a fundamental toolbox component like normal equations solving. We use this for processing xfel data, and would like the opportunity to test any changes through a pull request, prior to having them committed to the main branch. Nick Sauter Nicholas K. Sauter, Ph. D. Senior Scientist, Molecular Biophysics & Integrated Bioimaging Division Lawrence Berkeley National Laboratory 1 Cyclotron Rd., Bldg. 33R0345 Berkeley, CA 94720 (510) 486-5713 On Wed, Sep 5, 2018 at 5:29 AM, CCTBX commit < diamondlightsource.jenkins(a)gmail.com> wrote: > Repository : ssh://g18-sc-serv-04.diamond.ac.uk/cctbx > On branch : master > > ------------------------------ > > > commit 9339fd5f7d240f0d6f85dd57ce42e796d19608f1 > Author: pcxod <oleg_dolomanov(a)hotmail.com> > Date: Wed Sep 5 13:29:29 2018 +0100 > > re-defining the shift/est convergence limit in terms of > crystallographic rather than independent parameters to make it easier to > relate to the convergence reported in the CIF; also caching the shifts for > further analysis and reporting; > > > ------------------------------ > > > 9339fd5f7d240f0d6f85dd57ce42e796d19608f1 > scitbx/lstbx/normal_eqns_solving.py | 17 +++++++++++------ > 1 file changed, 11 insertions(+), 6 deletions(-) > > diff --git a/scitbx/lstbx/normal_eqns_solving.py > b/scitbx/lstbx/normal_eqns_solving.py > index 660304eab..45f070622 100644 > --- a/scitbx/lstbx/normal_eqns_solving.py > +++ b/scitbx/lstbx/normal_eqns_solving.py > @@ -140,15 +140,20 @@ class iterations(object): > a = self.non_linear_ls.normal_matrix_packed_u() > a.matrix_packed_u_diagonal_add_in_place(value*a. > matrix_packed_u_diagonal()) > > - def do_scale_shifts(self, max_shift_over_esd): > + def do_scale_shifts(self, limit_shift_over_su): > x = self.non_linear_ls.step() > esd = self.non_linear_ls.covariance_matrix().matrix_packed_u_ > diagonal() > - x_over_esd = flex.abs(x/flex.sqrt(esd)) > - max_val = flex.max(x_over_esd) > - if max_val < self.convergence_as_shift_over_esd: > + ls_shifts_over_su = flex.abs(x/flex.sqrt(esd)) > + #max shift for the LS > + self.max_ls_shift_over_su = flex.max(ls_shifts_over_su) > + jac_tr = self.non_linear_ls.actual.\ > + reparametrisation.jacobian_transpose_matching_grad_fc() > + self.shifts_over_su = jac_tr.transpose() * ls_shifts_over_su > + self.max_shift_over_su = flex.max(self.shifts_over_su) > + if self.max_shift_over_su < self.convergence_as_shift_over_esd: > return True > - if max_val > max_shift_over_esd: > - shift_scale = max_shift_over_esd/max_val > + if self.max_ls_shift_over_su > limit_shift_over_su: > + shift_scale = limit_shift_over_su/self.max_ls_shift_over_su > x *= shift_scale > return False > > > ------------------------------ > > To unsubscribe from the CCTBX-COMMIT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCTBX-COMMIT&A=1 >

2 3

Adding more parameters to xray::scatterer for anharmonic thermal displacements
by Luc J. Bourhis 22 Aug '18

22 Aug '18

Hi, we are working with Michal Chodkiewicz (Warsaw University) to add anharmonic thermal tensors to smtbx refinement. I was thinking to add one pointer to xray::scatterer, which can be NULL. When it is not so, it would point to an object which can compute the value and the derivatives for that thermal factor. That means we would have a base class with virtual methods, but I would say that is our problem! The issue for the rest of the cctbx community is the extra storage of that pointer in that class. Would that be all right? I remember quite a few years ago Ralf saying he wanted to replace the ADP's by a pointer to an external storage to save space. Our idea is along the same line. Best wishes, Luc

3 2

model selection
by Pavel Afonine 16 Aug '18

16 Aug '18

Currently model class has three selection methods: def selection(self, selstr, optional=True): def select(self, selection): def iselection(self, selstr): which is hideously confusing with zero chance to remember, and also inconsistent with the rest. Most objects in cctbx have ".select(self, selection)" methods, while being inconsistent about what they expect: iselection or boolean selection as "selection" argument. Some smart ones though can take both int or bool selections (figure out type automatically, which is trivial). Can we consolidate all three into one ".select()" that would allow taking bool or int or str? Or you think there are philosophical arguments against it? Pavel On 8/16/18 15:00, CCTBX commit wrote: > Repository : ssh://g18-sc-serv-04.diamond.ac.uk/cctbx > On branch : master > > ------------------------------------------------------------------------ > > > commit c98b44997e8eb7bf53ee828f510b933cd5167758 > Author: Oleg Sobolev <osobolev(a)lbl.gov> > Date: Thu Aug 16 15:00:20 2018 -0700 > > Proper use of model class > > > ------------------------------------------------------------------------ > > > c98b44997e8eb7bf53ee828f510b933cd5167758 > mmtbx/model/model.py | 3 +-- > 1 file changed, 1 insertion(+), 2 deletions(-) > > diff --git a/mmtbx/model/model.py b/mmtbx/model/model.py > index 6f2247452..87412f95c 100644 > --- a/mmtbx/model/model.py > +++ b/mmtbx/model/model.py > @@ -2312,8 +2312,7 @@ class manager(object): > sizes = flex.int() > h = self.get_hierarchy() > if(macro_molecule_only): > - asc = h.atom_selection_cache() > - s = asc.selection("protein or nucleotide") > + s = self.selection("protein or nucleotide") > h = h.select(s) > for r in h.residue_groups(): > sizes.append(r.atoms().size())

2 3

Extracting data from MTZ
by David Waterman 14 Aug '18

14 Aug '18

Hi all, I have a script that extracts Fobs and Fcalc from an MTZ file produced by Refmac for some analysis. I was just doing this in a trivial way: fobs = m.extract_reals("F").data fc = m.extract_reals("FC_ALL").data and this worked fine, until I came across a file with missing observations, so that the lengths of fobs and fc do not match. Can anybody advise a better way to do this please? I'm inexperienced with iotbx.mtz. I don't need anything other than the values of the structure factors, but I need each element of fobs and fc to contain the equivalent values. Thanks -- David

3 3

How does Jenkins work?
by Takanori Nakane 28 Jul '18

28 Jul '18

Hi, Why does Jenkins still run tests on my old commits on my deleted (dxtbx-sacla) branch? The test failure is probably caused by my commit dc17165 but I committed a fix 5c7416b and confirmed that it passes the tests. So I merged my topic branch to master and deleted the branch from GitHub. I know how git works but I am new to the practice in the cctbx repository (like using rebase instead of merge). If I am doing something wrong, could you please point it to me? Best regards, Takanori Nakane > <html><head></head><body><table style="width:100%; background-color: > #F59400; color: #FFF; border-radius: 0.5em; margin-bottom: 0.5em"><tr><td > style="margin: 0.5em 1.25em 0.5em 0.7em; font-weight: bold; font-family: > sans-serif; font-size: 110%"><a > href="http://jenkins.diamond.ac.uk:8080/job/cctbx_branch_tests/145/" > style="color:#FFF; text-decoration: none"><big>Build CCTBX Branch Tests is > unstable</big></a></td></tr></table><br/><table style="width:100%; > background-color: #F59400; color: #FFF; border-radius: 0.5em; > margin-bottom: 0.5em"><tr><td style="margin: 0.5em 1.25em 0.5em 0.7em; > font-weight: bold; font-family: sans-serif; font-size: 110%"><a > href="http://jenkins.diamond.ac.uk:8080/job/cctbx_branch_tests/145/testReport" > style="color:#FFF; text-decoration: none">3 out of 940 tests failed (132 > skipped)</a></td></tr></table><table style="margin: 0.5em 0 1em > 2em"><tr><td><pre style="font-size:80%">3 tests failed. > FAILED: > dxtbx.build_dials.modules.cctbx_project.dxtbx.tests.test_regression_images.test_no_multiple_format_understanding[SACLA_MPCCD_Cheetah/run266702-0-subset.h5] > Error Message: > exit code 1 > Stack Trace: > FAILED: > dxtbx.build_dials.modules.cctbx_project.dxtbx.tests.test_regression_images.test_no_multiple_format_understanding[putative_imgCIF_HDF5_mapping/minicbf.h5] > Error Message: > exit code 1 > Stack Trace: > FAILED: > dxtbx.build_dials.modules.cctbx_project.dxtbx.tests.test_regression_images.test_no_multiple_format_understanding[putative_imgCIF_HDF5_mapping/X4_wide_M1S4_1.nxs] > Error Message: > exit code 1 > Stack Trace: > </pre></td></tr></table><table style="width:100%; background-color: > #F59400; color: #FFF; border-radius: 0.5em; margin-bottom: 0.5em"><tr><td > style="margin: 0.5em 1.25em 0.5em 0.7em; font-weight: bold; font-family: > sans-serif; font-size: 110%">Changes since the last successful > build</td></tr></table><table style="margin: 0.5em 0 1em > 2em"><tr><td><table style="padding: 0.1em 0.4em; background-color: > #F59400; color:#fff"><tr><td>145</td></tr></table></td><td>No changes > </td></tr></table><table style="width:100%; background-color: #CCC; color: > #000; border-radius: 0.5em; margin-bottom: 0.5em"><tr><td style="margin: > 0.5em 1.25em 0.5em 0.7em; font-weight: bold; font-family: sans-serif; > font-size: 110%">Build environment</td></tr></table><table style="margin: > 0.5em 0 1em 2em"><tr><td><span > style="font-size:130%"> [ </span>cctbx <strong>71a4ab94a > 2018-07-25 06:47:08 +0900</strong><span > style="font-size:130%"> | </span>DIALS regression > <strong>1924</strong>, PHENIX regression <strong>4419</strong>, DLS > Jenkins scripts <strong>8de8b58 2018-07-04 23:29:22 +0100</strong><span > style="font-size:130%"> ] </span></td></tr></table><span > style="color:#CCC;font-size:80%">mail template revision > 2487</span></body></html> > <br> > <hr> > <p align="center">To unsubscribe from the CCTBX-COMMIT list, click the > following link:<br> > <a > href="https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCTBX-COMMIT&A=1" > target="_blank">https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCTBX-COMMIT&A=1</a> > </p>

4 5

mmtbx wilson_scaling in a small molecule context
by ben.williams＠diamond.ac.uk 23 Jul '18

23 Jul '18

Hello any and all, I was looking to make use of the functionality of wilson_scaling (Wilson plot, etc.) from mmtbx.scaling.data_statistics, in the context of small molecule data. I'm new to mmtbx, so here are two (groups of) questions for the enlightened: 1. Designed, as it is, with MX in mind, wilson_scaling's __init__ demands as an argument the number of protein residues, in order to form an estimate of the contents of the asymmetric unit. If this class were to be used in a small molecule context, what would be a sensible value to use? Would spoofing n_residues with an arbitrary small number (1?) be a robust bodge? Is it ever likely to howl? 2. Being crystals of small molecules, the samples in question may have inversion centres, mirror planes. Having been designed as a tool for MX, will wilson_scaling throw a wobbly when it sees my data? Many thanks, Ben Williams Diamond Light Source -- 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

2 1

subset of reflections from mtz object
by Robert Oeffner 18 Jul '18

18 Jul '18

Hi, I'm not as well versed using iotbx.mtz as I ought to be. I'd like to make a subset of reflections from an mtz file bounded by a chosen dmin and dmax, i.e. a resolution shell of reflections. What is the best way of doing this in python? Many thanks, Rob -- Robert Oeffner, Ph.D. Research Associate, The Read Group Department of Haematology, Cambridge Institute for Medical Research University of Cambridge Cambridge Biomedical Campus Wellcome Trust/MRC Building Hills Road Cambridge CB2 0XY www.cimr.cam.ac.uk/investigators/read/index.html tel: +44(0)1223 763234

2 1

Citation for CCTBX
by Thomas, Jens 17 Jul '18

17 Jul '18

Hi, I'm updating the references printed by AMPLE and would like to cite CCTBX. Is there a recommended citation or way to acknowledge the use of CCTBX in a program? Best wishes, Jens

2 2

cctbx debug build windows
by Pascal 10 Jul '18

10 Jul '18

Hi, How do you build a debug version of cctbx on windows? After getting an environement working with bootstrap, I reconfigured with configure.py --build=debug and it is now failing when linking against python27_d.lib Any advice? Pascal

3 2

Deprecating legacy support (CentOS 5, Windows 32-bit) in CCTBX and Phenix
by Billy Poon 06 Jul '18

06 Jul '18

Hi everyone, The upcoming Phenix 1.14 official release will still have installers for CentOS 5 and Windows 32-bit, but since CentOS is no longer supporting CentOS 5, and RedHat is only supporting RHEL5 through their Extended Life Cycle Support Add-On (until November 30, 2020), we are planning on deprecating CentOS 5 support (32-bit and 64-bit). In addition, we are planning on deprecating 32-bit support for Windows because only a few percent (< 5% for both Windows and CentOS 5) of our Phenix downloads are for 32-bit versions. Please let us know if support for CentOS 5 (32-bit and/or 64-bit) or 32-bit Windows is a requirement for your systems. If so, also please describe your setup. Thanks! -- 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

2 4

Install OpenBLAS or MKL in base
by Luc Bourhis 22 Jun '18

22 Jun '18

Hi, years ago, I had wrote on this discussion list about a project of mine to dramatically accelerate scitbx.lstbx by using optimised BLAS libraries. That work had been dormant on a branch but now we are planning to move forward with the help of Pascal Parlois who will do the actual coding in the coming months. In order for this new code to be exercised by nightly tests, we, the smtbx people, need to write code so that that optimised BLAS library is installed during bootstrap. Right now, as a stopgap, I used conda to install either OpenBLAS and MKL but that won’t do with the cctbx philosophy. There are basically two choices: either OpenBLAS or MKL. When I started this project, I chose OpenBLAS because MKL was not freely redistributable, and I had got the green light to install it as needed. However now MKL has become completely free, thus becoming a possible choice. MKL is more performant on Intel but OpenBLAS is better on AMD (OpenBLAS actually runs on pretty much any processor out there but we don’t care in the context of cctbx): c.f. Julia people conclusions <https://discourse.julialang.org/t/openblas-is-faster-than-intel-mkl-on-amd-…> Now I realise that most of you may not care one way or another!?! But we won’t move forward before we got the green light… Note that I am taking about installing a BLAS usable from C++ here, not getting a BLAS-accelerated numpy. The latter could be an alternative though. But that would require to modify the bootstrap code to compile a MKL- or OpenBLAS-enabled numpy anyway. Best wishes, Luc J Bourhis

6 22

Fwd: buildbot failure in Phenix on cctbx-ci-ci
by Graeme.Winter＠Diamond.ac.uk 05 Jun '18

05 Jun '18

Hi Folks, Am I alone in finding this kind of message ** very ** annoying I did not touch this file I have no business touching this file If I do fix this then it may cause conflicts for others, which will no doubt annoy them far more than the odd extra space in the code However I am also now to blame for breaking the Phenix build, in the run up to a release This is no a happy place Suggestions? Thanks & cheerio Graeme Begin forwarded message: From: phenix(a)phenix-online.org<mailto:[email protected]> Subject: buildbot failure in Phenix on cctbx-ci-ci Date: 4 June 2018 at 12:11:19 BST To: graeme.winter(a)gmail.com<mailto:[email protected]> Cc: ASBrewster(a)LBL.Gov<mailto:[email protected]>, NWMoriarty(a)LBL.Gov<mailto:[email protected]> Build status: FAILURE Buildslave for this Build: ci Complete logs for all build steps: http://cci-vm-6.lbl.gov:8010/builders/cctbx-ci-ci/builds/5580 Build Reason: The SingleBranchScheduler scheduler named 'cctbx-ci.poll' triggered this build Build Source Stamp: clipper: [branch master] HEAD cbflib: [branch master] HEAD cctbx_project: [branch master] 4de5e7f82b0302632282f78c6dda8b999cf6abf6 annlib_adaptbx: [branch master] HEAD tntbx: [branch master] HEAD ccp4io_adaptbx: [branch master] HEAD boost: [branch master] HEAD gui_resources: [branch master] HEAD Blamelist: graeme-winter If you got an email and you didn't touch this file, it may because someone commited this file before you with an error and hasn't fixed it yet. You might have noticed the error if you ran libtbx.find_clutter on the entire tree. Detailed log of last build step: http://cci-vm-6.lbl.gov:8010/builders/cctbx-ci-ci/builds/5580/steps/test ALL clutter/logs/stdio<http://cci-vm-6.lbl.gov:8010/builders/cctbx-ci-ci/builds/5580/steps/test%20…> Last 80 lines of "test ALL clutter.stdio" iota/command_line/iota_single_image.py: tabs or trailing whitespace=2, #10, #11 *** To clean up please use: libtbx.clean_clutter *** -The Buildbot -- 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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