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@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@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@gmail.com>
Sent: Monday, August 12, 2019 3:34 PM
To: Charitha Belluru Shetty <charitha-belluru.b.shetty@gsk.com>
Cc: Nigel Moriarty (nwmoriarty@lbl.gov) <nwmoriarty@lbl.gov>; cctbxbb@phenix-online.org; Robert Nolte <robert.t.nolte@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

 

 

 

 

 

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