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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov On Mon, Aug 12, 2019 at 2:58 PM Robert Nolte 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 *Sent:* Monday, August 12, 2019 5:55 PM *To:* Robert Nolte *Cc:* Charitha Belluru Shetty ; Christopher Williams ; [email protected] *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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov

On Mon, Aug 12, 2019 at 2:44 PM Robert Nolte 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 *Sent:* Monday, August 12, 2019 4:52 PM *To:* Charitha Belluru Shetty *Cc:* Christopher Williams ; [email protected]; Robert Nolte *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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov

On Mon, Aug 12, 2019 at 1:14 PM Charitha Belluru Shetty < [email protected]> 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 *Sent:* Monday, August 12, 2019 4:08 PM *To:* Charitha Belluru Shetty *Cc:* Christopher Williams ; [email protected]; Robert Nolte *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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov

On Mon, Aug 12, 2019 at 12:43 PM Charitha Belluru Shetty < [email protected]> 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 *Sent:* Monday, August 12, 2019 3:34 PM *To:* Charitha Belluru Shetty *Cc:* Nigel Moriarty ([email protected]) ; [email protected]; Robert Nolte *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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