Dear Nigel, Switching to rosetta 3.7 did the trick. Thanks a lot for the tip. Ludovic.

On 07 Nov 2016, at 18:39, Nigel Moriarty wrote:

Ludovic

Can you move to Rosetta 3.7 and let me know if it still fails?

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 http://cci.lbl.gov/ On Thu, Nov 3, 2016 at 9:16 AM, ludovic Pecqueur mailto:[email protected]> wrote: Dear Phenix developers,

I installed the latest phenix version today (1.11.1-2575) on Centos 7.2 I have rosetta_2016.13.58602

When I try to compile the rosetta interface (after exporting PHENIX_ROSETTA_PATH), compilation fails (see end of message for errors).

When I compile the rosetta interface using phenix 1.11-2567, compilation goes to completion without errors.

If you have any idea of the change between the two versions leading to this issue.

Thank you for your help,

Ludovic.

######################## Error message:

Substituting phenix.python into build shell scripts update_options.sh update_ResidueType_enum_files.sh /usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/rosetta_src_2016.13.58602_bundle/main/source

~> phenix.python scons.py bin mode=release extras=python -j 8

scons: Reading SConscript files ... Running versioning script ... fatal: Not a git repository (or any parent up to mount point /usr/local) Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). Done. (0.0 seconds) file ./options.dox being updated file ./full-options-list.md http://full-options-list.md/ being updated Number of option files updated: 2 Total 3657 options. Finished updating ResidueProperty code -- no changes needed Finished updating VariantType code -- no changes needed scons: done reading SConscript files. scons: Building targets ... g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/python/protocols/hybridization/CartesianSampler.os -c -std=c++98 -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/hybridization/CartesianSampler.cc In file included from src/protocols/hybridization/CartesianSampler.cc:17:0: src/core/scoring/cryst/PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory #include "Python.h" ^ compilation terminated. g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/python/protocols/cryst/cryst_movers.os -c -std=c++98 -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/cryst/cryst_movers.cc In file included from src/protocols/cryst/cryst_movers.cc:16:0: src/core/scoring/cryst/PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory #include "Python.h" ^ compilation terminated. gcc -o build/external/release/linux/3.10/64/x86/gcc/4.8/python/libsqlite3.so -shared build/external/release/linux/3.10/64/x86/gcc/4.8/python/dbio/sqlite3/sqlite3.os -L/usr/lib -L/usr/local/lib -Lexternal/lib -lpython2.7 -ldl -lpthread -lutil g++ -o build/external/release/linux/3.10/64/x86/gcc/4.8/python/libcifparse.so -Wl,-rpath=/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/rosetta_src_2016.13.58602_bundle/main/source/build/external/release/linux/3.10/64/x86/gcc/4.8/python -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib -shared build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/BlockIO.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifDataInfo.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifExcept.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifFile.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifFileReadDef.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifParentChild.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifParserBase.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifScannerBase.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifString.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DataInfo.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DicFile.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DICParserBase.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DICScannerBase.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/Exceptions.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/GenCont.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/GenString.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/ISTable.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/ITTable.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/mapped_ptr_vector.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/mapped_vector.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/ParentChild.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/RcsbFile.! os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/RcsbPlatform.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/Serializer.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/TableFile.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/TTable.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifParser.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifScanner.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DICParser.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DICScanner.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/regcomp.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/regerror.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/regexec.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/regfree.os -Lexternal/lib -Lbuild/external/release/linux/3.10/64/x86/gcc/4.8/python -Lexternal -L/usr/lib -L/usr/local/lib -lpython2.7 -ldl -lpthread -lutil g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/python/core/scoring/cryst/PhenixInterface.os -c -std=c++98 -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/core/scoring/cryst/PhenixInterface.cc In file included from src/core/scoring/cryst/PhenixInterface.cc:15:0: src/core/scoring/cryst/PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory #include "Python.h" ^ compilation terminated. g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/python/core/scoring/cryst/XtalMLEnergy.os -c -std=c++98 -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/core/scoring/cryst/XtalMLEnergy.cc In file included from src/core/scoring/cryst/XtalMLEnergy.cc:16:0: src/core/scoring/cryst/PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory #include "Python.h" ^ compilation terminated. scons: *** [build/src/release/linux/3.10/64/x86/gcc/4.8/python/protocols/hybridization/CartesianSampler.os] Error 1 scons: *** [build/src/release/linux/3.10/64/x86/gcc/4.8/python/protocols/cryst/cryst_movers.os] Error 1 scons: *** [build/src/release/linux/3.10/64/x86/gcc/4.8/python/core/scoring/cryst/PhenixInterface.os] Error 1 scons: *** [build/src/release/linux/3.10/64/x86/gcc/4.8/python/core/scoring/cryst/XtalMLEnergy.os] Error 1 scons: building terminated because of errors.

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Dear Reza, We do have a new method to do that in a development version of Phaser, which should become part of the official release at some point in the not so distant future. This is part of some wider work to adapt Phaser’s algorithms for real space molecular replacement to work better in the cryo-EM docking problem. So far, the magnification factor refinement seems to be pretty robust in our tests. If you have a particular urgent case at hand, there’s a workaround you could apply. Basically, we already had the machinery to do what is needed, but in the other direction: the released version of Phaser can refine the magnification factor for a cryo-EM reconstruction being used to solve a crystal structure. The trick is that you have to treat the cryo-EM data as the diffraction data and turn the atomic model into a density model (e.g. by putting it into a P1 cell 3-4 times the molecular width in each direction and running phenix.fmodel), and then refine the cell scale parameter as well as the rotation and translation parameters. If you want more information, get in touch directly and I can give you a sample script! Best wishes, Randy Read ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hills Road E-mail: [email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

On 3 Apr 2017, at 22:30, Reza Khayat wrote:

Hi,

Is there a method to refine the pixel size of an image reconstruction if the PDB has been docked in? Thanks.

Best wishes, Reza

Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031 From: [email protected] on behalf of [email protected] Sent: Tuesday, November 8, 2016 10:28 AM To: Nigel Moriarty Cc: [email protected] Subject: Re: [phenixbb] Cannot compile rosetta interface Centos 7 with 1.11.1

Dear Nigel,

Switching to rosetta 3.7 did the trick.

Thanks a lot for the tip.

Ludovic.

...

On 07 Nov 2016, at 18:39, Nigel Moriarty wrote:

Ludovic

Can you move to Rosetta 3.7 and let me know if it still fails?

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 Thu, Nov 3, 2016 at 9:16 AM, ludovic Pecqueur wrote: Dear Phenix developers,

I installed the latest phenix version today (1.11.1-2575) on Centos 7.2 I have rosetta_2016.13.58602

When I try to compile the rosetta interface (after exporting PHENIX_ROSETTA_PATH), compilation fails (see end of message for errors).

When I compile the rosetta interface using phenix 1.11-2567, compilation goes to completion without errors.

If you have any idea of the change between the two versions leading to this issue.

Thank you for your help,

Ludovic.

######################## Error message:

Substituting phenix.python into build shell scripts update_options.sh update_ResidueType_enum_files.sh /usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/rosetta_src_2016.13.58602_bundle/main/source

~> phenix.python scons.py bin mode=release extras=python -j 8

scons: Reading SConscript files ... Running versioning script ... fatal: Not a git repository (or any parent up to mount point /usr/local) Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). Done. (0.0 seconds) file ./options.dox being updated file ./full-options-list.md being updated Number of option files updated: 2 Total 3657 options. Finished updating ResidueProperty code -- no changes needed Finished updating VariantType code -- no changes needed scons: done reading SConscript files. scons: Building targets ... g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/python/protocols/hybridization/CartesianSampler.os -c -std=c++98 -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/hybridization/CartesianSampler.cc In file included from src/protocols/hybridization/CartesianSampler.cc:17:0: src/core/scoring/cryst/PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory #include "Python.h" ^ compilation terminated. g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/python/protocols/cryst/cryst_movers.os -c -std=c++98 -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/cryst/cryst_movers.cc In file included from src/protocols/cryst/cryst_movers.cc:16:0: src/core/scoring/cryst/PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory #include "Python.h" ^ compilation terminated. gcc -o build/external/release/linux/3.10/64/x86/gcc/4.8/python/libsqlite3.so -shared build/external/release/linux/3.10/64/x86/gcc/4.8/python/dbio/sqlite3/sqlite3.os -L/usr/lib -L/usr/local/lib -Lexternal/lib -lpython2.7 -ldl -lpthread -lutil g++ -o build/external/release/linux/3.10/64/x86/gcc/4.8/python/libcifparse.so -Wl,-rpath=/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/rosetta_src_2016.13.58602_bundle/main/source/build/external/release/linux/3.10/64/x86/gcc/4.8/python -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib -shared build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/BlockIO.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifDataInfo.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifExcept.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifFile.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifFileReadDef.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifParentChild.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifParserBase.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifScannerBase.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifString.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DataInfo.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DicFile.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DICParserBase.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DICScannerBase.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/Exceptions.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/GenCont.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/GenString.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/ISTable.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/ITTable.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/mapped_ptr_vector.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/mapped_vector.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/ParentChild.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/RcsbFile.! os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/RcsbPlatform.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/Serializer.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/TableFile.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/TTable.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifParser.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifScanner.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DICParser.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DICScanner.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/regcomp.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/regerror.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/regexec.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/regfree.os -Lexternal/lib -Lbuild/external/release/linux/3.10/64/x86/gcc/4.8/python -Lexternal -L/usr/lib -L/usr/local/lib -lpython2.7 -ldl -lpthread -lutil g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/python/core/scoring/cryst/PhenixInterface.os -c -std=c++98 -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/core/scoring/cryst/PhenixInterface.cc In file included from src/core/scoring/cryst/PhenixInterface.cc:15:0: src/core/scoring/cryst/PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory #include "Python.h" ^ compilation terminated. g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/python/core/scoring/cryst/XtalMLEnergy.os -c -std=c++98 -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/core/scoring/cryst/XtalMLEnergy.cc In file included from src/core/scoring/cryst/XtalMLEnergy.cc:16:0: src/core/scoring/cryst/PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory #include "Python.h" ^ compilation terminated. scons: *** [build/src/release/linux/3.10/64/x86/gcc/4.8/python/protocols/hybridization/CartesianSampler.os] Error 1 scons: *** [build/src/release/linux/3.10/64/x86/gcc/4.8/python/protocols/cryst/cryst_movers.os] Error 1 scons: *** [build/src/release/linux/3.10/64/x86/gcc/4.8/python/core/scoring/cryst/PhenixInterface.os] Error 1 scons: *** [build/src/release/linux/3.10/64/x86/gcc/4.8/python/core/scoring/cryst/XtalMLEnergy.os] Error 1 scons: building terminated because of errors.

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No, no tools to abuse file formats, sorry 🙂 Pavel On Apr 20, 2017 3:10 PM, "Reza Khayat" wrote:

Hi,

Is there a phenix program that will insert the calculated CC (between the PDB and map) into the B-factor column? Thanks.

Best wishes, Reza

Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031 ------------------------------ *From:* [email protected] on behalf of [email protected] < [email protected]> *Sent:* Tuesday, November 8, 2016 10:28 AM *To:* Nigel Moriarty *Cc:* [email protected] *Subject:* Re: [phenixbb] Cannot compile rosetta interface Centos 7 with 1.11.1

Dear Nigel,

Switching to rosetta 3.7 did the trick.

Thanks a lot for the tip.

Ludovic.

On 07 Nov 2016, at 18:39, Nigel Moriarty wrote:

Ludovic

Can you move to Rosetta 3.7 and let me know if it still fails?

Cheers

Nigel

--- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 <947%2020%2082%2035> Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov https://urldefense.proofpoint.com/v2/url?u=http-3A__cci.lbl.gov_&d=DgMFAw&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=jCBuhFtksZ8bTlBMxgH6J9UDJ3CkcE-GQK2yZyIY3mg&m=CclpQbOUSrklcMjwFZmST7ev5xmpm7vPsNVtOHsU1GA&s=j9KRfzD1wS0qoGc9M1kgp2NfeTcgpdZ63qi0nzh4Wdw&e=

On Thu, Nov 3, 2016 at 9:16 AM, ludovic Pecqueur < [email protected]> wrote:

...

Dear Phenix developers,

I installed the latest phenix version today (1.11.1-2575) on Centos 7.2 I have rosetta_2016.13.58602

When I try to compile the rosetta interface (after exporting PHENIX_ROSETTA_PATH), compilation fails (see end of message for errors).

When I compile the rosetta interface using phenix 1.11-2567, compilation goes to completion without errors.

If you have any idea of the change between the two versions leading to this issue.

Thank you for your help,

Ludovic.

######################## Error message:

Substituting phenix.python into build shell scripts update_options.sh update_ResidueType_enum_files.sh /usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/rosetta_sr c_2016.13.58602_bundle/main/source

~> phenix.python scons.py bin mode=release extras=python -j 8

scons: Reading SConscript files ... Running versioning script ... fatal: Not a git repository (or any parent up to mount point /usr/local) Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). Done. (0.0 seconds) file ./options.dox being updated file ./full-options-list.md https://urldefense.proofpoint.com/v2/url?u=http-3A__full-2Doptions-2Dlist.md_&d=DgMFAw&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=jCBuhFtksZ8bTlBMxgH6J9UDJ3CkcE-GQK2yZyIY3mg&m=CclpQbOUSrklcMjwFZmST7ev5xmpm7vPsNVtOHsU1GA&s=QQ-WkxsPQmBAfCDpGq6Kiqi769wKOQiKKsMiZgaaIFs&e= being updated Number of option files updated: 2 Total 3657 options. Finished updating ResidueProperty code -- no changes needed Finished updating VariantType code -- no changes needed scons: done reading SConscript files. scons: Building targets ... g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/python/protocols /hybridization/CartesianSampler.os -c -std=c++98 -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/hybridization/CartesianSampler.cc https://urldefense.proofpoint.com/v2/url?u=http-3A__cartesiansampler.cc&d=DgMFAw&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=jCBuhFtksZ8bTlBMxgH6J9UDJ3CkcE-GQK2yZyIY3mg&m=CclpQbOUSrklcMjwFZmST7ev5xmpm7vPsNVtOHsU1GA&s=s1h3iBFqQztjSfFsFE-tj-D2VWkeV7BFeDkTFNrnHnw&e= In file included from src/protocols/hybridization/Ca rtesianSampler.cc:17:0: src/core/scoring/cryst/PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory #include "Python.h" ^ compilation terminated. g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/python/protocols/cryst/cryst_movers.os -c -std=c++98 -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/cryst/cryst_movers.cc In file included from src/protocols/cryst/cryst_movers.cc:16:0: src/core/scoring/cryst/PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory #include "Python.h" ^ compilation terminated. gcc -o build/external/release/linux/3.10/64/x86/gcc/4.8/python/libsqlite3.so -shared build/external/release/linux/3.10/64/x86/gcc/4.8/python/dbio/sqlite3/sqlite3.os -L/usr/lib -L/usr/local/lib -Lexternal/lib -lpython2.7 -ldl -lpthread -lutil g++ -o build/external/release/linux/3.10/64/x86/gcc/4.8/python/libcifparse.so -Wl,-rpath=/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_ refine/rosetta_src_2016.13.58602_bundle/main/source/ build/external/release/linux/3.10/64/x86/gcc/4.8/python -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib -shared build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/BlockIO.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifDataInfo.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifExcept.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifFile.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifFileReadDef.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifParentChild.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifParserBase.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifScannerBase.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifString.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DataInfo.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DicFile.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DICParserBase.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DICScannerBase.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/Exceptions.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/GenCont.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/GenString.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/ISTable.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/ITTable.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/mapped_ptr_vector.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/mapped_vector.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/ParentChild.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifp arse/RcsbFile.! os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/RcsbPlatform.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/Serializer.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/TableFile.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/TTable.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifParser.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifScanner.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DICParser.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DICScanner.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/regcomp.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/regerror.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/regexec.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/regfree.os -Lexternal/lib -Lbuild/external/release/linux/3.10/64/x86/gcc/4.8/python -Lexternal -L/usr/lib -L/usr/local/lib -lpython2.7 -ldl -lpthread -lutil g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/python/core/scoring/cryst/PhenixInterface.os -c -std=c++98 -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/core/scoring/cryst/PhenixInterface.cc In file included from src/core/scoring/cryst/PhenixInterface.cc:15:0: src/core/scoring/cryst/PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory #include "Python.h" ^ compilation terminated. g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/python/core/scoring/cryst/XtalMLEnergy.os -c -std=c++98 -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/core/scoring/cryst/XtalMLEnergy.cc In file included from src/core/scoring/cryst/XtalMLEnergy.cc:16:0: src/core/scoring/cryst/PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory #include "Python.h" ^ compilation terminated. scons: *** [build/src/release/linux/3.10/64/x86/gcc/4.8/python/protocol s/hybridization/CartesianSampler.os] Error 1 scons: *** [build/src/release/linux/3.10/64/x86/gcc/4.8/python/protocols/cryst/cryst_movers.os] Error 1 scons: *** [build/src/release/linux/3.10/64/x86/gcc/4.8/python/core/scoring/cryst/PhenixInterface.os] Error 1 scons: *** [build/src/release/linux/3.10/64/x86/gcc/4.8/python/core/scoring/cryst/XtalMLEnergy.os] Error 1 scons: building terminated because of errors.

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It can be done with a very simple python or perl script that parses both the PDB file and the file with CC values, and then replaces corresponding B-factors with CC. 

Oleg

 
Oleg Borbulevych, Ph.D.
Staff Scientist
QuantumBio, Inc.
2790 W. College Ave.
State College, PA 16801
E-mail: [email protected], [email protected]
Linkedin Professional Profile: http://www.linkedin.com/pub/oleg-borbulevych/22/454/b80


-----Original Message-----
From: "Tim Gruene" 
Sent: Friday, April 21, 2017 3:59am
To: "PHENIX user mailing list" 
Subject: Re: [phenixbb] Calculating CC and inserting it into B-factor

_______________________________________________
phenixbb mailing list
[email protected]
http://phenix-online.org/mailman/listinfo/phenixbb
Unsubscribe: [email protected] Reza,

this could be achieved with some command line tools. 
If you have the CC per atom in the same order as the atoms in the PDB file,

I would strip the PDB file off anything but the ATOM cards, remove everything 
per line beyond the occupancy and paste the two files together. 
You can add the header afterwards.

Best regards,
Tim

On Thursday 20 April 2017 10:07:11 PM Reza Khayat wrote:
> Hi,
> 
> 
> Is there a phenix program that will insert the calculated CC (between the
> PDB and map) into the B-factor column? Thanks.
> 
> 
> Best wishes,
> Reza
> 
> 
> Reza Khayat, PhD
> Assistant Professor
> City College of New York
> Department of Chemistry
> New York, NY 10031
> ________________________________
> From: [email protected]
>  on behalf of
> [email protected]
>  Sent: Tuesday, November 8, 2016
> 10:28 AM
> To: Nigel Moriarty
> Cc: [email protected]
> Subject: Re: [phenixbb] Cannot compile rosetta interface Centos 7 with
> 1.11.1
> 
> Dear Nigel,
> 
> Switching to rosetta 3.7 did the trick.
> 
> Thanks a lot for the tip.
> 
> Ludovic.
> 
> 
> On 07 Nov 2016, at 18:39, Nigel Moriarty
> > wrote:
> 
> Ludovic
> 
> Can you move to Rosetta 3.7 and let me know if it still fails?
> 
> 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 _&d=DgIFAw&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=jCBuhFtksZ8bTlBMx
> gH6J9UDJ3CkcE-GQK2yZyIY3mg&m=CclpQbOUSrklcMjwFZmST7ev5xmpm7vPsNVtOHsU1GA&s=j
> 9KRfzD1wS0qoGc9M1kgp2NfeTcgpdZ63qi0nzh4Wdw&e= >
> 
> On Thu, Nov 3, 2016 at 9:16 AM, ludovic Pecqueur
>  rance.fr>> wrote: Dear Phenix developers,
> 
> I installed the latest phenix version today (1.11.1-2575) on Centos 7.2
> I have rosetta_2016.13.58602
> 
> When I try to compile the rosetta interface (after exporting
> PHENIX_ROSETTA_PATH), compilation fails (see end of message for errors).
> 
> When I compile the rosetta interface using phenix 1.11-2567, compilation
> goes to completion without errors.
> 
> If you have any idea of the change between the two versions leading to this
> issue.
> 
> Thank you for your help,
> 
> Ludovic.
> 
> ########################
> Error message:
> 
> Substituting phenix.python into build shell scripts
>   update_options.sh
>   update_ResidueType_enum_files.sh
> /usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/rosetta_src_2016.13.58602_
> bundle/main/source
> 
>   ~> phenix.python scons.py bin mode=release extras=python  -j 8
> 
> scons: Reading SConscript files ...
> Running versioning script ... fatal: Not a git repository (or any parent up
> to mount point /usr/local) Stopping at filesystem boundary
> (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). Done. (0.0 seconds)
> file ./options.dox being updated
> file
> ./full-options-list.md full-2Doptions-2Dlist.md_&d=DgIFAw&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtI
> MGmo&r=jCBuhFtksZ8bTlBMxgH6J9UDJ3CkcE-GQK2yZyIY3mg&m=CclpQbOUSrklcMjwFZmST7e
> v5xmpm7vPsNVtOHsU1GA&s=QQ-WkxsPQmBAfCDpGq6Kiqi769wKOQiKKsMiZgaaIFs&e= >
> being updated Number of option files updated: 2
> Total 3657 options.
> Finished updating ResidueProperty code -- no changes needed
> Finished updating VariantType code -- no changes needed
> scons: done reading SConscript files.
> scons: Building targets ...
> g++ -o
> build/src/release/linux/3.10/64/x86/gcc/4.8/python/protocols/hybridization/
> CartesianSampler.os -c -std=c++98 -ffor-scope -isystem
> external/boost_1_55_0/ -isystem external/ -isystem external/include/
> -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Wno-long-long
> -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math
> -funroll-loops -finline-functions -finline-limit=20000 -s
> -Wno-unused-variable -Wno-unused-parameter -fPIC
> -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED
> -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG
> -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8
> -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux
> -Iexternal/boost_1_55_0 -Iexternal -Iexternal/dbio -I/usr/include
> -I/usr/local/include -Iexternal/include/python2.7
> src/protocols/hybridization/CartesianSampler.cc nt.com/v2/url?u=http-3A__cartesiansampler.cc&d=DgIFAw&c=4NmamNZG3KTnUCoC6Ino
> LJ6KV1tbVKrkZXHRwtIMGmo&r=jCBuhFtksZ8bTlBMxgH6J9UDJ3CkcE-GQK2yZyIY3mg&m=Cclp
> QbOUSrklcMjwFZmST7ev5xmpm7vPsNVtOHsU1GA&s=s1h3iBFqQztjSfFsFE-tj-D2VWkeV7BFeD
> kTFNrnHnw&e= > In file included from
> src/protocols/hybridization/CartesianSampler.cc:17:0:
> src/core/scoring/cryst/PhenixInterface.hh:18:20: fatal error: Python.h: No
> such file or directory #include "Python.h"
>                     ^
> compilation terminated.
> g++ -o
> build/src/release/linux/3.10/64/x86/gcc/4.8/python/protocols/cryst/cryst_mo
> vers.os -c -std=c++98 -ffor-scope -isystem external/boost_1_55_0/ -isystem
> external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall
> -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2
> -mtune=generic -O3 -ffast-math -funroll-loops -finline-functions
> -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC
> -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED
> -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG
> -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8
> -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux
> -Iexternal/boost_1_55_0 -Iexternal -Iexternal/dbio -I/usr/include
> -I/usr/local/include -Iexternal/include/python2.7
> src/protocols/cryst/cryst_movers.cc In file included from
> src/protocols/cryst/cryst_movers.cc:16:0:
> src/core/scoring/cryst/PhenixInterface.hh:18:20: fatal error: Python.h: No
> such file or directory #include "Python.h"
>                     ^
> compilation terminated.
> gcc -o build/external/release/linux/3.10/64/x86/gcc/4.8/python/libsqlite3.so
> -shared
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/dbio/sqlite3/sqlite
> 3.os -L/usr/lib -L/usr/local/lib -Lexternal/lib -lpython2.7 -ldl -lpthread
> -lutil g++ -o
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/libcifparse.so
> -Wl,-rpath=/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/rosetta_src_20
> 16.13.58602_bundle/main/source/build/external/release/linux/3.10/64/x86/gcc/
> 4.8/python -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib -shared
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/BlockIO.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifDataInf
> o.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifExcept.
> os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifFile.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifFileRea
> dDef.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifParentC
> hild.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifParserB
> ase.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifScanner
> Base.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifString.
> os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DataInfo.o
> s
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DicFile.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DICParserB
> ase.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DICScanner
> Base.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/Exceptions
> .os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/GenCont.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/GenString.
> os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/ISTable.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/ITTable.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/mapped_ptr
> _vector.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/mapped_vec
> tor.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/ParentChil
> d.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/RcsbFile.!
> os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/RcsbPlatfo
> rm.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/Serializer
> .os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/TableFile.
> os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/TTable.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifParser.
> os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifScanner
> .os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DICParser.
> os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DICScanner
> .os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/regcomp.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/regerror.o
> s
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/regexec.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/regfree.os
> -Lexternal/lib -Lbuild/external/release/linux/3.10/64/x86/gcc/4.8/python
> -Lexternal -L/usr/lib -L/usr/local/lib -lpython2.7 -ldl -lpthread -lutil
> g++ -o
> build/src/release/linux/3.10/64/x86/gcc/4.8/python/core/scoring/cryst/Pheni
> xInterface.os -c -std=c++98 -ffor-scope -isystem external/boost_1_55_0/
> -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe
> -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2
> -mtune=generic -O3 -ffast-math -funroll-loops -finline-functions
> -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC
> -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED
> -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG
> -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8
> -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux
> -Iexternal/boost_1_55_0 -Iexternal -Iexternal/dbio -I/usr/include
> -I/usr/local/include -Iexternal/include/python2.7
> src/core/scoring/cryst/PhenixInterface.cc In file included from
> src/core/scoring/cryst/PhenixInterface.cc:15:0:
> src/core/scoring/cryst/PhenixInterface.hh:18:20: fatal error: Python.h: No
> such file or directory #include "Python.h"
>                     ^
> compilation terminated.
> g++ -o
> build/src/release/linux/3.10/64/x86/gcc/4.8/python/core/scoring/cryst/XtalM
> LEnergy.os -c -std=c++98 -ffor-scope -isystem external/boost_1_55_0/
> -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe
> -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2
> -mtune=generic -O3 -ffast-math -funroll-loops -finline-functions
> -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC
> -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED
> -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG
> -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8
> -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux
> -Iexternal/boost_1_55_0 -Iexternal -Iexternal/dbio -I/usr/include
> -I/usr/local/include -Iexternal/include/python2.7
> src/core/scoring/cryst/XtalMLEnergy.cc In file included from
> src/core/scoring/cryst/XtalMLEnergy.cc:16:0:
> src/core/scoring/cryst/PhenixInterface.hh:18:20: fatal error: Python.h: No
> such file or directory #include "Python.h"
>                     ^
> compilation terminated.
> scons: ***
> [build/src/release/linux/3.10/64/x86/gcc/4.8/python/protocols/hybridization
> /CartesianSampler.os] Error 1 scons: ***
> [build/src/release/linux/3.10/64/x86/gcc/4.8/python/protocols/cryst/cryst_m
> overs.os] Error 1 scons: ***
> [build/src/release/linux/3.10/64/x86/gcc/4.8/python/core/scoring/cryst/Phen
> ixInterface.os] Error 1 scons: ***
> [build/src/release/linux/3.10/64/x86/gcc/4.8/python/core/scoring/cryst/Xtal
> MLEnergy.os] Error 1 scons: building terminated because of errors.
> 
> 
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-- 
--
Paul Scherrer Institut
Dr. Tim Gruene
- persoenlich -
Principal Investigator
Biology and Chemistry
OFLC/104
CH-5232 Villigen PSI

Phone: +41 (0)56 310 5297

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