Hi Nigel,
xcode version is now 2343.
rosetta.run_tests does not seem to be a command available:


Seba@host028:~> xcode-select --version
xcode-select version 2343.
Seba@host028:~> rosetta.            
rosetta.build_phenix_interface            rosetta.relax_simple                      
rosetta.build_phenix_interface_1.10-2155  rosetta.relax_simple_1.10-2155            
Seba@host028:~> rosetta.run_tests
bash: rosetta.run_tests: command not found
Seba@host028:~> 


As mentioned I have just used the command:

rosetta.build_phenix_interface nproc=X

which seemed to build everything it had too without errors.

Rosetta_refine seems now to be running fine:

======================= ROSETTA/PHENIX X-ray refinement =======================

Output directory:
  /GoogleDrive/Crystallography_Unit_cloud/NuMA-LGN/xtal/phenix/rosetta_refine_161

             ----------Setting up input files for Rosetta----------            

/Applications/rosetta_src_2016.32.58837_bundle/main/source
/Applications/rosetta_src_2016.32.58837_bundle/main/source
|-starting model--------------------------------------------------------------|
| target_work(ml) = 6.38521  r_work = 0.1996  r_free = 0.2388                 |
|-----------------------------------------------------------------------------|

  Validation statistics (starting model):
    Ramachandran outliers =   2.16 %
                  favored =  92.60 %
    Rotamer outliers      =   4.46 %
    C-beta deviations     =    92
    Clashscore            =   6.96
    MolProbity score      =   2.34


Rosetta command-line arguments:
  -parser:protocol /Applications/rosetta_src_2016.32.58837_bundle/main/source/src/apps/public/crystal_refinement/low_resolution_refine.xml

[…]

  -parser:script_vars bfactstrat=individual
  -parser:script_vars map_type=Auto
  -score:weights talaris2013_cart
  -nstruct 1
  -database /Applications/rosetta_src_2016.32.58837_bundle/main/database

Generating 5 models on 5 processors...


Thanks again,
S


On 12 Sep 2016, at 17:09, Nigel Moriarty <[email protected]> wrote:

Sebastiano

It's not a bother and I'm glad you find the solution. Can you email me directly with the version of XCode you have and whether 

rosetta.run_tests

succeeds.



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, Sep 12, 2016 at 7:39 AM, Sebastiano Pasqualato <[email protected]> wrote:

OK the problem seems to be solved by running:

xcode-select —install

thanks anyway,
sorry for bothering,
ciao,
S

On 12 Sep 2016, at 16:22, Sebastiano Pasqualato <sebastiano.pasqualato@GMAIL.COM> wrote:


Hi there,
I am trying to run Phenix Rosetta Refinement on my laptop, which is running MacOSX 10.11.6 (El Capitan) with XQuartz 2.7.9.
I have followed the instructions on this page:


and specifically 

Once you have both a Phenix installation and a Rosetta source distribution, you can build the hybrid system with this command (located in the Phenix tree):

rosetta.build_phenix_interface nproc=X

Unfortunately, when I do that, the building does not proceed flawlessly, but instead stops with the message the I report below.
Has someone gone through the same and can tell me how to set up Rosetta to be used with Phenix?

Thanks in advance for the help,
Sebastiano

Seba@host028:~> rosetta.build_phenix_interface nproc=8
False
scons: Reading SConscript files ...
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
Running versioning script ... xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
Done. (0.0 seconds)
Number of option files updated: 0
Total 3741 options.
Finished updating ResidueProperty code -- no changes needed
Finished updating VariantType code -- no changes needed
scons: done reading SConscript files.
scons: Building targets ...
clang++ -o build/src/release/macos/15.6/64/x86/clang/python/apps/public/AbinitioRelax.o -c -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -std=c++11 -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -O3 -Wno-unused-variable -Wno-unused-parameter -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DCXX11 -DPTR_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/apps/public/AbinitioRelax.cc
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
clang++ -o build/src/release/macos/15.6/64/x86/clang/python/devel/init.os -c -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -std=c++11 -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -O3 -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DCXX11 -DPTR_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/devel/init.cc
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
clang++ -o build/src/release/macos/15.6/64/x86/clang/python/devel/svn_version.os -c -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -std=c++11 -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -O3 -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DCXX11 -DPTR_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/devel/svn_version.cc
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
clang++ -o build/src/release/macos/15.6/64/x86/clang/python/protocols/init/init.os -c -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -std=c++11 -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -O3 -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DCXX11 -DPTR_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/init/init.cc
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
clang++ -o build/src/release/macos/15.6/64/x86/clang/python/protocols/match/output/DownstreamRMSEvaluator.os -c -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -std=c++11 -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -O3 -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DCXX11 -DPTR_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/match/output/DownstreamRMSEvaluator.cc
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
clang++ -o build/src/release/macos/15.6/64/x86/clang/python/protocols/match/output/LimitHitsPerRotamerFilter.os -c -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -std=c++11 -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -O3 -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DCXX11 -DPTR_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/match/output/LimitHitsPerRotamerFilter.cc
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
clang++ -o build/src/release/macos/15.6/64/x86/clang/python/protocols/match/output/MatchConsolidator.os -c -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -std=c++11 -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -O3 -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DCXX11 -DPTR_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/match/output/MatchConsolidator.cc
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
scons: *** [build/src/release/macos/15.6/64/x86/clang/python/apps/public/AbinitioRelax.o] Error 1
clang++ -o build/src/release/macos/15.6/64/x86/clang/python/protocols/match/output/MatchEvaluator.os -c -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -std=c++11 -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -O3 -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DCXX11 -DPTR_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/match/output/MatchEvaluator.cc
scons: *** [build/src/release/macos/15.6/64/x86/clang/python/devel/init.os] Error 1
scons: *** [build/src/release/macos/15.6/64/x86/clang/python/devel/svn_version.os] Error 1
scons: *** [build/src/release/macos/15.6/64/x86/clang/python/protocols/init/init.os] Error 1
scons: *** [build/src/release/macos/15.6/64/x86/clang/python/protocols/match/output/DownstreamRMSEvaluator.os] Error 1
scons: *** [build/src/release/macos/15.6/64/x86/clang/python/protocols/match/output/LimitHitsPerRotamerFilter.os] Error 1
scons: *** [build/src/release/macos/15.6/64/x86/clang/python/protocols/match/output/MatchConsolidator.os] Error 1
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
scons: *** [build/src/release/macos/15.6/64/x86/clang/python/protocols/match/output/MatchEvaluator.os] Error 1
scons: building terminated because of errors.
Seba@host028:~> 

-- 
Sebastiano Pasqualato, PhD
Crystallography Unit
Department of Experimental Oncology
European Institute of Oncology
IFOM-IEO Campus
via Adamello, 16
20139 - Milano
Italy

tel +39 02 9437 5167
fax +39 02 9437 5990



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