[phenixbb] rosetta installation

Sebastiano Pasqualato sebastiano.pasqualato at gmail.com
Mon Sep 12 09:21:36 PDT 2016 

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


Seba at host028:~> xcode-select --version
xcode-select version 2343.
Seba at host028:~> rosetta.            
rosetta.build_phenix_interface            rosetta.relax_simple                      
rosetta.build_phenix_interface_1.10-2155  rosetta.relax_simple_1.10-2155            
Seba at host028:~> rosetta.run_tests
bash: rosetta.run_tests: command not found
Seba at 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 <nwmoriarty at lbl.gov> 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 : NWMoriarty at LBL.gov
> Fax   : 510-486-5909       Web  : CCI.LBL.gov <http://cci.lbl.gov/>
> On Mon, Sep 12, 2016 at 7:39 AM, Sebastiano Pasqualato <sebastiano.pasqualato at gmail.com <mailto:sebastiano.pasqualato at gmail.com>> 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 at GMAIL.COM <mailto:sebastiano.pasqualato at 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:
>> 
>> https://www.phenix-online.org/documentation/reference/rosetta_refine.html <https://www.phenix-online.org/documentation/reference/rosetta_refine.html>
>> 
>> 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 at 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 <http://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 <http://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 <http://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 <http://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 <http://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 <http://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 <http://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 at 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 <tel:%2B39%2002%209437%205167>
>> fax +39 02 9437 5990 <tel:%2B39%2002%209437%205990>
>> web http://is.gd/IEOXtalUnit <http://is.gd/IEOXtalUnit>
> 
> 
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