<div dir="ltr"><div><div><div><div><div><div>I am having some trouble setting up <span class="gmail-il">phenix</span>.rosetta_refine on my Kubuntu 16.04 LTS-system.<br><br>I've been following the instructions found here: <a href="https://www.phenix-online.org/documentation/reference/rosetta_install.html">https://www.phenix-online.org/documentation/reference/rosetta_install.html</a><br><br>The installation/compilation of Rosetta as such (rosetta_src_2016.37.58930_bundle.tgz) worked fine, and so did installing the latest version of <span class="gmail-il">Phenix - here, I've tried both the binary available for download (</span><span class="gmail-il">phenix</span>-installer-1.10.1-2155-<wbr>intel-linux-2.6-x86_64-<wbr>centos6) and a self-compiled version (phenix-installer-1.11-2567-source).<br><br></div>But when running<br><br></div>rosetta.build_phenix_interface<br><br></div>(both with nproc=6 or no multiple processor options set), the compilation crashes at some point. This takes quite a while, and I suspect most parts get compiled, but it does not run to completion.<br><br></div>Any ideas? I attach the output of the error message below.<br><br><br></div>Best wishes,<br><br></div>Gerhard<br><div><div><div><div><div><div><br><br><div><br></div><div>------ stdout ----<br>g++ -o build/src/release/linux/4.4/64/x86/gcc/5.4/python/core/scoring/cryst/PhenixInterface.os -c -std=c++11 -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_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/5.4 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/core/scoring/cryst/PhenixInterface.cc<br>src/core/scoring/cryst/PhenixInterface.cc: In member function 'void core::scoring::cryst::PhenixInterface::fitBfactors(core::pose::Pose&)':<br>src/core/scoring/cryst/PhenixInterface.cc:253:34: error: no matching function for call to 'core::pose::Pose::dump_pdb(char [256], const char [2])'<br> pose_asu.dump_pdb( pdbout , "1" );<br> ^<br>In file included from src/core/scoring/cryst/PhenixInterface.cc:18:0:<br>src/core/pose/Pose.hh:1518:2: note: candidate: bool core::pose::Pose::dump_pdb(const string&) const<br> dump_pdb(std::string const & file_name) const;<br> ^<br>src/core/pose/Pose.hh:1518:2: note: candidate expects 1 argument, 2 provided<br>src/core/pose/Pose.hh:1521:2: note: candidate: void core::pose::Pose::dump_pdb(std::ostream&) const<br> dump_pdb(std::ostream & out) const;<br> ^<br>src/core/pose/Pose.hh:1521:2: note: candidate expects 1 argument, 2 provided<br>src/core/pose/Pose.hh:1525:2: note: candidate: void core::pose::Pose::dump_pdb(std::ostream&, const utility::vector1<long unsigned int>&) const<br> dump_pdb(<br> ^<br>src/core/pose/Pose.hh:1525:2: note: no known conversion for argument 1 from 'char [256]' to 'std::ostream& {aka std::basic_ostream<char>&}'<br>src/core/scoring/cryst/PhenixInterface.cc: In member function 'void core::scoring::cryst::PhenixInterface::initialize_target_evaluator(const core::pose::Pose&, std::__cxx11::string)':<br>src/core/scoring/cryst/PhenixInterface.cc:916:34: error: no matching function for call to 'core::pose::Pose::dump_pdb(char [256], const char [2])'<br> pose_asu.dump_pdb( buffer , "1" );<br> ^<br>In file included from src/core/scoring/cryst/PhenixInterface.cc:18:0:<br>src/core/pose/Pose.hh:1518:2: note: candidate: bool core::pose::Pose::dump_pdb(const string&) const<br> dump_pdb(std::string const & file_name) const;<br> ^<br>src/core/pose/Pose.hh:1518:2: note: candidate expects 1 argument, 2 provided<br>src/core/pose/Pose.hh:1521:2: note: candidate: void core::pose::Pose::dump_pdb(std::ostream&) const<br> dump_pdb(std::ostream & out) const;<br> ^<br>src/core/pose/Pose.hh:1521:2: note: candidate expects 1 argument, 2 provided<br>src/core/pose/Pose.hh:1525:2: note: candidate: void core::pose::Pose::dump_pdb(std::ostream&, const utility::vector1<long unsigned int>&) const<br> dump_pdb(<br> ^<br>src/core/pose/Pose.hh:1525:2: note: no known conversion for argument 1 from 'char [256]' to 'std::ostream& {aka std::basic_ostream<char>&}'<br>src/core/scoring/cryst/PhenixInterface.cc: In member function 'void core::scoring::cryst::PhenixInterface::fitBfactors(core::pose::Pose&)':<br>src/core/scoring/cryst/PhenixInterface.cc:244:25: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result]<br> chdir(tempdir_.c_str());<br> ^<br>src/core/scoring/cryst/PhenixInterface.cc:375:13: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result]<br> chdir("..");<br> ^<br>src/core/scoring/cryst/PhenixInterface.cc: In member function 'void core::scoring::cryst::PhenixInterface::initialize_target_evaluator(const core::pose::Pose&, std::__cxx11::string)':<br>src/core/scoring/cryst/PhenixInterface.cc:914:25: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result]<br> chdir(tempdir_.c_str());<br> ^<br>src/core/scoring/cryst/PhenixInterface.cc:1080:13: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result]<br> chdir("..");<br> ^<br>src/core/scoring/cryst/PhenixInterface.cc: In member function 'std::__cxx11::string core::scoring::cryst::PhenixInterface::calculateDensityMap(core::pose::Pose&, bool)':<br>src/core/scoring/cryst/PhenixInterface.cc:1100:25: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result]<br> chdir(tempdir_.c_str());<br> ^<br>src/core/scoring/cryst/PhenixInterface.cc:1109:13: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result]<br> chdir("..");<br> ^<br>scons: *** [build/src/release/linux/4.4/64/x86/gcc/5.4/python/core/scoring/cryst/PhenixInterface.os] Error 1<br>scons: building terminated because of errors.<br></div><div>--------- stdout end ------<br></div><div><div><div class="gmail_signature"><br><br>--<br>Gerhard Fischer, PhD<br>Postdoctoral Research Associate<br><br>University of Cambridge<br>Department of Biochemistry<br>80 Tennis Court Road<br>CB2 1GA Cambridge<br>United Kingdom<br><br>---<br>This e-mail message (including any attachments) is for the sole use of<br>the intended recipient(s) and may contain confidential and privileged<br>information. If the reader of this message is not the intended<br>recipient, you are hereby notified that any dissemination, distribution<br>or copying of this message (including any attachments) is strictly<br>prohibited.<br><br>If you have received this message in error, please contact<br>the sender by reply e-mail message and destroy all copies of the<br>original message (including attachments).</div></div>
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