I'm having difficulty in installing the dspp package -- I've installed boost 1.78 and libcif++ from source code and the issue I've having seems like to be related to the failure of linking zlib and bzip2 to dssp and boost. Please find the error message below:
CMakeFiles/mkdssp.dir/src/mkdssp.cpp.o: In function d_main(int, char const**)': mkdssp.cpp:(.text+0x1aed): undefined reference to boost::iostreams::zlib::default_strategy'
mkdssp.cpp:(.text+0x1af3): undefined reference to boost::iostreams::zlib::deflated' mkdssp.cpp:(.text+0x1af9): undefined reference to boost::iostreams::zlib::default_compression'
CMakeFiles/mkdssp.dir/src/mkdssp.cpp.o: In function boost::iostreams::basic_gzip_compressor<std::allocator<char> >::basic_gzip_compressor(boost::iostreams::gzip_params const&, long)': mkdssp.cpp:(.text._ZN5boost9iostreams21basic_gzip_compressorISaIcEEC2ERKNS0_11gzip_paramsEl[_ZN5boost9iostreams21basic_gzip_compressorISaIcEEC5ERKNS0_11gzip_paramsEl]+0x1a7): undefined reference to boost::iostreams::zlib::best_compression'
mkdssp.cpp:(.text._ZN5boost9iostreams21basic_gzip_compressorISaIcEEC2ERKNS0_11gzip_paramsEl[_ZN5boost9iostreams21basic_gzip_compressorISaIcEEC5ERKNS0_11gzip_paramsEl]+0x1c6): undefined reference to boost::iostreams::zlib::best_speed' CMakeFiles/mkdssp.dir/src/mkdssp.cpp.o: In function boost::iostreams::detail::zlib_compressor_impl<std::allocator >::zlib_compressor_impl(boost::iostreams::zlib_params const&)':
mkdssp.cpp:(.text._ZN5boost9iostreams6detail20zlib_compressor_implISaIcEEC2ERKNS0_11zlib_paramsE[_ZN5boost9iostreams6detail20zlib_compressor_implISaIcEEC5ERKNS0_11zlib_paramsE]+0x19): undefined reference to boost::iostreams::detail::zlib_base::zlib_base()' mkdssp.cpp:(.text._ZN5boost9iostreams6detail20zlib_compressor_implISaIcEEC2ERKNS0_11zlib_paramsE[_ZN5boost9iostreams6detail20zlib_compressor_implISaIcEEC5ERKNS0_11zlib_paramsE]+0x5e): undefined reference to boost::iostreams::detail::zlib_base::~zlib_base()'
CMakeFiles/mkdssp.dir/src/mkdssp.cpp.o: In function boost::iostreams::detail::zlib_compressor_impl<std::allocator<char> >::~zlib_compressor_impl()': mkdssp.cpp:(.text._ZN5boost9iostreams6detail20zlib_compressor_implISaIcEED2Ev[_ZN5boost9iostreams6detail20zlib_compressor_implISaIcEED5Ev]+0x1e): undefined reference to boost::iostreams::detail::zlib_base::reset(bool, bool)'
mkdssp.cpp:(.text._ZN5boost9iostreams6detail20zlib_compressor_implISaIcEED2Ev[_ZN5boost9iostreams6detail20zlib_compressor_implISaIcEED5Ev]+0x36): undefined reference to boost::iostreams::detail::zlib_base::~zlib_base()' CMakeFiles/mkdssp.dir/src/mkdssp.cpp.o: In function void boost::iostreams::detail::zlib_base::init<std::allocator >(boost::iostreams::zlib_params const&, bool, boost::iostreams::detail::zlib_allocator<std::allocator, boost::iostreams::detail::zlib_allocator_traits<std::allocator >::type>&)':
mkdssp.cpp:(.text._ZN5boost9iostreams6detail9zlib_base4initISaIcEEEvRKNS0_11zlib_paramsEbRNS1_14zlib_allocatorIT_NS1_21zlib_allocator_traitsIS9_E4typeEEE[_ZN5boost9iostreams6detail9zlib_base4initISaIcEEEvRKNS0_11zlib_paramsEbRNS1_14zlib_allocatorIT_NS1_21zlib_allocator_traitsIS9_E4typeEEE]+0x5f): undefined reference to boost::iostreams::detail::zlib_base::do_init(boost::iostreams::zlib_params const&, bool, void* (*)(void*, unsigned int, unsigned int), void (*)(void*, void*), void*)' CMakeFiles/mkdssp.dir/src/mkdssp.cpp.o: In function boost::iostreams::detail::zlib_compressor_impl<std::allocator >::filter(char const*&, char const*, char*&, char*, bool)':
mkdssp.cpp:(.text._ZN5boost9iostreams6detail20zlib_compressor_implISaIcEE6filterERPKcS6_RPcS8_b[_ZN5boost9iostreams6detail20zlib_compressor_implISaIcEE6filterERPKcS6_RPcS8_b]+0x3d): undefined reference to boost::iostreams::detail::zlib_base::before(char const*&, char const*, char*&, char*)' mkdssp.cpp:(.text._ZN5boost9iostreams6detail20zlib_compressor_implISaIcEE6filterERPKcS6_RPcS8_b[_ZN5boost9iostreams6detail20zlib_compressor_implISaIcEE6filterERPKcS6_RPcS8_b]+0x4d): undefined reference to boost::iostreams::zlib::finish'
mkdssp.cpp:(.text._ZN5boost9iostreams6detail20zlib_compressor_implISaIcEE6filterERPKcS6_RPcS8_b[_ZN5boost9iostreams6detail20zlib_compressor_implISaIcEE6filterERPKcS6_RPcS8_b]+0x55): undefined reference to boost::iostreams::zlib::no_flush' mkdssp.cpp:(.text._ZN5boost9iostreams6detail20zlib_compressor_implISaIcEE6filterERPKcS6_RPcS8_b[_ZN5boost9iostreams6detail20zlib_compressor_implISaIcEE6filterERPKcS6_RPcS8_b]+0x5f): undefined reference to boost::iostreams::detail::zlib_base::xdeflate(int)'
mkdssp.cpp:(.text._ZN5boost9iostreams6detail20zlib_compressor_implISaIcEE6filterERPKcS6_RPcS8_b[_ZN5boost9iostreams6detail20zlib_compressor_implISaIcEE6filterERPKcS6_RPcS8_b]+0x7b): undefined reference to boost::iostreams::detail::zlib_base::after(char const*&, char*&, bool)' mkdssp.cpp:(.text._ZN5boost9iostreams6detail20zlib_compressor_implISaIcEE6filterERPKcS6_RPcS8_b[_ZN5boost9iostreams6detail20zlib_compressor_implISaIcEE6filterERPKcS6_RPcS8_b]+0x85): undefined reference to boost::iostreams::zlib_error::check(int)'
mkdssp.cpp:(.text._ZN5boost9iostreams6detail20zlib_compressor_implISaIcEE6filterERPKcS6_RPcS8_b[_ZN5boost9iostreams6detail20zlib_compressor_implISaIcEE6filterERPKcS6_RPcS8_b]+0x8b): undefined reference to boost::iostreams::zlib::stream_end' CMakeFiles/mkdssp.dir/src/mkdssp.cpp.o: In function boost::iostreams::detail::zlib_compressor_impl<std::allocator >::close()':
mkdssp.cpp:(.text._ZN5boost9iostreams6detail20zlib_compressor_implISaIcEE5closeEv[_ZN5boost9iostreams6detail20zlib_compressor_implISaIcEE5closeEv]+0x1e): undefined reference to boost::iostreams::detail::zlib_base::reset(bool, bool)' /home/chengeng/.local/lib/libcifpp.a(Cif++.cpp.o): In function cif::File::save(std::filesystem::__cxx11::path const&)':
Cif++.cpp:(.text+0x124e3): undefined reference to boost::iostreams::zlib::default_strategy' Cif++.cpp:(.text+0x124ec): undefined reference to boost::iostreams::zlib::deflated'
Cif++.cpp:(.text+0x124f5): undefined reference to boost::iostreams::zlib::default_compression' /home/chengeng/.local/lib/libcifpp.a(Cif++.cpp.o): In function boost::iostreams::gzip_error::gzip_error(int)':
Cif++.cpp:(.text._ZN5boost9iostreams10gzip_errorC2Ei[_ZN5boost9iostreams10gzip_errorC5Ei]+0x69): undefined reference to boost::iostreams::zlib::okay' /home/chengeng/.local/lib/libcifpp.a(Cif++.cpp.o): In function boost::iostreams::detail::gzip_header::gzip_header()':
Cif++.cpp:(.text._ZN5boost9iostreams6detail11gzip_headerC2Ev[_ZN5boost9iostreams6detail11gzip_headerC5Ev]+0x31): undefined reference to boost::iostreams::detail::gzip_header::reset()' /home/chengeng/.local/lib/libcifpp.a(Cif++.cpp.o): In function boost::iostreams::detail::gzip_footer::gzip_footer()':
Cif++.cpp:(.text._ZN5boost9iostreams6detail11gzip_footerC2Ev[_ZN5boost9iostreams6detail11gzip_footerC5Ev]+0x14): undefined reference to boost::iostreams::detail::gzip_footer::reset()' /home/chengeng/.local/lib/libcifpp.a(Cif++.cpp.o): In function boost::iostreams::basic_gzip_decompressor<std::allocator >::make_params(int)':
Cif++.cpp:(.text._ZN5boost9iostreams23basic_gzip_decompressorISaIcEE11make_paramsEi[_ZN5boost9iostreams23basic_gzip_decompressorISaIcEE11make_paramsEi]+0x68): undefined reference to boost::iostreams::zlib::default_strategy' Cif++.cpp:(.text._ZN5boost9iostreams23basic_gzip_decompressorISaIcEE11make_paramsEi[_ZN5boost9iostreams23basic_gzip_decompressorISaIcEE11make_paramsEi]+0x71): undefined reference to boost::iostreams::zlib::deflated'
Cif++.cpp:(.text._ZN5boost9iostreams23basic_gzip_decompressorISaIcEE11make_paramsEi[_ZN5boost9iostreams23basic_gzip_decompressorISaIcEE11make_paramsEi]+0x7a): undefined reference to boost::iostreams::zlib::default_compression' /home/chengeng/.local/lib/libcifpp.a(Cif++.cpp.o): In function boost::iostreams::detail::zlib_decompressor_impl<std::allocator >::zlib_decompressor_impl(boost::iostreams::zlib_params const&)':
Cif++.cpp:(.text._ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEEC2ERKNS0_11zlib_paramsE[_ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEEC5ERKNS0_11zlib_paramsE]+0x19): undefined reference to boost::iostreams::detail::zlib_base::zlib_base()' Cif++.cpp:(.text._ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEEC2ERKNS0_11zlib_paramsE[_ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEEC5ERKNS0_11zlib_paramsE]+0x66): undefined reference to boost::iostreams::detail::zlib_base::~zlib_base()'
/home/chengeng/.local/lib/libcifpp.a(Cif++.cpp.o): In function boost::iostreams::detail::zlib_decompressor_impl<std::allocator<char> >::~zlib_decompressor_impl()': Cif++.cpp:(.text._ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEED2Ev[_ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEED5Ev]+0x1e): undefined reference to boost::iostreams::detail::zlib_base::reset(bool, bool)'
Cif++.cpp:(.text._ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEED2Ev[_ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEED5Ev]+0x36): undefined reference to boost::iostreams::detail::zlib_base::~zlib_base()' /home/chengeng/.local/lib/libcifpp.a(Cif++.cpp.o): In function long boost::iostreams::basic_gzip_decompressor<std::allocator >::write<boost::iostreams::detail::linked_streambuf<char, std::char_traits > >(boost::iostreams::detail::linked_streambuf<char, std::char_traits >&, char const*, long)':
Cif++.cpp:(.text._ZN5boost9iostreams23basic_gzip_decompressorISaIcEE5writeINS0_6detail16linked_streambufIcSt11char_traitsIcEEEEElRT_PKcl[_ZN5boost9iostreams23basic_gzip_decompressorISaIcEE5writeINS0_6detail16linked_streambufIcSt11char_traitsIcEEEEElRT_PKcl]+0x67): undefined reference to boost::iostreams::detail::gzip_header::reset()' Cif++.cpp:(.text._ZN5boost9iostreams23basic_gzip_decompressorISaIcEE5writeINS0_6detail16linked_streambufIcSt11char_traitsIcEEEEElRT_PKcl[_ZN5boost9iostreams23basic_gzip_decompressorISaIcEE5writeINS0_6detail16linked_streambufIcSt11char_traitsIcEEEEElRT_PKcl]+0x77): undefined reference to boost::iostreams::detail::gzip_footer::reset()'
Cif++.cpp:(.text._ZN5boost9iostreams23basic_gzip_decompressorISaIcEE5writeINS0_6detail16linked_streambufIcSt11char_traitsIcEEEEElRT_PKcl[_ZN5boost9iostreams23basic_gzip_decompressorISaIcEE5writeINS0_6detail16linked_streambufIcSt11char_traitsIcEEEEElRT_PKcl]+0xba): undefined reference to boost::iostreams::detail::gzip_header::process(char)' Cif++.cpp:(.text._ZN5boost9iostreams23basic_gzip_decompressorISaIcEE5writeINS0_6detail16linked_streambufIcSt11char_traitsIcEEEEElRT_PKcl[_ZN5boost9iostreams23basic_gzip_decompressorISaIcEE5writeINS0_6detail16linked_streambufIcSt11char_traitsIcEEEEElRT_PKcl]+0x20b): undefined reference to boost::iostreams::detail::gzip_footer::process(char)'
/home/chengeng/.local/lib/libcifpp.a(Cif++.cpp.o): In function boost::iostreams::detail::zlib_decompressor_impl<std::allocator<char> >::filter(char const*&, char const*, char*&, char*, bool)': Cif++.cpp:(.text._ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEE6filterERPKcS6_RPcS8_b[_ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEE6filterERPKcS6_RPcS8_b]+0x3d): undefined reference to boost::iostreams::detail::zlib_base::before(char const*&, char const*, char*&, char*)'
Cif++.cpp:(.text._ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEE6filterERPKcS6_RPcS8_b[_ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEE6filterERPKcS6_RPcS8_b]+0x48): undefined reference to boost::iostreams::zlib::sync_flush' Cif++.cpp:(.text._ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEE6filterERPKcS6_RPcS8_b[_ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEE6filterERPKcS6_RPcS8_b]+0x54): undefined reference to boost::iostreams::detail::zlib_base::xinflate(int)'
Cif++.cpp:(.text._ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEE6filterERPKcS6_RPcS8_b[_ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEE6filterERPKcS6_RPcS8_b]+0x70): undefined reference to boost::iostreams::detail::zlib_base::after(char const*&, char*&, bool)' Cif++.cpp:(.text._ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEE6filterERPKcS6_RPcS8_b[_ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEE6filterERPKcS6_RPcS8_b]+0x7a): undefined reference to boost::iostreams::zlib_error::check(int)'
Cif++.cpp:(.text._ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEE6filterERPKcS6_RPcS8_b[_ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEE6filterERPKcS6_RPcS8_b]+0x81): undefined reference to boost::iostreams::zlib::stream_end' /home/chengeng/.local/lib/libcifpp.a(Cif++.cpp.o): In function boost::iostreams::detail::zlib_decompressor_impl<std::allocator >::close()':
Cif++.cpp:(.text._ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEE5closeEv[_ZN5boost9iostreams6detail22zlib_decompressor_implISaIcEE5closeEv]+0x26): undefined reference to boost::iostreams::detail::zlib_base::reset(bool, bool)' /home/chengeng/.local/lib/libcifpp.a(Cif++.cpp.o): In function long boost::iostreams::basic_gzip_decompressor<std::allocator >::read<boost::iostreams::detail::linked_streambuf<char, std::char_traits > >(boost::iostreams::detail::linked_streambuf<char, std::char_traits >&, char*, long)':
Cif++.cpp:(.text._ZN5boost9iostreams23basic_gzip_decompressorISaIcEE4readINS0_6detail16linked_streambufIcSt11char_traitsIcEEEEElRT_Pcl[_ZN5boost9iostreams23basic_gzip_decompressorISaIcEE4readINS0_6detail16linked_streambufIcSt11char_traitsIcEEEEElRT_Pcl]+0xc4): undefined reference to boost::iostreams::detail::gzip_header::reset()' Cif++.cpp:(.text._ZN5boost9iostreams23basic_gzip_decompressorISaIcEE4readINS0_6detail16linked_streambufIcSt11char_traitsIcEEEEElRT_Pcl[_ZN5boost9iostreams23basic_gzip_decompressorISaIcEE4readINS0_6detail16linked_streambufIcSt11char_traitsIcEEEEElRT_Pcl]+0xd7): undefined reference to boost::iostreams::detail::gzip_footer::reset()'
Cif++.cpp:(.text._ZN5boost9iostreams23basic_gzip_decompressorISaIcEE4readINS0_6detail16linked_streambufIcSt11char_traitsIcEEEEElRT_Pcl[_ZN5boost9iostreams23basic_gzip_decompressorISaIcEE4readINS0_6detail16linked_streambufIcSt11char_traitsIcEEEEElRT_Pcl]+0x160): undefined reference to boost::iostreams::detail::gzip_header::process(char)' Cif++.cpp:(.text._ZN5boost9iostreams23basic_gzip_decompressorISaIcEE4readINS0_6detail16linked_streambufIcSt11char_traitsIcEEEEElRT_Pcl[_ZN5boost9iostreams23basic_gzip_decompressorISaIcEE4readINS0_6detail16linked_streambufIcSt11char_traitsIcEEEEElRT_Pcl]+0x2dd): undefined reference to boost::iostreams::detail::gzip_footer::process(char)'
Cif++.cpp:(.text._ZN5boost9iostreams23basic_gzip_decompressorISaIcEE4readINS0_6detail16linked_streambufIcSt11char_traitsIcEEEEElRT_Pcl[_ZN5boost9iostreams23basic_gzip_decompressorISaIcEE4readINS0_6detail16linked_streambufIcSt11char_traitsIcEEEEElRT_Pcl]+0x3d1): undefined reference to boost::iostreams::detail::gzip_header::reset()' Cif++.cpp:(.text._ZN5boost9iostreams23basic_gzip_decompressorISaIcEE4readINS0_6detail16linked_streambufIcSt11char_traitsIcEEEEElRT_Pcl[_ZN5boost9iostreams23basic_gzip_decompressorISaIcEE4readINS0_6detail16linked_streambufIcSt11char_traitsIcEEEEElRT_Pcl]+0x3e4): undefined reference to boost::iostreams::detail::gzip_footer::reset()'
/home/chengeng/.local/lib/libcifpp.a(Structure.cpp.o): In function mmcif::FileImpl::save(std::filesystem::__cxx11::path const&)': Structure.cpp:(.text+0xeec): undefined reference to boost::iostreams::zlib::default_strategy'
Structure.cpp:(.text+0xef5): undefined reference to boost::iostreams::zlib::deflated' Structure.cpp:(.text+0xefe): undefined reference to boost::iostreams::zlib::default_compression'
collect2: error: ld returned 1 exit status
CMakeFiles/mkdssp.dir/build.make:117: recipe for target 'mkdssp' failed
make[2]: *** [mkdssp] Error 1
CMakeFiles/Makefile2:814: recipe for target 'CMakeFiles/mkdssp.dir/all' failed
make[1]: *** [CMakeFiles/mkdssp.dir/all] Error 2
Makefile:145: recipe for target 'all' failed
make: *** [all] Error 2
I've tried multiple approaches but had zero success.
install zlib and bzip2 using sudo apt-get install libbz2-dev zlib1g-dev, compile boost then compile dssp -- doesn't work
compile boost including flags such as -sZLIB_INCLUDE=xyz in order to specify the path of zlib/bzip2 for boost then compile dssp -- doesn't work
have zlib and bzip2 package files ready and/or specify their path (e.g. using zlib : 1.2.10 : /home/chengeng/Downloads/zlib-1.2.10 ;) in the user-config.jam file so that they can be built by boost before compiling dssp -- doesn't work
install zlib and bzip2 packages from source code in the default path and/or specify their path (e.g. using zlib : 1.2.10 : /usr/local/include /usr/local/lib ;) in the user-config.jam file so that they can be built by boost before compiling dssp -- doesn't work
In this case, could you help me with installation? My OS is Ubuntu 18.04 and I'm using gcc 10. I would really appreciate it if you could tell me the version of zlib, bzip2 and boost you are using when you compile this dssp package. Many thanks!
This error is generated by AlphaFold predicted structures, which do not have a CRYST1 record. IMHO this is overly stringent, should be a warning or not checked at all. I realize I can work around this by inserting a fake CRYST1 record, but this is very expensive for high-throughput applications, I'm dealing with 10^5 or 10^6 structures per batch.
I tried to fix this myself but got stuck trying to build libcifpp, I was unable to resolve this error:
CMake Error at /usr/share/cmake-3.22/Modules/FindPackageHandleStandardArgs.cmake:230 (message):
Could NOT find ZLIB (missing: ZLIB_LIBRARY ZLIB_INCLUDE_DIR)
I tried installing zlib through apt (on Ubuntu) and also downloading and re-building from the zlib source then setting environment variables ZLIB_LIBRARY and ZLIB_INCLUDE_DIR, without success.
mostly we refer to pre-computed DSSP files, e.g., via rsync -avz --delete rsync://rsync.cmbi.umcn.nl/dssp-from-mmcif/ /path_to_dssp/
from the DSSP website.
For a pipeline working with MD simulation data, we need to compute DSSP files on our own and are therefore using your software. Now we stumbled over two things:
The DSSP files we create with your software do not contain the extra columns introduced for large structures / mmCIF, such as CHAIN and AUTHCHAIN. Is it possible to get these extra colums? I have not found an option in the help.
Your software seems not to be able to create DSSP files for large structures. It worked well when annotating the mmCIF, but when run with the option to create a DSSP file, chains with IDs of more than two characters are ignored. Interestingly, it seems that your software uses the PDB-style chain IDs (A..ZZZZ) instead of the author-given chain IDs (arbitrary) for this, even though author-given chain IDs are written to the DSSP file in the end. That would mean that your software only can correctly process up to 24 chains (A..Z).
Hope to hear from you. I also want to quickly thank for your last answer regarding the standalone version. We are still trying to compile it due to some errors and the issue was then already closed, but your answer really helped us.
i'm using docker.
i want to install in my container.
"""
when i installed mrc , i encountered error
./configure
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking whether g++ supports C++17 features with -std=c++17... yes
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for boostlib >= 1.65.1 (106501)... yes
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether the Boost::Program_Options library is available... yes
checking for main in -lboost_program_options... yes
checking how to run the C++ preprocessor... g++ -std=c++17 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking elf.h usability... yes
checking elf.h presence... yes
checking for elf.h... yes
checking filesystem usability... no
checking filesystem presence... no
checking for filesystem... no
configure: error: The file is missing, perhaps you should install a more recent libstdc++ implementation.
"""
gcc --version
gcc (Ubuntu 9.3.0-11ubuntu0~18.04.1) 9.3.0
Copyright (C) 2019 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.
make --version
GNU Make 4.1
Built for x86_64-pc-linux-gnu
Copyright (C) 1988-2014 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later http://gnu.org/licenses/gpl.html
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
I used a simple test script to check if dssp works well, as below:
class Test_Dssp():
def init(self):
self.parser = Bio.PDB.PDBParser()
def test_dssp(self, inputfile, pdbname):
structure = self.parser.get_structure(pdbname,inputfile)
for model in structure:
dssp = DSSP(model,inputfile, dssp='/MAPATH/mambaforge/envs/Geopacker01/bin/dssp')
print(type(dssp))
if name == "main":
inputfile = '/MYPATH/example/3MPC_A.pdb'
pdbname = '3MPC'
if 1:
Test = Test_Dssp()
Test.test_dssp(inputfile, pdbname)
else:
dssp_tuple = dssp_dict_from_pdb_file(inputfile)
dssp_dict = dssp_tuple[0]
print(dssp_dict['A',(' ', 1, ' ')])
And the error occured:
UserWarning: /MYPATHi/mambaforge/envs/Geopacker01/bin/mkdssp: symbol lookup error: /MYPATH/mambaforge/envs/Geopacker01/bin/mkdssp: undefined symbol: _ZNK5boost15program_options22error_with_option_name23substitute_placeholdersERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE
warnings.warn(err)
Traceback (most recent call last):
File "my_scripts/test_dssp.py", line 26, in
Test.test_dssp(inputfile, pdbname)
File "my_scripts/test_dssp.py", line 18, in test_dssp
dssp = DSSP(model,inputfile, dssp='/MYPATH/mambaforge/envs/Geopacker01/bin/mkdssp')
File "MYPATH/mambaforge/envs/Geopacker01/lib/python3.6/site-packages/Bio/PDB/DSSP.py", line 438, in init
dssp_dict, dssp_keys = dssp_dict_from_pdb_file(in_file, dssp)
File "/MYPATH/mambaforge/envs/Geopacker01/lib/python3.6/site-packages/Bio/PDB/DSSP.py", line 254, in dssp_dict_from_pdb_file
raise Exception("DSSP failed to produce an output")
Exception: DSSP failed to produce an output
It's almost the simplest case, I don't know why this error.
The dssp is installed by "conda install -c salilab dssp", while the version is 3.0.0
I ran into an error during the installation under macOS Big Sur (11.6.1).
Would be nice If you could help me with this, as I'm really looking forward to use your package :)
cmake --build . --config Release
[ 16%] Building CXX object CMakeFiles/mkdssp.dir/src/dssp.cpp.o
[ 33%] Building CXX object CMakeFiles/mkdssp.dir/src/mkdssp.cpp.o
[ 50%] Linking CXX executable mkdssp
[ 50%] Built target mkdssp
[ 66%] Building CXX object CMakeFiles/unit-test.dir/test/unit-test.cpp.o
/Users/<>/dssp/test/unit-test.cpp:108:12: error: 'datablock' is a private member of 'mmcif::Structure'
structure.datablock()["software"].erase("name"_key == "dssp");
^
/usr/local/include/cif++/Structure.hpp:529:18: note: declared private here
cif::Datablock &datablock() const;
^
/Users/<>/dssp/test/unit-test.cpp:109:5: error: 'datablock' is a private member of 'mmcif::Structure'
rs.datablock()["software"].erase("name"_key == "dssp");
^
/usr/local/include/cif++/Structure.hpp:529:18: note: declared private here
cif::Datablock &datablock() const;
^
/Users/till/dssp/test/unit-test.cpp:114:24: error: 'datablock' is a private member of 'mmcif::Structure'
BOOST_CHECK(structure.datablock() == rs.datablock());
^
/usr/local/include/cif++/Structure.hpp:529:18: note: declared private here
cif::Datablock &datablock() const;
^
/Users/<>/dssp/test/unit-test.cpp:114:42: error: 'datablock' is a private member of 'mmcif::Structure'
BOOST_CHECK(structure.datablock() == rs.datablock());
^
/usr/local/include/cif++/Structure.hpp:529:18: note: declared private here
cif::Datablock &datablock() const;
^
4 errors generated.
make[2]: *** [CMakeFiles/unit-test.dir/test/unit-test.cpp.o] Error 1
make[1]: *** [CMakeFiles/unit-test.dir/all] Error 2
make: *** [all] Error 2
If stop == True then since bool stop = t == dssp.end(); it means that t == dssp.end() and therefore accessing t->ss() will cause a heap buffer overflow.
I think the solution is to move:
if (stop)
break;
above the if (lastSS != t->ss()) check:
if (stop) {
break;
}
if (lastSS != t->ss()) {
st = t;
lastSS = t->ss();
}
The code goes awry with some standard PDBs like 7rkf.pdb . The problem is with the dihedral calculation where it calculates the phi, psi's as 360, 360 for a bunch of residues (especially in Chain R) Any standard program like Pymol shows the residues in this chain as a helix - implying that pymol managed to compute the dihedrals correctly.
Correcting this error can hugely increase the utility of this program.
I've been trying to DSSP program on Ubuntu 20.04, when I run the configure file I get an error saying configure: error: libz not found - compressed files not supported.
I tried to install libz using the command sudo apt-get install -y libz-dev for which I get the following response: Note, selecting 'zlib1g-dev' instead of 'libz-dev' zlib1g-dev is already the newest version (1:1.2.11.dfsg-2ubuntu1.2)
When the problem still persisted, i installed libz from source from here, but the problem still persists. Could anyone please help me? I am new to linux so please give responses that are a little noob friendly with distinct commands.
I just reported this as an issue in biopython here: biopython/biopython#3505
but after looking closer at it, I think it might actually be an issue in dssp rather than biopython.
The issue is that when I run the dssp on the file: '2mys.cif', which contains 3 chain_ids 'A','B','C' then I only get the dssp results from the first chain_id, 'A', but not for the other two chains, which I believe I should be getting.
I got this error after run "make"
Is there anything that I miss? I already have install the libcif++
make
fatal: your current branch 'master' does not have any commits yet
fatal: your current branch 'master' does not have any commits yet
src/mkdssp.cpp
src/mkdssp.cpp: In function ‘int d_main(int, const char**)’:
src/mkdssp.cpp:532:8: error: ‘addFileResource’ is not a member of ‘cif’
532 | cif::addFileResource("components.cif", vm["compounds"].asstd::string());
| ^~~~~~~~~~~~~~~
src/mkdssp.cpp:534:8: error: ‘addFileResource’ is not a member of ‘cif’
534 | cif::addFileResource("components.cif", vm["components"].asstd::string());
| ^~~~~~~~~~~~~~~
src/mkdssp.cpp:542:8: error: ‘addFileResource’ is not a member of ‘cif’
542 | cif::addFileResource("mmcif_pdbx_v50.dic", vm["mmcif-dictionary"].asstd::string());
| ^~~~~~~~~~~~~~~
src/mkdssp.cpp: At global scope:
src/mkdssp.cpp:638:1: fatal error: opening dependency file obj/mkdssp.d: Permission denied
638 | }
| ^
compilation terminated.
make: *** [GNUmakefile:97: obj/mkdssp.o] Error 1
Hello, I just cloned out the latest version (4.0.6). As I follow the instructions in the README, this happens:
$ cmake --build . --config Release
Scanning dependencies of target unit-test
[ 16%] Building CXX object CMakeFiles/unit-test.dir/test/unit-test.cpp.o
[ 33%] Building CXX object CMakeFiles/unit-test.dir/src/dssp.cpp.o
[ 50%] Linking CXX executable unit-test
/usr/bin/ld: CMakeFiles/unit-test.dir/test/unit-test.cpp.o: relocation R_X86_64_32 against symbol `typeinfo for std::exception@@GLIBCXX_3.4' can not be used when making a PDE object; recompile with -fPIE
/usr/bin/ld: CMakeFiles/unit-test.dir/src/dssp.cpp.o: relocation R_X86_64_32 against symbol `__gxx_personality_v0@@CXXABI_1.3' can not be used when making a PDE object; recompile with -fPIE
collect2: error: ld returned 1 exit status
make[2]: *** [CMakeFiles/unit-test.dir/build.make:103: unit-test] Error 1
make[1]: *** [CMakeFiles/Makefile2:106: CMakeFiles/unit-test.dir/all] Error 2
make: *** [Makefile:141: all] Error 2
It says I must recompile with -fPIE, but how do I make the makefile do that?
System: "Ubuntu 20.04.1 LTS"
Thank you for sharing this program. Unfortunately I am having problems installing it. Could you help me?
I installed mrc and libcif++ but my the dssp configuration has trouble finding this libcif++ install.
(base) jarek@jrk:~/Documents/dssp$ sudo ./configure
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking whether g++ supports C++17 features with -std=c++17... yes
checking whether C++ compiler accepts -fstandalone-debug... no
checking for a BSD-compatible install... /usr/bin/install -c
checking for pkg-config... no
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for a sed that does not truncate output... /usr/bin/sed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking whether gcc is Clang... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking whether more special flags are required for pthreads... no
checking for PTHREAD_PRIO_INHERIT... yes
checking for mrc... /usr/local/bin/mrc
checking how to run the C++ preprocessor... g++ -std=c++17 -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking filesystem usability... yes
checking filesystem presence... yes
checking for filesystem... yes
checking for boostlib >= 1.65.1 (106501)... yes
checking whether the Boost::IOStreams library is available... yes
checking for exit in -lboost_iostreams... yes
checking whether the Boost::Program_Options library is available... yes
checking for exit in -lboost_program_options... yes
checking whether the Boost::Date_Time library is available... yes
checking for exit in -lboost_date_time... yes
checking whether the Boost::Regex library is available... yes
checking for exit in -lboost_regex... yes
checking need to link zlib... no
checking need to link bzip2... no
checking cif++/Cif++.hpp usability... yes
checking cif++/Cif++.hpp presence... yes
checking for cif++/Cif++.hpp... yes
checking for cif++/Cif++.hpp... (cached) yes
checking for main in -lcifpp... no
configure: error: libcif++ not found
The installation of libcif++ seemed successful:
./configure
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking whether g++ supports C++17 features with -std=c++17... yes
checking whether C++ compiler accepts -fstandalone-debug... no
checking how to run the C++ preprocessor... g++ -std=c++17 -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking filesystem usability... yes
checking filesystem presence... yes
checking for filesystem... yes
checking for a BSD-compatible install... /usr/bin/install -c
checking for pkg-config... no
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for a sed that does not truncate output... /usr/bin/sed
checking how to run the C preprocessor... gcc -E
checking whether gcc is Clang... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking whether more special flags are required for pthreads... no
checking for PTHREAD_PRIO_INHERIT... yes
checking how to print strings... printf
checking for a sed that does not truncate output... (cached) /usr/bin/sed
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking for gawk... gawk
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for mt... mt
checking if mt is a manifest tool... no
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking how to run the C++ preprocessor... g++ -std=c++17 -E
checking for ld used by g++ -std=c++17... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ -std=c++17 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ -std=c++17 option to produce PIC... -fPIC -DPIC
checking if g++ -std=c++17 PIC flag -fPIC -DPIC works... yes
checking if g++ -std=c++17 static flag -static works... yes
checking if g++ -std=c++17 supports -c -o file.o... yes
checking if g++ -std=c++17 supports -c -o file.o... (cached) yes
checking whether the g++ -std=c++17 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for mrc... /usr/local/bin/mrc
checking for filesystem... (cached) yes
checking for floor... yes
checking for pow... yes
checking for rint... yes
checking for sqrt... yes
checking for strchr... yes
checking for strerror... yes
checking sys/ioctl.h usability... yes
checking sys/ioctl.h presence... yes
checking for sys/ioctl.h... yes
checking termios.h usability... yes
checking termios.h presence... yes
checking for termios.h... yes
checking for stdbool.h that conforms to C99... no
checking for _Bool... no
checking for ptrdiff_t... yes
checking whether make sets $(MAKE)... yes
checking for boostlib >= 1.71 (107100)... yes
checking whether the Boost::IOStreams library is available... yes
checking for exit in -lboost_iostreams... yes
checking whether the Boost::Date_Time library is available... yes
checking for exit in -lboost_date_time... yes
checking whether the Boost::Regex library is available... yes
checking for exit in -lboost_regex... yes
checking need to link zlib... no
checking need to link bzip2... no
configure: creating ./config.status
config.status: creating GNUmakefile
config.status: creating libcifpp.pc
config.status: creating tools/update-dictionary-script
config.status: creating src/Config.hpp
config.status: executing libtool commands
(base) jarek@jrk:~/Documents/libcifpp$ make
mkdir -p obj
>> src/AtomType.cpp
>> src/BondMap.cpp
>> src/Cif2PDB.cpp
>> src/Cif++.cpp
>> src/CifParser.cpp
rm -f version-info-*.txt
>> src/CifUtils.cpp
>> src/CifValidator.cpp
>> src/Compound.cpp
>> src/PDB2Cif.cpp
>> src/PDB2CifRemark3.cpp
>> src/Point.cpp
>> src/Secondary.cpp
>> src/Structure.cpp
>> src/Symmetry.cpp
>> src/TlsParser.cpp
/bin/sh /home/jarek/Documents/libcifpp/libtool --silent --tag=CXX --mode=link g++ -std=c++17 -I/usr/include -g -O2 -pthread -Wall -Wno-multichar -I include -O2 -DCACHE_DIR='"/var/cache/libcifpp"' -DDATA_DIR='"/usr/local/share/libcifpp"' -DUSE_RSRC=1 -DNDEBUG -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -version-info 1:1:1 -o libcifpp.la -rpath /usr/local/lib obj/AtomType.lo obj/BondMap.lo obj/Cif2PDB.lo obj/Cif++.lo obj/CifParser.lo obj/CifUtils.lo obj/CifValidator.lo obj/Compound.lo obj/PDB2Cif.lo obj/PDB2CifRemark3.lo obj/Point.lo obj/Secondary.lo obj/Structure.lo obj/Symmetry.lo obj/TlsParser.lo -lboost_iostreams -lboost_date_time -lboost_regex -lz -lbz2
(base) jarek@jrk:~/Documents/libcifpp$ sudo make install
mkdir -p data
wget -O data/components.cif.gz ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz
--2021-05-21 15:04:31-- ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz
=> ‘data/components.cif.gz’
Resolving ftp.wwpdb.org (ftp.wwpdb.org)... 128.6.158.66
Connecting to ftp.wwpdb.org (ftp.wwpdb.org)|128.6.158.66|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done. ==> PWD ... done.
==> TYPE I ... done. ==> CWD (1) /pub/pdb/data/monomers ... done.
==> SIZE components.cif.gz ... 78506636
==> PASV ... done. ==> RETR components.cif.gz ... done.
Length: 78506636 (75M) (unauthoritative)
components.cif.gz 100%[====================================================================================>] 74,87M 1,30MB/s in 59s
2021-05-21 15:05:32 (1,27 MB/s) - ‘data/components.cif.gz’ saved [78506636]
install -d /usr/local/share/libcifpp
install -m644 data/components.cif.gz /usr/local/share/libcifpp/
install -d /usr/local/lib
/bin/sh /home/jarek/Documents/libcifpp/libtool --mode=install install libcifpp.la /usr/local/lib
libtool: install: install .libs/libcifpp.lai /usr/local/lib/libcifpp.la
libtool: install: install .libs/libcifpp.a /usr/local/lib/libcifpp.a
libtool: install: chmod 644 /usr/local/lib/libcifpp.a
libtool: install: ranlib /usr/local/lib/libcifpp.a
libtool: finish: PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin:/sbin" ldconfig -n /usr/local/lib
----------------------------------------------------------------------
Libraries have been installed in:
/usr/local/lib
If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the '-LLIBDIR'
flag during linking and do at least one of the following:
- add LIBDIR to the 'LD_LIBRARY_PATH' environment variable
during execution
- add LIBDIR to the 'LD_RUN_PATH' environment variable
during linking
- use the '-Wl,-rpath -Wl,LIBDIR' linker flag
- have your system administrator add LIBDIR to '/etc/ld.so.conf'
See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
install -d /usr/local/share/libcifpp
for d in mmcif_ddl.dic mmcif_pdbx_v50.dic; do \
install -m644 rsrc/$d /usr/local/share/libcifpp; \
gzip -f /usr/local/share/libcifpp/$d; \
done
install -d /var/cache/libcifpp
install -d /etc/cron.weekly
if [ ! -f /etc/libcifpp.conf ] ; then \
echo "# Uncomment the next line to enable automatic updates" > /etc/libcifpp.conf; \
echo "# update=true" >> /etc/libcifpp.conf; \
echo ""; \
echo "Update the /etc/libcifpp.conf file to enable automatic updates"; \
echo ""; \
fi
install -m755 tools/update-dictionary-script /etc/cron.weekly/libcifpp
install -d /usr/local/include/cif++
for f in AtomType.hpp BondMap.hpp CifParser.hpp Compound.hpp PDB2CifRemark3.hpp Structure.hpp Cif2PDB.hpp CifUtils.hpp Point.hpp Symmetry.hpp Cif++.hpp CifValidator.hpp PDB2Cif.hpp Secondary.hpp TlsParser.hpp; do install include/cif++/$f /usr/local/include/cif++/$f; done
install -d /usr/local/lib/pkgconfig
install -m 644 libcifpp.pc /usr/local/lib/pkgconfig/libcifpp.pc
Do you have a suggestion on how to install the dssp?
Kind regards,
Jarek
I noticed that for at least one AF model - AF-P29376-F1-model_v3.pdb - which has some regions that are very glycine rich, the SSE reported is PP, which I understand to be polypro helix.
Dear Developer,
Recently, I have installed dssp under ubuntu version 18 and the dssp program works fine as a stand alone version but if I call the function within the gromacs do_dssp wrapper function, it fails to execute the command and after a prolonged time , there is no output generated by the system.
There is no way I could figure out where the issue is from, could you please help me to fix it.
Regards,
Nataraj
I recently tried to use dssp with Concoord, but no version from 2. until 4. worked. Older versions of dssp have been shown to have worked, but those are not available anymore.
I just wanted to ask if you happened to know what could cause this.
Dssp 2.2.1 I found on Debian, at least told me it was a bad lexical cast. Every other version just told me "empty protein, or no valid complete residues".
Using any dssp as a standalone worked perfectly fine.
Hi, Thanks for your work. I am trying to install dssp and ran into a problem.
The configuration is file ./configure --with-cif++=/home/yy/libcifpp
However, when I build with make I get the following error: /usr/local/bin/mrc -o obj/mkdssp_rsrc.o /home/yy/libcifpp/rsrc/mmcif_pdbx_v50.dic /usr/local/bin/mrc: error while loading shared libraries: libboost_program_options.so.1.66.0: cannot open shared object file: No such file or directory make: *** [GNUmakefile:139: obj/mkdssp_rsrc.o] Error 127
Hi - I have successfully installed DSSP after installing boost and libcifpp libraries. The dssp runs but shows this warning:
mkdssp 4bgq.pdb no compound information library was found, resulting data may be incorrect or incomplete
Then the generated output does not have the secondary structure assignment. Any solution to this issue? What compound information library is it looking for?
I've been trying to set up a workflow involving dssp so that I can apply it to many frames of a trajectory. Part of that is writing out my trajectory into several pdb files for dssp to use. The issue is that my pdbs do not have the normal remarks including journal information and the sort after going through this process.
Start of one of the pdbs:
CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P1 1
ATOM 1 N ALA X 1 -12.935 14.720 12.724 1.00 0.00 PROT
ATOM 2 HT1 ALA X 1 -12.744 14.789 13.744 1.00 0.00 PROT
I saw in issue #1 that the cryst1 line is required and I have it but I still get this error from dssp when trying to run one of these pdb files:
Expected record HEADER but found CRYST1
Expected record TITLE but found CRYST1
Expected record COMPND but found CRYST1
Expected record SOURCE but found CRYST1
Expected record KEYWDS but found CRYST1
Expected record EXPDTA but found CRYST1
Expected record AUTHOR but found CRYST1
Could not load the mon_lib_list.cif file from CCP4, please make sure you have installed CCP4 and sourced the environment.
missing mandatory field entity_id for Category struct_asym
missing mandatory field type_symbol for Category atom_site
Resulting mmCIF file is not valid!
missing mandatory field entity_id for Category struct_asym
missing mandatory field type_symbol for Category atom_site
Invalid mmCIF file.
Not a known element:
I have successfully used dssp on files containing these remarks (right off of the PDB) but get this error otherwise.
Hi - I have a DSSP set up in my Mac which works perfectly. This is the command I use: mkdssp 1mot.pdb -o 1mot.dssp
But that same command is not generating any SS assignment on AlphaFold generated pdb files. It only outputs the header, without any secondary structure assignment. Please find a sample AlphaFold generated pdb file and the output via the links.
While the command is not working, it also doesn't throw any error that I could dig into. Any help to resolve this, and to generate DSSP outputs on AlphaFold structures will be extremely helpful. Thank you!
명령어 'cmake' 을(를) 찾을 수 없습니다. 그러나 다음을 통해 설치할 수 있습니다:
(cannot find command 'cmake'. but you can install by this:)
sudo snap install cmake # version 3.21.4, or
sudo apt install cmake # version 3.16.3-1ubuntu1
'snap info cmake'에서 추가적인 버전을 확인하십시오.
(Check out the additional version in 'snap info cmake'.)
I success git clone and make build directory, but failed where cmake .. , it prints upper message.
I am using Ubuntu 20.04 LTS, and I tried substitute cmake to make but it failed by:
make: '..'을(를) 위해 할 일이 없습니다.
(make: There's nothing to do something for '..')
I'm running into an issue during install that it cannot find something in the ./doc dir. This checks out as the ./doc dir does not exist. Guessing this is ultimately a problem with something in the $ make?
Any help is appreciated!
Nick
$ ./configure
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking whether g++ supports C++17 features with -std=c++17... yes
checking whether C++ compiler accepts -fstandalone-debug... no
checking for a BSD-compatible install... /usr/bin/install -c
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking build system type...
x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for a sed that does not truncate output... /bin/sed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking whether gcc is Clang... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking whether more special flags are required for pthreads... no
checking for PTHREAD_PRIO_INHERIT... yes
checking for mrc... no
configure: WARNING: The mrc application was not found, not using resources.
checking how to run the C++ preprocessor... g++ -std=c++17 -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking filesystem usability... yes
checking filesystem presence... yes
checking for filesystem... yes
checking for boostlib >= 1.65.1 (106501)... yes
checking whether the Boost::IOStreams library is available... yes
checking for exit in -lboost_iostreams... yes
checking whether the Boost::Program_Options library is available... yes
checking for exit in -lboost_program_options... yes
checking whether the Boost::Date_Time library is available... yes
checking for exit in -lboost_date_time... yes
checking whether the Boost::Regex library is available... yes
checking for exit in -lboost_regex... yes
checking for CIFPP... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for main in -lz... yes
checking bzlib.h usability... yes
checking bzlib.h presence... yes
checking for bzlib.h... yes
checking for main in -lbz2... yes
configure: creating ./config.status
config.status: creating GNUmakefile
config.status: creating src/config.hpp
$ make
mkdir -p obj
rm -f version-info-*.txt
src/mkdssp.cpp
-> mkdssp
nfrazee@cable:~
$ sudo make install
install -d /usr/local/bin
install mkdssp /usr/local/bin/mkdssp
install -d /usr/local/share/man/man1
install -m 644 doc/mkdssp.1 /usr/local/share/man/man1/mkdssp.1;
install: cannot stat 'doc/mkdssp.1': No such file or directory
make: *** [GNUmakefile:164: install] Error 1
Trying to build the program from source code seems to fail on OSX (10.15), due to an issue related to the boost dependency licudata. This issue has been reported by others in separate applications as well: Ref. 1, Ref. 2.
Based on some of the comments from those issues, I was able to resolve the installation here by removing the following lines from the CMakeLists.txt file (148–150, primarily the Boost_USE_STATIC_LIBS setting):
I am having a (really) hard time compiling DSSP/libcifpp/mrc on Windows.
First mrc:
$ ./configure --with-boost="E:\Boost175"
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.exe
checking for suffix of executables... .exe
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking whether g++ supports C++17 features with -std=c++17... yes
checking build system type... x86_64-pc-mingw64
checking host system type... x86_64-pc-mingw64
checking forboostlib >= 1.65.1 (106501) includesin"E:\Boost175/include"... no
checking for boostlib >= 1.65.1 (106501)... yes
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether the Boost::Program_Options library is available... yes
checking formainin -lboost_program_options... no
checking formainin -lboost_program_options-boost_program_options... no
configure: error: Could not link against boost_program_options-boost_program_options !
Then libcifpp:
$ ./configure --with-boost="E:\Boost175"
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.exe
checking for suffix of executables... .exe
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking whether g++ supports C++17 features with -std=c++17... yes
checking whether C++ compiler accepts -fstandalone-debug... no
checking how to run the C++ preprocessor... g++ -std=c++17 -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking filesystem usability... no
checking filesystem presence... yes
configure: WARNING: filesystem: present but cannot be compiled
configure: WARNING: filesystem: check for missing prerequisite headers?
configure: WARNING: filesystem: see the Autoconf documentation
configure: WARNING: filesystem: section "Present But Cannot Be Compiled"
configure: WARNING: filesystem: proceeding with the compiler's resultconfigure: WARNING: ## --------------------------------- ##configure: WARNING: ## Report this to [email protected] ##configure: WARNING: ## --------------------------------- ##checking for filesystem... noconfigure: error: The file <filesystem> is missing, perhaps you should install a more recent libstdc++ implementation.
Would that be possible to get a build/release for Windows (and others) ?
Maybe a CMake version for the compilation tools ?
I hope you are doing well. I have an issue installing DSSP4.0. when I run "cmake --build . --config Release", I get the following error.
[ 12%] Generating mkdssp_rsrc.obj, ALL
/usr/local/bin/mrc: error while loading shared libraries: libboost_program_options.so.1.80.0: cannot open shared object file: No such file or directory
gmake[2]: *** [CMakeFiles/mkdssp.dir/build.make:74: mkdssp_rsrc.obj] Error 127
gmake[1]: *** [CMakeFiles/Makefile2:814: CMakeFiles/mkdssp.dir/all] Error 2
gmake: *** [Makefile:146: all] Error 2
I have /usr/local/bin/mrc and the "libboost_program_options.so.1.80.0" is in "/opt/boost/lib/libboost_program_options.so.1.80.0".
I would appreciate it if you could help me with this problem.
This is the CMakeCache.txt content:
This is the CMakeCache file.
For build in directory: ~/softwares/dssp/build
It was generated by CMake: /usr/bin/cmake
You can edit this file to change values found and used by cmake.
If you do not want to change any of the values, simply exit the editor.
If you do want to change a value, simply edit, save, and exit the editor.
The syntax for the file is as follows:
KEY:TYPE=VALUE
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TYPE is a hint to GUIs for the type of VALUE, DO NOT EDIT TYPE!.
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//Should Dart server send email when build errors are found in
// Continuous builds?
DELIVER_CONTINUOUS_EMAIL:BOOL=Off
//Build an installer
DSSP_BUILD_INSTALLER:BOOL=OFF
//TRUE if we can run a program using std::filesystem
Filesystem_FOUND:BOOL=1
//Path to a program.
GITCOMMAND:FILEPATH=/usr/bin/git
//Git command line client
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USE_RSRC:BOOL=ON
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COVERAGE_COMMAND-ADVANCED:INTERNAL=1
//ADVANCED property for variable: COVERAGE_EXTRA_FLAGS
COVERAGE_EXTRA_FLAGS-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CTEST_SUBMIT_RETRY_COUNT
CTEST_SUBMIT_RETRY_COUNT-ADVANCED:INTERNAL=1
//ADVANCED property for variable: CTEST_SUBMIT_RETRY_DELAY
CTEST_SUBMIT_RETRY_DELAY-ADVANCED:INTERNAL=1
//Test CXX_FILESYSTEM_NO_LINK_NEEDED
CXX_FILESYSTEM_NO_LINK_NEEDED:INTERNAL=
//Test CXX_FILESYSTEM_STDCPPFS_NEEDED
CXX_FILESYSTEM_STDCPPFS_NEEDED:INTERNAL=1
//ADVANCED property for variable: DART_BUILD_ERROR_REPORT_LIMIT
DART_BUILD_ERROR_REPORT_LIMIT-ADVANCED:INTERNAL=1
//ADVANCED property for variable: DART_BUILD_WARNING_REPORT_LIMIT
DART_BUILD_WARNING_REPORT_LIMIT-ADVANCED:INTERNAL=1
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DART_ROOT-ADVANCED:INTERNAL=1
//ADVANCED property for variable: DART_TESTING_TIMEOUT
DART_TESTING_TIMEOUT-ADVANCED:INTERNAL=1
//ADVANCED property for variable: DART_VERBOSE_BUILD
DART_VERBOSE_BUILD-ADVANCED:INTERNAL=1
//ADVANCED property for variable: DELIVER_CONTINUOUS_EMAIL
DELIVER_CONTINUOUS_EMAIL-ADVANCED:INTERNAL=1
//Details about finding Boost
FIND_PACKAGE_MESSAGE_DETAILS_Boost:INTERNAL=[/opt/boost/lib/cmake/Boost-1.80.0/BoostConfig.cmake][cfound components: date_time program_options ][v1.80.0()]
//Details about finding Mrc
FIND_PACKAGE_MESSAGE_DETAILS_Mrc:INTERNAL=[/usr/local/bin/mrc][v()]
//Details about finding Threads
FIND_PACKAGE_MESSAGE_DETAILS_Threads:INTERNAL=[TRUE][v()]
//Details about finding ZLIB
FIND_PACKAGE_MESSAGE_DETAILS_ZLIB:INTERNAL=[/usr/lib64/libz.so][/usr/include][v1.2.11()]
//ADVANCED property for variable: GITCOMMAND
GITCOMMAND-ADVANCED:INTERNAL=1
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GIT_EXECUTABLE-ADVANCED:INTERNAL=1
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GUNZIPCOMMAND-ADVANCED:INTERNAL=1
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MRC_EXECUTABLE-ADVANCED:INTERNAL=1
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_CXX_FILESYSTEM_HAVE_HEADER-ADVANCED:INTERNAL=1
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_CXX_FILESYSTEM_HAVE_HEADER:INTERNAL=1
//CMAKE_INSTALL_PREFIX during last run
_GNUInstallDirs_LAST_CMAKE_INSTALL_PREFIX:INTERNAL=~/.local
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boost_regex_DIR-ADVANCED:INTERNAL=1
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boost_system_DIR-ADVANCED:INTERNAL=1
when I run command cmake --build . --config Release, an error has shown: /home/localuser/boost/lib/libboost_iostreams.a(zlib.o): In function boost::iostreams::detail::zlib_base::after(char const*&, char*&, bool)':
zlib.cpp:(.text+0x138): undefined reference to crc32' /home/localuser/boost/lib/libboost_iostreams.a(zlib.o): In function boost::iostreams::detail::zlib_base::reset(bool, bool)':
zlib.cpp:(.text+0x1b1): undefined reference to deflateReset' zlib.cpp:(.text+0x1c6): undefined reference to inflateEnd'
zlib.cpp:(.text+0x1d9): undefined reference to inflateReset' zlib.cpp:(.text+0x1f1): undefined reference to deflateEnd'
/home/localuser/boost/lib/libboost_iostreams.a(zlib.o): In function boost::iostreams::detail::zlib_base::do_init(boost::iostreams::zlib_params const&, bool, void* (*)(void*, unsigned int, unsigned int), void (*)(void*, void*), void*)': zlib.cpp:(.text+0x3f3): undefined reference to inflateInit2_'
zlib.cpp:(.text+0x447): undefined reference to deflateInit2_' /home/localuser/boost/lib/libboost_iostreams.a(zlib.o): In function boost::iostreams::detail::zlib_base::xdeflate(int)':
zlib.cpp:(.text+0x184): undefined reference to deflate' /home/localuser/boost/lib/libboost_iostreams.a(zlib.o): In function boost::iostreams::detail::zlib_base::xinflate(int)':
zlib.cpp:(.text+0x194): undefined reference to inflate'
I am trying to test rsync but not working. I have all permissions since this is my own laptop and I get the same issue from both my laptop and linux server from clientserver.c
macbook
% rsync -v -avz rsync://rsync.cmbi.umcn.nl/dssp_redo/5gq9.dssp .
opening tcp connection to rsync.cmbi.umcn.nl port 873
rsync: failed to connect to rsync.cmbi.umcn.nl: Connection refused (61)
rsync error: error in socket IO (code 10) at /AppleInternal/Library/BuildRoots/a0876c02-1788-11ed-b9c4-96898e02b808/Library/Caches/com.apple.xbs/Sources/rsync/rsync/clientserver.c(106) [receiver=2.6.9]
centos server
$ rsync -v -avz rsync://rsync.cmbi.umcn.nl/dssp_redo/5gq9.dssp .
opening tcp connection to rsync.cmbi.umcn.nl port 873
rsync: failed to connect to rsync.cmbi.umcn.nl (131.174.161.51): Connection refused (111)
rsync error: error in socket IO (code 10) at clientserver.c(125) [Receiver=3.1.2]
Hi
I am using mkdssp for my own database. For some pdb files the server gives the massage below.
can you tell me what is causing it？
Thanks a lot.
mkdssp: /libcifpp/src/PDB2Cif.cpp:5512: PDBFileParser::ParseCoordinate(int)::<lambda(atomRec&, atomRec&)>: Assertion `d != 0' failed.
Ubuntu Linux 16.04 LTS latest patches, BOOST 1.74.0, libcif++ and MRC are installed successfully. Configure finishes successfully, but make fails:
./configure
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++-9 accepts -g... yes
checking whether g++-9 supports C++17 features with -std=c++17... yes
checking whether C++ compiler accepts -fstandalone-debug... no
checking for a BSD-compatible install... /usr/bin/install -c
checking for mrc... /usr/local/bin/mrc
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for gcc... gcc-9
checking whether we are using the GNU C compiler... yes
checking whether gcc-9 accepts -g... yes
checking for gcc-9 option to accept ISO C89... none needed
checking for a sed that does not truncate output... /bin/sed
checking how to run the C preprocessor... gcc-9 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking whether gcc-9 is Clang... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking whether more special flags are required for pthreads... no
checking for PTHREAD_PRIO_INHERIT... yes
checking how to run the C++ preprocessor... g++-9 -std=c++17 -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking filesystem usability... yes
checking filesystem presence... yes
checking for filesystem... yes
checking for boostlib >= 1.65.1 (106501)... configure: We will use a staged boost library from /root/boost_1_74_0
yes
checking whether the Boost::IOStreams library is available... yes
checking for exit in -lboost_iostreams... yes
checking whether the Boost::Program_Options library is available... yes
checking for exit in -lboost_program_options... yes
checking whether the Boost::Date_Time library is available... yes
checking for exit in -lboost_date_time... yes
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for pkg-config... /usr/bin/pkg-config
checking for CIFPP... yes
configure: creating ./config.status
config.status: creating GNUmakefile
config.status: creating src/config.hpp
root@host:~/dssp# make -j4
fatal: Not a git repository (or any of the parent directories): .git
fatal: Not a git repository (or any of the parent directories): .git
fatal: Not a git repository (or any of the parent directories): .git
mkdir -p obj
rm -f version-info-*.txt
fatal: Not a git repository (or any of the parent directories): .git
GNUmakefile:115: recipe for target 'version-info-.txt' failed
make: *** [version-info-.txt] Error 128
running on the original 101M entry produces a very short dssp file. Most residues are missing:
==== Secondary Structure Definition by the program DSSP, NKI version 3.0 ==== DATE=2021-11-25 .
REFERENCE W. KABSCH AND C.SANDER, BIOPOLYMERS 22 (1983) 2577-2637 .
HEADER OXYGEN TRANSPORT 13-DEC-97 101M .
COMPND MOL_ID: 1; MOLECULE: MYOGLOBIN; CHAIN: A; MUTATION: YES; ENGINEERED: YES .
SOURCE MOL_ID: 1; ORGANISM_COMMON: SPERM WHALE; CELLULAR_LOCATION: CYTOPLASM; ORGANISM_SCIENTIFIC: PHYSETER CATODON; ORG... .
AUTHOR R.D.Smith; J.S.Olson; G.N.Phillips Jr. .
6 5 0 0 0 TOTAL NUMBER OF RESIDUES, NUMBER OF CHAINS, NUMBER OF SS-BRIDGES(TOTAL,INTRACHAIN,INTERCHAIN) .
1513.3 ACCESSIBLE SURFACE OF PROTEIN (ANGSTROM**2) .
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(J) , SAME NUMBER PER 100 RESIDUES .
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS IN PARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES .
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS IN ANTIPARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES .
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-5), SAME NUMBER PER 100 RESIDUES .
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-4), SAME NUMBER PER 100 RESIDUES .
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-3), SAME NUMBER PER 100 RESIDUES .
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-2), SAME NUMBER PER 100 RESIDUES .
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-1), SAME NUMBER PER 100 RESIDUES .
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+0), SAME NUMBER PER 100 RESIDUES .
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+1), SAME NUMBER PER 100 RESIDUES .
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+2), SAME NUMBER PER 100 RESIDUES .
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+3), SAME NUMBER PER 100 RESIDUES .
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+4), SAME NUMBER PER 100 RESIDUES .
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+5), SAME NUMBER PER 100 RESIDUES .
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 *** HISTOGRAMS OF *** .
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 RESIDUES PER ALPHA HELIX .
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 PARALLEL BRIDGES PER LADDER .
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ANTIPARALLEL BRIDGES PER LADDER .
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 LADDERS PER SHEET .
# RESIDUE AA STRUCTURE BP1 BP2 ACC N-H-->O O-->H-N N-H-->O O-->H-N TCO KAPPA ALPHA PHI PSI X-CA Y-CA Z-CA
1 63 A K 0 0 316 0, 0.0 0, 0.0 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 360.0 44.4 10.0 15.5
2 ! 0 0 0 0, 0.0 0, 0.0 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 360.0 0.0 0.0 0.0
3 78 A K 0 0 206 1,-0.1 0, 0.0 3,-0.1 0, 0.0 0.000 360.0 360.0 360.0 -13.1 39.3 10.5 -7.3
4 79 A K 0 0 250 2,-0.1 -1,-0.1 0, 0.0 0, 0.0 0.865 360.0 360.0 52.6 360.0 36.2 12.5 -8.4
5 ! 0 0 0 0, 0.0 0, 0.0 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 360.0 0.0 0.0 0.0
6 82 A H 0 0 244 0, 0.0 -2,-0.1 0, 0.0 -3,-0.1 0.000 360.0 360.0 360.0 360.0 36.8 5.4 -6.4
7 ! 0 0 0 0, 0.0 0, 0.0 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 360.0 0.0 0.0 0.0
8 112 A I 0 0 282 0, 0.0 0, 0.0 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 360.0 28.8 19.6 6.5
9 ! 0 0 0 0, 0.0 0, 0.0 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 360.0 0.0 0.0 0.0
10 144 A A 0 0 215 0, 0.0 0, 0.0 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 360.0 25.7 -1.1 -2.9
Dear
I encountered some problems during the installation.
~/software/dssp-trunk$ ./configure
./configure: line 2068: syntax error near unexpected token noext' ./configure: line 2068: AX_CXX_COMPILE_STDCXX_17(noext)'
First, thanks for your work! I am having some issues ranning the ./configure command for the installation process. It seems like the problem is recognising the libz library, which is installed (when I ran the command sudo apt install zlib1g is stated that the library is already installed).
Can you provide any advice for this error?
Thanks in advance!
g for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking whether g++ supports C++17 features with -std=c++17... yes
checking whether C++ compiler accepts -fstandalone-debug... no
checking for a BSD-compatible install... /usr/bin/install -c
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for a sed that does not truncate output... /usr/bin/sed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking whether gcc is Clang... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking whether more special flags are required for pthreads... no
checking for PTHREAD_PRIO_INHERIT... yes
checking for mrc... no
configure: WARNING: The mrc application was not found, not using resources.
checking how to run the C++ preprocessor... g++ -std=c++17 -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking filesystem usability... yes
checking filesystem presence... yes
checking for filesystem... yes
checking for boostlib >= 1.65.1 (106501)... yes
checking whether the Boost::IOStreams library is available... yes
checking for exit in -lboost_iostreams... yes
checking whether the Boost::Program_Options library is available... yes
checking for exit in -lboost_program_options... yes
checking whether the Boost::Date_Time library is available... yes
checking for exit in -lboost_date_time... yes
checking whether the Boost::Regex library is available... yes
checking for exit in -lboost_regex... yes
checking need to link zlib... no
checking need to link bzip2... no
checking for CIFPP... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for main in -lz... no
configure: error: libz not found - compressed files not supported
I built and installed mkdssp from tag v4.0.0. When I run it however, I get the following error message:
$ mkdssp -v /srv/data/pdb/all/pdb1q5a.ent.gz /srv/data/dssp/1q5a.dssp
Error trying to load file "/srv/data/pdb/all/pdb1q5a.ent.gz"
Dictionary not found or defined (mmcif_pdbx)
The manual entry from mkdssp doesn't say anything about a dictionary. There is a file present though: rsrc/mmcif_pdbx.dic But I can't find any way to use it.
I am trying to build the dssp excutable, so I built first libcifpp in a directory "/apps/dssp/4.0" (cmake -DCMAKE_INSTALL_PREFIX=/apps/dssp/4.0 -DCMAKE_C_COMPILER=gcc-11 -DCMAKE_CXX_COMPILER=g++-11). This worked well but when I tried to build dssp (cmake -DCMAKE_INSTALL_PREFIX=/apps/dssp/4.0 -DCMAKE_C_COMPILER=gcc-11 -DCMAKE_CXX_COMPILER=g++-11) I get the error below. I am on an openSUSE-Tumbleweed machine and I have libconfig installed. My default compiler is GCC 12 but I am trying to build with GCC 11 because libcifpp does not build with GCC 12.
Do you have any idea why is this happening and how to fix it ?
Thank you
Best wishes
Vlad
---ERROR----
CMake Error at CMakeLists.txt:127 (target_link_libraries):
Target "mkdssp" links to:
libconfig::libconfig
but the target was not found. Possible reasons include:
* There is a typo in the target name.
* A find_package call is missing for an IMPORTED target.
* An ALIAS target is missing.
I've managed to get it to configure properly with libcif++ and boost (this was not easy!) but now when I try to make it I'm getting stuck.
If I use my system's default C++ compiler (g++) I get an extremely long error message starting with a complaint about the compiler not being from Intel:
error "This Intel <complex> is for use only with the Intel C++ compilers!"
But when I switch to an Intel C++ compiler that supports C++17 (icx), I get this error:
-> mkdssp
ld: obj/mkdssp.o: undefined reference to symbol '_ZNSt15basic_streambufIcSt11char_traitsIcEE8overflowEi@@GLIBCXX_3.4'
/cm/shared/apps/spack/cpu/opt/spack/linux-centos8-zen/gcc-8.3.1/anaconda3-2020.11-da3i7hmt6bdqbmuzq6pyt7kbm47wyrjp/lib/libstdc++.so.6: error adding symbols: DSO missing from command line
make: *** [GNUmakefile:147: mkdssp] Error 1
This seems to be indicating that it wants me to use a gcc compiler. When I try to configure with gcc, I get an error in the configuration itself:
configure: error: Could not link filesystem
And the other two compilers I've tried (icc and gcpc) fail to even get past the check for support for C++17 when configuring.
I'm trying to compile dssp with gcc 12.1.0 and running into some errors whose cause is not clear to me. I first built libcif++ from source and then ran the following in the dssp build directory:
-- The CXX compiler identification is GNU 12.1.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /gpfs/software/gcc/12.1.0/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Looking for C++ include filesystem -- Looking for C++ include filesystem - found -- Performing Test CXX_FILESYSTEM_NO_LINK_NEEDED -- Performing Test CXX_FILESYSTEM_NO_LINK_NEEDED - Success -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Found ZLIB: /usr/lib64/libz.so (found version "1.2.11") Using resources compiled with -- Configuring done -- Generating done -- Build files have been written to: /gpfs/software/dssp/build
we use a previous version of DSSP, where we have a standalone executable that we can easily transfer and run on different machines. Is this possible for DSSP4.0, as well?
I followed the installation instructions, including mrc, and am able to use mkdssp on my machine. The executable depends on Boost, stating
./mkdssp: error while loading shared libraries: libboost_program_options.so.1.73.0: cannot open shared object file: No such file or directory
after transferring to and running it on a different machine. Is it possible to create a standalone executable as before?
Dear authors, I wish to get accessible surface area values. Suppose a structure has two chains A,B, then when I pass the file (pdb or cif), DSSP calculates the ASA for all the chains present in it together. However, I want to calculate ASA, lets say, chain A and B separately and then together A,B. I could not find any help in the documentation on how to do it? Is it possible?
("output,o", po::value<std::string>(), "Output to this file")
("debug,d", po::value<int>(), "Debug level (for even more verbose output)")
("compounds", po::value<std::string>(), "Location of the components.cif file from CCD")
("components", po::value<std::string>(), "Location of the components.cif file from CCD, alias")
("extra-compounds", po::value<std::string>(), "File containing residue information for extra compounds in this specific target, should be either in CCD format or a CCP4 restraints file")
("mmcif-dictionary", po::value<std::string>(), "Path to the mmcif_pdbx.dic file to use instead of default")
I wonder why these are hidden from the --help considering I just had use for them. Can they not be unhidden?
I'm trying to install dssp, when I run "cmake .." in the directory build, I got an error below:
########################################
CMake Error at CMakeLists.txt:110 (find_package):
By not providing "Findlibconfig.cmake" in CMAKE_MODULE_PATH this project
has asked CMake to find a package configuration file provided by
"libconfig", but CMake did not find one.
Could not find a package configuration file provided by "libconfig" with
any of the following names:
libconfigConfig.cmake
libconfig-config.cmake
Add the installation prefix of "libconfig" to CMAKE_PREFIX_PATH or set
"libconfig_DIR" to a directory containing one of the above files. If
"libconfig" provides a separate development package or SDK, be sure it has
been installed.
#########################################
I have installed the two repo you mentioned above, and noticed https://github.com/mhekkel/libconfig.git has the file "libconfigCondig.cmake", so it confused me, to why the error still appears.
Dear developers,
i have encountered following issues during compiling mkdssp.cpp:
src/mkdssp.cpp: In function 'int d_main(int, const char**)':
src/mkdssp.cpp:532:8: error: 'addFileResource' is not a member of 'cif'
532 | cif::addFileResource("components.cif", vm["compounds"].asstd::string());
| ^~~~~~~~~~~~~~~
src/mkdssp.cpp:534:8: error: 'addFileResource' is not a member of 'cif'
534 | cif::addFileResource("components.cif", vm["components"].asstd::string());
| ^~~~~~~~~~~~~~~
src/mkdssp.cpp:542:8: error: 'addFileResource' is not a member of 'cif'
542 | cif::addFileResource("mmcif_pdbx_v50.dic", vm["mmcif-dictionary"].asstd::string());
| ^~~~~~~~~~~~~~~
make: *** [obj/mkdssp.o] Error 1
i have already installed libcifpp ver 1.0.0 and boost ver 1.76.0
the compilation is carried out with gnu compiler ver 9.3.0
what can i do with the problem??
thank you very much in advance
I was trying to download the official tarball for dssp-4.0.0 but I couldn't find it. Before cloning the git repo, I thought that maybe tagging a 4.0.0 release here would also help others (like other downstreams trying to package updated dssp for their distributions)
I am not able to use MRC while invoking cmake for DSSP installation:
cmake --cifpp_DIR=/home/peter/libcifpp/build/cifpp/ ..
-- Could NOT find Mrc (missing: MRC_EXECUTABLE)
CMake Warning at CMakeLists.txt:128 (find_package):
Found package configuration file:
/home/peter/mrc/mrc-config.cmake
but it set Mrc_FOUND to FALSE so package "Mrc" is considered to be NOT
FOUND.
CMake Warning at CMakeLists.txt:133 (message):
Not using resources since mrc was not found
-- Configuring done
-- Generating done
-- Build files have been written to: /home/peter/dssp/build
Could someone please highlight the issue here?
If I proceed without making any changes, I get the following errors in the next step:
cmake --build . --config Release
Scanning dependencies of target unit-test
[ 16%] Building CXX object CMakeFiles/unit-test.dir/test/unit-test.cpp.o
[ 33%] Building CXX object CMakeFiles/unit-test.dir/src/dssp.cpp.o
[ 50%] Linking CXX executable unit-test
/usr/bin/ld: CMakeFiles/unit-test.dir/src/dssp.cpp.o: in function `boost::date_time::month_formatter<boost::gregorian::greg_month, boost::date_time::iso_extended_format<char>, char>::format_month(boost::gregorian::greg_month const&, std::ostream&)':
dssp.cpp:(.text._ZN5boost9date_time15month_formatterINS_9gregorian10greg_monthENS0_19iso_extended_formatIcEEcE12format_monthERKS3_RSo[_ZN5boost9date_time15month_formatterINS_9gregorian10greg_monthENS0_19iso_extended_formatIcEEcE12format_monthERKS3_RSo]+0x4c): undefined reference to `boost::gregorian::greg_month::as_short_string() const'
/usr/bin/ld: dssp.cpp:(.text._ZN5boost9date_time15month_formatterINS_9gregorian10greg_monthENS0_19iso_extended_formatIcEEcE12format_monthERKS3_RSo[_ZN5boost9date_time15month_formatterINS_9gregorian10greg_monthENS0_19iso_extended_formatIcEEcE12format_monthERKS3_RSo]+0x6f): undefined reference to `boost::gregorian::greg_month::as_long_string() const'
collect2: error: ld returned 1 exit status
make[2]: *** [CMakeFiles/unit-test.dir/build.make:105: unit-test] Error 1
make[1]: *** [CMakeFiles/Makefile2:106: CMakeFiles/unit-test.dir/all] Error 2
make: *** [Makefile:141: all] Error 2
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