- IMP-dev - salilab.org

IMP 2.19.0 release
by Ben Webb 23 Jun '23

23 Jun '23

IMP 2.19.0 is now available. This contains serialization support for many commonly-used IMP classes, and support for capturing information on most IMP restraints in output RMF files. See https://integrativemodeling.org/2.19.0/doc/manual/changelog.html for the full change log. Check it out at https://integrativemodeling.org/ Ben -- ben(a)salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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installing IMP on google colab
by Barak Raveh 18 Jan '23

18 Jan '23

This shell snippet used to work for installing IMP on google colab, but it seems to have stopped working: !echo "deb https://integrativemodeling.org/latest/download/ $(lsb_release -cs)/" > /etc/apt/sources.list.d/salilab.list !apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 22A3BF2B !apt update !apt install imp Is it the proper way, and is it supposed to work at all? There seems to be an issue with the key. Thanks! Barak

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cmake - forcing the example module to be built
by Barak Raveh 21 Dec '22

21 Dec '22

Hi, How can I force a certain module to be built? Specifically, the example module is needed by ctest for running e.g. some of the IMP.core examples, but it is not a prerequisite for IMP.core, and it's disabled when I disable some other modules. -- Barak

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build error related to C++11 flag on Mac + conda
by Barak Raveh 19 Dec '22

19 Dec '22

I have been trying to build IMP from source on Conda on my mac. It mostly goes well except in one file it gets flustered by a for-range loop (see *Build output *below). If I build using the same cmd-line just with *--std=c++11*, or *std=c++14*, or *std=c++17*, it works just fine. Moreover, cmake does detect that it should work with C++11 (see *CMake output* below). Any ideas? Thanks! Barak *Build output:* (IMP_BUILD_py310) /Users/Shared/imp/fast_checks$ $ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -DIMPATOM_COMPILATION -DIMP_EXECUTABLE -Iinclude -I/Users/Shared/imp/repository/modules/core/dependency/python-ihm/src -isystem /opt/local/include/eigen3 -w -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.1.sdk -MD -MT modules/atom/benchmark/CMakeFiles/IMP.atom-benchmark_md_charmm.cpp.dir/benchmark_md_charmm.cpp.o -MF modules/atom/benchmark/CMakeFiles/IMP.atom-benchmark_md_charmm.cpp.dir/benchmark_md_charmm.cpp.o.d -o modules/atom/benchmark/CMakeFiles/IMP.atom-benchmark_md_charmm.cpp.dir/benchmark_md_charmm.cpp.o -c /Users/Shared/imp/repository/modules/atom/benchmark/benchmark_md_charmm.cpp /Users/Shared/imp/repository/modules/atom/benchmark/benchmark_md_charmm.cpp:69:30: error: unexpected ':' in nested name specifier; did you mean '::'? for(atom::Hierarchy atom : atoms) { ^ :: /Users/Shared/imp/repository/modules/atom/benchmark/benchmark_md_charmm.cpp:69:32: error: definition or redeclaration of 'atoms' not allowed inside a function for(atom::Hierarchy atom : atoms) { ~~~~~~ ^ /Users/Shared/imp/repository/modules/atom/benchmark/benchmark_md_charmm.cpp:69:32: error: no member named 'atoms' in namespace 'IMP::atom' for(atom::Hierarchy atom : atoms) { ~~~~~~ ^ /Users/Shared/imp/repository/modules/atom/benchmark/benchmark_md_charmm.cpp:69:37: error: expected ';' in 'for' statement specifier for(atom::Hierarchy atom : atoms) { ^ /Users/Shared/imp/repository/modules/atom/benchmark/benchmark_md_charmm.cpp:69:37: error: expected ';' in 'for' statement specifier /Users/Shared/imp/repository/modules/atom/benchmark/benchmark_md_charmm.cpp:70:17: error: unexpected namespace name 'atom': expected expression core::XYZ(atom).set_coordinates_are_optimized(true); ^ 6 errors generated. *CMake output:* -- The C compiler identification is AppleClang 13.0.0.13000029 -- The CXX compiler identification is AppleClang 13.0.0.13000029 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /Users/Shared/Miniconda/envs/IMP_BUILD_py310/bin/python3.1 (found version "3.10.8") found components: Interpreter Development NumPy Development.Module Development.Embed -- Running check_common_problems -- Running clean_build_dir -- Running setup_cmake -- clang version: 13.0.0 -- Using clang C++11 (or later) support

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IMP 2.18.0 release
by Ben Webb 15 Dec '22

15 Dec '22

IMP 2.18.0 is now available. This contains minor updates, including preliminary support for serialization, improvements in constructing topology from primary sequence, and support for the PrISM method for annotation of ensemble precision. See https://integrativemodeling.org/2.18.0/doc/manual/changelog.html for the full change log. Check it out at https://integrativemodeling.org/ Ben -- ben(a)salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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Precision for integrative models
by Shruthi Viswanath 02 Jul '22

02 Jul '22

Hello IMP users, We recently developed PrISM, <https://urldefense.com/v3/__https://doi.org/10.1093/bioinformatics/btac400_… > a simple tool to annotate regions of high and low precision in integrative models. It is implemented as part of the IMP analysis pipeline (sampcon) and detailed usage is at github https://urldefense.com/v3/__https://github.com/isblab/prism__;!!LQC6Cpwp!vk… . We hope it is useful for your systems. Happy to hear any feedback on the method. Best Shruthi

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IMP 2.17.0 release
by Ben Webb 23 Jun '22

23 Jun '22

IMP 2.17.0 is now available. This contains minor updates, with a number of performance improvements and support for newer C++ standards. See https://integrativemodeling.org/2.17.0/doc/manual/changelog.html for the full change log. Check it out at https://integrativemodeling.org/ Ben -- ben(a)salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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IMP 2.16.0 release
by Ben Webb 16 Dec '21

16 Dec '21

IMP 2.16.0 is now available. This contains major updates, notably improved NumPy integration, support for Python 3.10, and a faster scoring function for Monte Carlo sampling. See https://integrativemodeling.org/2.16.0/doc/manual/changelog.html for the full change log. Check it out at https://integrativemodeling.org/ Ben -- ben(a)salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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IMP 2.15.0 release
by Ben Webb 02 Jun '21

02 Jun '21

IMP 2.15.0 is now available. This is contains minor updates, most notably improved handling of MRC files, a new scoring function for cryo-EM data, and support for Apple Silicon. See https://integrativemodeling.org/2.15.0/doc/manual/changelog.html for the full change log. Check it out at https://integrativemodeling.org/ Ben -- ben(a)salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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Imp_sampcon representation resolution
by Jan Kosinski 25 Feb '21

25 Feb '21

Hi all and Shruthi, Actually, since we are talking about imp_sampcon: One feature request I would have for imp_sampcon is an option to select a representation resolution desired for rmsd computations. Would speed up a lot for those who used multiple resolutions. I think one would have to just add an option to the main script and pass an argument to get_rmfs_coordinates and get_rmfs_coordinates_one_rmf in rmsd_calculation.py. Best, Jan

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