March 2015 - IMP-users

how do I build working pmi rnapolii examples ?
by Isabelle Phan 25 Mar '16

25 Mar '16

Hello Ben, How do I install working examples for pmi rnapolii? I need to run the analysis on my model and could not match the IMP tutorial for rnapolii with my old code. They had diverged too much. So I installed 2.4.0 stable release. This does not seem to have working examples for rnapolii. The code only has modules/pmi/broken-examples/rnapolii I tried pulling from the development version, but that does not seem to include working examples either. Am grateful for any help, Isabelle

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Re: [IMP-users] IMP-CGAL4.5.2-Surface_mesh_simplification’ is not a namespace-name
by Ben Webb 16 Mar '15

16 Mar '15

On 03/14/2015 01:50 AM, 陈同 wrote: > I have to add the following lines to CMakeLists.txt. (Listing here for > newbies like me.) While that (in principle) should work, you don't need to edit CMakeLists.txt. Either run ccmake (rather than cmake) and edit the variables in the CMake cache, or you can specify them on the command line when you run cmake. e.g. this is how we run cmake on a 64-bit RHEL5 system (which is too old to have recent enough Boost or HDF5 libraries): cmake28 .. -DCMAKE_INCLUDE_PATH=/usr/include/boost141;/usr/include/hdf518/ -DCMAKE_LIBRARY_PATH=/usr/lib64/boost141;/usr/lib64/hdf518 Ben -- ben(a)salilab.org http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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Re: [IMP-users] IMP-CGAL4.5.2-Surface_mesh_simplification’ is not a namespace-name
by Ben Webb 13 Mar '15

13 Mar '15

On 3/12/15 11:26 PM, 陈同 wrote: > This software recommends install IMP: *IMP version 2.0.1* and *IMP > version 2.1.1.* Ah, looks like they didn't test it with any newer versions of IMP. Well, a newer version of IMP might work. Or you can just apply the patch from my previous email to IMP 2.1.1 - that part of the code hasn't changed for a while. Ben -- ben(a)salilab.org http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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IMP-CGAL4.5.2-Surface_mesh_simplification’ is not a namespace-name
by 陈同 12 Mar '15

12 Mar '15

Hi, all, when installing IMP (2.1.1), I met following errors, Built target RMF-rmf_slice [ 34%] Built target RMF-rmf_pdb [ 34%] Built target RMF-rmf_transform [ 34%] Built target RMF-rmf_validate [ 35%] Built target RMF-rmf_xml [ 35%] Built target RMF-rmf_update [ 35%] Building CXX object modules/cgal/src/CMakeFiles/IMP.cgal-lib.dir/__/__/__/src/cgal_all.cpp.o [ 37%] [ 37%] [ 37%] Built target _RMF_HDF5 Built target RMF-test_associations Built target _RMF [ 37%] Built target RMF-test_buffer [ 37%] Built target RMF-test_fill [ 38%] Built target IMP.benchmark-doc [ 38%] [ 38%] Built target RMF-test_json_encode_decode Built target RMF.benchmark_rmf [ 38%] Built target IMP.kmeans-doc [ 38%] [ 38%] Built target IMP.mpi-doc Built target IMP.test-doc [ 39%] Built target RMF.benchmark_size In file included from /imp5/imp/src/cgal_all.cpp:5: imp-2.1.1/modules/cgal/src/internal/polyhedrons.cpp: In function ‘std::pair<IMP::base::Vector<IMP::algebra::VectorD<3> >, IMP::base::Vector<int> > IMP::cgal::internal::get_skin_surface(const IMP::algebra::Sphere3Ds&)’: imp5/imp-2.1.1/modules/cgal/src/internal/polyhedrons.cpp:275: error: ‘Surface_mesh_simplification’ is not a namespace-name imp5/imp-2.1.1/modules/cgal/src/internal/polyhedrons.cpp:275: error: expected namespace-name before ‘;’ token make[2]: *** [modules/cgal/src/CMakeFiles/IMP.cgal-lib.dir/__/__/__/src/cgal_all.cpp.o] Error 1 make[1]: *** [modules/cgal/src/CMakeFiles/IMP.cgal-lib.dir/all] Error 2 make: *** [all] Error 2 I am using CGAL-4.5.2 and mpfr-3.1.1, could anybody tell me what is wrong? Thanks! Best, Tong Chen

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IMP 2.4.0 release
by Ben Webb 02 Mar '15

02 Mar '15

IMP 2.4.0 is now available. This is a bug fix and minor update release. Most notably Python 3 is now supported, and command line tools ("applications") are now part of regular IMP modules. See https://github.com/salilab/imp/releases/tag/2.4.0 for the full change log. Check it out at http://integrativemodeling.org/ Ben -- ben(a)salilab.org http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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