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273 discussions

remove DiameterRestraint
by harianto tjong 16 Mar '14

16 Mar '14

Dear IMP users or developers, I run the code example http://salilab.org/imp/2.1.1/doc/html/core_2restrain_diameter_8py-example.h… It runs smoothly. But when I add at the end of the code: m.remove_restraint(r) then it will be Segmentation fault. Anyone knows how to remove this restraint appropriately? Thank you. Best, Harianto.

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RNA / DNA in IMP?
by Barak Raveh 13 Mar '14

13 Mar '14

Anyone has experience with working with nucleic acids in IMP? Does it have any existing nucleic acids support? -- Barak

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changing the default installed /usr/share/IMP path (IMP-2.1.1-1.el5.centos.x86_64.rpm/IMP-devel-2.1.1-1.el5.centos.x86_64.rpm)
by Tru Huynh 04 Dec '13

04 Dec '13

Hello, I am trying to install the prebuilt IMP rpms for CentOS-5 x86_64 in some different place, ie /usr/ -> nfs mounted /c5/shared/imp/2.1.1-1.el5.centos.x86_64 I have rpm2cpio the contents, redefined the required PATH/PYTHONPATH but I am stuck at the /usr/shared/IMP which seems to be hardcoded in lib64/libimp_base.so file. Is there a way to override that /usr/shared/IMP path with some environment variables? or some magic IMP.base.set_data_path ? testcase: <cut imp.py> import IMP import IMP.atom import IMP.multifit m=IMP.kernel.Model() mp0 = IMP.atom.read_pdb('/Bis/home/tru/0.pdb',m) </cut> $ python imp.py Traceback (most recent call last): File "imp.py", line 5, in ? mp0 = IMP.atom.read_pdb('/Bis/home/tru/0.pdb',m) File "/c5/shared/imp/2.1.1-1.el5.centos.x86_64/lib64/python2.4/site-packages/IMP/atom/__init__.py", line 10442, in read_pdb return _IMP_atom.read_pdb(*args) _IMP_base.IOException: Unable to find data file top.lib in [/usr/share/IMP]. IMP is not installed or set up correctly. begin Model 0::do_destroy: Destroying model end Model 0::do_destroy top.lib in my setup is /c5/shared/imp/2.1.1-1.el5.centos.x86_64/share/IMP/atom/top.lib and not in /usr/share/IMP/atom/top.lib Thanks Tru -- Dr Tru Huynh | http://www.pasteur.fr/recherche/unites/Binfs/ mailto:tru@pasteur.fr | tel/fax +33 1 45 68 87 37/19 Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France

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Fwd: FW: FW: Installing IMP on Ubuntu
by Nan Zhao 19 Nov '13

19 Nov '13

Finally made most modules work by installing several packages. Module CGal still could be found, after installing libcgal9. If libcgal-dev package was installed, the building can not finish with an error something like "not complete, error 2". Alan

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Re: [IMP-users] FW: Installing IMP on Ubuntu
by Nan Zhao 15 Nov '13

15 Nov '13

>Does "import IMP.multifit" work from a Python interpreter? It sounds like some of your environment variables aren't set. Did you use the setup_environment script? "import IMP.multifit" does not work. I did use setup_enviroment script. But not all modules could be found. >And they are...? Besides multifit, I also noticed that em2d, emagefit, cnmultifit, numpy, could not be found. (Many other modules and applications work well.) Alan Nan (Alan) Zhao, Ph.D. Assistant Research Professor Department of Basic Sciences College of Veterinary Medicine P.O.Box 6100 Mississippi State, MS 39762 Phone: 662-325-1208 Email: nzhao(a)cvm.msstate.edu On Fri, Nov 15, 2013 at 3:23 PM, Nan (Alan) Zhao <nzhao(a)cvm.msstate.edu>wrote: > > > -----Original Message----- > From: imp-users-bounces(a)salilab.org [mailto:imp-users-bounces@salilab.org] > On Behalf Of Ben Webb > Sent: Friday, November 15, 2013 10:14 AM > To: Help and discussion for users of IMP > Subject: Re: [IMP-users] Installing IMP on Ubuntu > > On 11/15/13 6:54 AM, Nan Zhao wrote: > > I am new to IMP and tried to install it on a Ubuntu server. It worked > > well mostly and after building, I am able to use basic applications > > and modules. However, I just noticed that not all modules are > > installed. For example, if I run multifit.py, Error shows "No module > named > multifit". > > Does "import IMP.multifit" work from a Python interpreter? It sounds like > some of your environment variables aren't set. Did you use the > setup_environment script? > > > There are more than just this one. > > And they are...? > > > /usr/local/src/imp_release/doxygen/generated/all.dox:9: warning: > > unable to resolve reference to `impcgal' for \ref command > > This is just related to the documentation - nothing to worry about. > > BEn > -- > ben(a)salilab.org http://salilab.org/~ben/ > "It is a capital mistake to theorize before one has data." > - Sir Arthur Conan Doyle > _______________________________________________ > IMP-users mailing list > IMP-users(a)salilab.org > https://salilab.org/mailman/listinfo/imp-users > >

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Installing IMP on Ubuntu
by Nan Zhao 15 Nov '13

15 Nov '13

Hi all, I am new to IMP and tried to install it on a Ubuntu server. It worked well mostly and after building, I am able to use basic applications and modules. However, I just noticed that not all modules are installed. For example, if I run multifit.py, Error shows "No module named multifit". There are more than just this one. After building, I got some warnings as following: /usr/local/src/imp_release/doxygen/generated/all.dox:9: warning: unable to resolve reference to `impcgal' for \ref command /usr/local/src/imp_release/doxygen/generated/all.dox:10: warning: unable to resolve reference to `impcnmultifit' for \ref command /usr/local/src/imp_release/doxygen/generated/all.dox:16: warning: unable to resolve reference to `impem2d' for \ref command /usr/local/src/imp_release/doxygen/generated/all.dox:18: warning: unable to resolve reference to `impgsl' for \ref command /usr/local/src/imp_release/doxygen/generated/all.dox:25: warning: unable to resolve reference to `impmpi' for \ref command /usr/local/src/imp_release/doxygen/generated/all.dox:26: warning: unable to resolve reference to `impmultifit' for \ref command /usr/local/src/imp_release/doxygen/generated/all.dox:40: warning: unable to resolve reference to `impEMageFit' for \ref command /usr/local/src/imp_release/doxygen/generated/all.dox:41: warning: unable to resolve reference to `impcnmultifit_tools' for \ref command /usr/local/src/imp_release/doxygen/generated/all.dox:47: warning: unable to resolve reference to `impmultifit_tools' for \ref command /usr/local/src/imp_release/doxygen/generated/all.dox:50: warning: unable to resolve reference to `impsaxs_merge' for \ref command /usr/local/src/imp_release/doxygen/generated/function_example_index.md:32: warning: unable to resolve reference to `IMP::atom::Atom::get_is_setup()' for \ref command /usr/local/src/imp_release/doxygen/generated/function_example_index.md:98: warning: unable to resolve reference to `IMP::core::RigidBody::get_is_setup()' for \ref command /usr/local/src/imp_release/doxygen/generated/installation.md:188: warning: unable to resolve reference to `CGAL' for \ref command /usr/local/src/imp_release/doxygen/generated/installation.md:191: warning: unable to resolve reference to `GSL' for \ref command /usr/local/src/imp_release/doxygen/generated/installation.md:192: warning: unable to resolve reference to `OpenCV' for \ref command /usr/local/src/imp_release/doxygen/generated/installation.md:193: warning: unable to resolve reference to `impmpi' for \ref command /usr/local/src/imp_release/include/IMP/algebra/vector_search.h:49: warning: unable to resolve reference to `CGAL' for \ref command /usr/local/src/imp_release/include/IMP/core/XYZR.h:99: warning: unable to resolve reference to `cgal' for \ref command /usr/local/src/imp_release/include/IMP/core/BoxSweepClosePairsFinder.h:22: warning: unable to resolve reference to `CGAL' for \ref command /usr/local/src/imp_release/include/IMP/core/CoverRefined.h:37: warning: unable to resolve reference to `CGAL' for \ref command /usr/local/src/imp_release/include/IMP/core/RigidClosePairsFinder.h:57: warning: unable to resolve reference to `CGAL' for \ref command /usr/local/src/imp/doc/tutorial/emagefit_3sfd.dox:7: warning: unable to resolve reference to `impEMageFit' for \ref command /usr/local/src/imp/doc/tutorial/multifit_3sfd.dox:7: warning: unable to resolve reference to `impmultifit_tools' for \ref command /usr/local/src/imp/doc/tutorial/cnmultifit_groel.dox:7: warning: unable to resolve reference to `impcnmultifit_tools' for \ref command Does any one know what the problem could be? Thanks. BTW, I just built it at a local directory but did not install it. I change environment variables whenever I use it.

2 1

How to represent a protein-protein interaction network in IMP
by Hongzhu Cui 01 Nov '13

01 Nov '13

Hi, all, Recently, I have a project with IMP. Basically, we need to represent a protein-protein interaction network in IMP, and then we add some restraints to see how we could optimize this network. But I stuck on this problem, and I did not find any similar example in the Manual documentation. Thanks & Regards, Hongzhu

2 3

IMP 2.1 release
by Daniel Russel 24 Oct '13

24 Oct '13

IMP 2.1 has been released. You can either get the source from the master branch (https://github.com/salilab/imp/tree/master) or binary installers from the downloads tab (http://integrativemodeling.org/download.html). See the release notes (https://github.com/salilab/imp/releases/tag/2.1.0) for a list of changes.

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Installing IMP on Ubuntu 12.04
by Steven Howell 10 Sep '13

10 Sep '13

Greetings IMP users, I am failing to successfully setup IMP 2.0.1 on my Ubuntu 12.04 system. Following the directions in the IMP documentation, I installed the mandatory packages - cmake - libboost-all-dev - libhdf5-serial-1.8.4 - swig as well as the optional packages - gsl-bin - ann-tools - libcgal8 - google-perftools When I run, 'cmake ../imp -DCMAKE_BUILD_TYPE=Release', I get the fatal error: -- Could NOT find HDF5 (missing: HDF5_LIBRARIES HDF5_INCLUDE_DIRS) CMake Error at /usr/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:91 (MESSAGE): Could NOT find HDF5 (missing: HDF5_LIBRARIES HDF5_INCLUDE_DIRS) I attempted installing different libhdf5 versions, lam, openmpi, and mpich, but received the same error for each. Additionally, all of optional packages I installed fail to be detected. Initially gsl and cgal are both detected but then upon configuration they are no longer found. ... -- Different data/build_info/sorted_modules +cgal +gsl ... -- Configuring module cgal ... CGAL not found Different data/build_info/sorted_modules -cgal ... -- Configuring module gsl ... GSL not found Different data/build_info/sorted_modules -gsl ... Is this a problem with a different native installation path for programs in Ubuntu vs Fedora/RedHad? What is the best work around to overcome these errors? Thank you for any help. Steven Howell Ph.D. Candidate Department of Physics The George Washington University Corcoran 203, 725 21st St, NW Washington, DC 20052 Lab: 202.994.3414

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Disabling logs in IMP
by Dan Cohen 04 Aug '13

04 Aug '13

Hello all, I would like first to say that IMP has been a great help for me and I have been using it extensively in my current project. Thank you! I just pulled the latest IMP from the git and built it after doing : cmake ../imp-source/ -DCMAKE_BUILD_TYPE=Release Suddenly when running code using IMP (python bindings) I'm getting tons of logs (for each creation/destruction of a Model object for example) I thought I was building in release so why do I get all of those logs? Can I disable them? You can see below the output of the cmake command. I'm using cmake version 2.8.7 Thank you, Dany * * *Example for some logs : * Matched Atom N of residue 525 with [] and 1 end search begin search: Matched Atom CA of residue 525 with [] and 1 end search begin search: Matched Atom C of residue 525 with [] and 1 end search begin search: Matched Atom O of residue 525 with [] and 1 end search begin search: Matched Atom CB of residue 525 with [] and 1 end search begin search: Matched Atom CG of residue 525 with [] and 1 end search begin search: Matched Atom CD of residue 525 with [] and 1 end search Matched PRO with [4365, 4367, 4368, 4369, 4370, 4371, 4372] and 1 end search Matched Chain E with [0, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, ,...] and 1 end search Matched 1oel_E.pdb: with [0, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, ,...] and 1 end search * * *The cmake output : * $ cmake ../imp-source/ -DCMAKE_BUILD_TYPE=Release -- The C compiler identification is GNU -- The CXX compiler identification is GNU -- Check for working C compiler: /usr/bin/gcc -- Check for working C compiler: /usr/bin/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Running check_common_problems -- Running setup_cmake -- Wrong doxygen version at /usr/bin/doxygen. Found 1.7.6.1, but needed 1.8.4 -- Will download doxygen from http://ftp.stack.nl/pub/users/dimitri/doxygen-1.8.4.linux.bin.tar.gz -- Running setup_doxygen -- Python version is 2.7 -- Found PythonLibs: /usr/lib/libpython2.7.so (found suitable exact version "2.7.3") -- Running setup -- Running setup_containers -- Running setup_all -- Running setup_module_alias for compatibility -- Setting up alias for module base as compatibility -- Running setup_module_alias for kernel -- Setting up alias for module kernel as -- Boost version: 1.46.1 -- Found the following Boost libraries: -- system -- filesystem -- thread -- program_options -- Performing Test IMP_COMPILER_HAS_AUTO -- Performing Test IMP_COMPILER_HAS_AUTO - Failed -- Performing Test IMP_COMPILER_HAS_DEBUG_VECTOR -- Performing Test IMP_COMPILER_HAS_DEBUG_VECTOR - Success -- checking for module 'gperftools' -- package 'gperftools' not found GPerfTools not found -- checking for module 'log4cxx' -- package 'log4cxx' not found -- Found LOG4CXX -- Performing Test Log4CXX_found -- Performing Test Log4CXX_found - Success -- Found Log4CXX -- checking for module 'tcmalloc_heapchecker' -- package 'tcmalloc_heapchecker' not found TCMalloc_HeapChecker not found -- checking for module 'tcmalloc_heapprofiler' -- package 'tcmalloc_heapprofiler' not found TCMalloc_HeapProfiler not found -- Running generate paths.cpp Configuring module base ... yes -- Running setup_swig_wrappers base Configuring module benchmark ... yes -- Running setup_swig_wrappers benchmark -- Build type: Release -- USING CXXFLAGS = ' -O3 -DNDEBUG' -- USING EXEFLAGS = ' ' -- Targetting Unix Makefiles -- Using /usr/bin/c++ compiler. -- Updating CMAKE_CXX_FLAGS Configuring module cgal ... yes -- Running setup_swig_wrappers cgal Configuring module kmeans ... yes -- Running setup_swig_wrappers kmeans -- Found MPI_C: /usr/local/lib/openmpi-1.4.1/lib/libmpi.so;/usr/local/lib/openmpi-1.4.1/lib/libopen-rte.so;/usr/local/lib/openmpi-1.4.1/lib/libopen-pal.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libnsl.so;/usr/lib/x86_64-linux-gnu/libutil.so;/usr/lib/x86_64-linux-gnu/libm.so;/usr/lib/x86_64-linux-gnu/libdl.so -- Found MPI_CXX: /usr/local/lib/openmpi-1.4.1/lib/libmpi_cxx.so;/usr/local/lib/openmpi-1.4.1/lib/libmpi.so;/usr/local/lib/openmpi-1.4.1/lib/libopen-rte.so;/usr/local/lib/openmpi-1.4.1/lib/libopen-pal.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libnsl.so;/usr/lib/x86_64-linux-gnu/libutil.so;/usr/lib/x86_64-linux-gnu/libm.so;/usr/lib/x86_64-linux-gnu/libdl.so -- MPI found Configuring module mpi ... yes -- Running setup_swig_wrappers mpi Configuring module test ... yes -- Running setup_swig_wrappers test -- checking for module 'ann' -- package 'ann' not found ANN not found Configuring module algebra ... yes -- Running setup_swig_wrappers algebra Configuring module kernel ... yes -- Running setup_swig_wrappers kernel Configuring module display ... yes -- Running setup_swig_wrappers display -- checking for module 'gsl' -- found gsl, version 1.15 -- Found GSL -- Performing Test GSL_found -- Performing Test GSL_found - Success -- Found GSL Configuring module gsl ... yes -- Running setup_swig_wrappers gsl Configuring module parallel ... yes -- Running setup_swig_wrappers parallel Configuring module score_functor ... yes -- Running setup_swig_wrappers score_functor Configuring module statistics ... yes -- Running setup_swig_wrappers statistics Configuring module system ... yes -- Running setup_swig_wrappers system Configuring module core ... yes -- Running setup_swig_wrappers core Configuring module container ... yes -- Running setup_swig_wrappers container Configuring module modeller ... yes -- Running setup_swig_wrappers modeller Configuring module symmetry ... yes -- Running setup_swig_wrappers symmetry Configuring module atom ... yes -- Running setup_swig_wrappers atom Configuring module scratch ... yes -- Running setup_swig_wrappers scratch Configuring module em ... yes -- Running setup_swig_wrappers em Configuring module kinematics ... yes -- Running setup_swig_wrappers kinematics Configuring module misc ... yes -- Running setup_swig_wrappers misc -- Performing Test RMF_environment -- Performing Test RMF_environment - Failed -- checking for module 'RMF' -- package 'RMF' not found -- Building internal RMF -- checking for module 'log4cxx' -- package 'log4cxx' not found -- Found Log4CXX -- Logging enabled -- Found HDF5: debug;/usr/lib/libhdf5.so;optimized;/usr/lib/libhdf5.so -- Found SWIG: swig (found version "2.0.4") -- /usr/include/python2.7 -- benchmark_size -- benchmark_rmf -- Found Doxygen: /usr/bin/doxygen -- Updating paths for RMF <> Configuring module rmf ... yes -- Running setup_swig_wrappers rmf Configuring module rotamer ... yes -- Running setup_swig_wrappers rotamer Configuring module saxs ... yes -- Running setup_swig_wrappers saxs -- checking for module 'hdf5' -- package 'hdf5' not found -- Found HDF5 -- Performing Test HDF5_found -- Performing Test HDF5_found - Success -- Found HDF5 Configuring module domino ... yes -- Running setup_swig_wrappers domino -- checking for module 'cholmod' -- package 'cholmod' not found CHOLMOD not found -- checking for module 'eigen3' -- package 'eigen3' not found Eigen3 not found Configuring module isd ... Eigen3 not found Different data/build_info/sorted_modules -isd Module IMP.isd disabled Configuring module restrainer ... yes -- Running setup_swig_wrappers restrainer -- checking for module 'fftw3' -- found fftw3, version 3.3.3 -- Found FFTW3 -- Performing Test FFTW3_found -- Performing Test FFTW3_found - Success -- Found FFTW3 -- checking for module 'opencv21' -- package 'opencv21' not found OpenCV21 not found -- checking for module 'opencv22' -- package 'opencv22' not found OpenCV22 not found em2d is disabled Different data/build_info/sorted_modules -em2d Module IMP.em2d disabled -- checking for module 'exampledependency' -- package 'exampledependency' not found ExampleDependency not found Configuring module example ... yes -- Running setup_swig_wrappers example Configuring module multifit ... yes -- Running setup_swig_wrappers multifit Configuring module pepdock ... yes -- Running setup_swig_wrappers pepdock -- checking for module 'libtau' -- package 'libtau' not found libTau not found Configuring module cnmultifit ... libTau not found Different data/build_info/sorted_modules -cnmultifit Module IMP.cnmultifit disabled -- Running setup_swig_dependencies -- Creating thread pool with 16 Configuring application EMageFit ... no Different data/build_info/applications -EMageFit Application EMageFit disabled Configuring application cnmultifit_tools ... no Different data/build_info/applications -cnmultifit_tools Application cnmultifit_tools disabled Configuring application em_tools ... yes Configuring application example_app ... yes Configuring application foxs ... yes Configuring application integrative_docking ... yes Configuring application ligand_score ... yes Configuring application multifit_tools ... yes Configuring application pdb_tools ... yes Configuring application rmf_tools ... yes Configuring application saxs_merge ... no Different data/build_info/applications -saxs_merge Application saxs_merge disabled Configuring application saxs_tools ... yes -- Running setup_doxygen_config -- Running setup_imppy -- Configuring done

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