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274 discussions

IMP 2.6.1 release
by Ben Webb 14 Apr '16

14 Apr '16

IMP 2.6.1 is now available. This corrects a few minor bugs and documentation issues in the previous release (2.6.0). See https://integrativemodeling.org/2.6.1/doc/manual/changelog.html for the full change log. Check it out at https://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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slow MC optimizer
by Joseph Eschweiler 14 Apr '16

14 Apr '16

Hello, I'm using the MC optimizer to optimize protein complexes represented by spheres. My script loops through various sets of restraints (either distance or MS-connectivity) and generates an ensemble of structures for each restraint set. My problem is that the speed of the optimizer changes drastically each time over the loop, and there is no correlation between the complexity of the restraint set and the speed of the optimizer. The speed usually varies between 10 and 30 models per second, but will sometimes slow to 1 model/10minutes forces me to terminate the script. I always initialize each optmization cycle with new random coordinates, so I know I'm not simply getting stuck in a local minima, and I know the restraint sets themselves are all fine since I could loop over the same restraint set many times and the speed would change unpredictably. I've also tried setting up a completely new model instance for each restraint set, which doesn't solve the problem either. for restraint set: for oc in range(self.optimization_cycles): for particle in self.system.ds: ## RANDOMIZE COORDINATES init_coors = IMP.algebra.get_random_vector_in(self.system.bb ) particle.set_coordinates(init_coors) T = self.initial_temperature for mc in range(self.mc_cool_cycles): ## DO THE ANNEALING MC T = 0.99*T self.optimizer.set_kt(T) self.optimizer.optimize(self.mc_cool_steps) Any input is greatly appreciated. Joe -- Joseph D. Eschweiler Ph.D. Candidate | Ruotolo Group Department of Chemistry University of Michigan

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IMP 2.6.0 release
by Ben Webb 28 Mar '16

28 Mar '16

IMP 2.6.0 is now available. This is a bugfix and minor update release. Most notably we include most of the functionality of PMI2. This is an improved version of PMI that is faster than PMI1, more modular, and easier to use. See the IMP::pmi module docs for more information. This release also includes a number of bug fixes, most notably in the creation of sampled electron microscopy density maps. See the https://integrativemodeling.org/2.6.0/doc/manual/changelog.html for the full change log. Check it out at https://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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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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MP.em.EnvelopeFitRestraint class
by Karine VOLTZ 05 Feb '16

05 Feb '16

Dear IMP-users, I have a question regarding the IMP.em.EnvelopeFitRestraint class: As a simple test I just tried to evaluate this restraint with an EM density map and a set of particles corresponding to each subunits that fill the map. As coordinates for each particle, I have assigned a random vector belonging to the boundingbox of the density map. Depending on the coordinates of the particles, sometimes the restraint is correctly calculated, sometimes I get the following error message: File "/usr/local/lib/IMP-python/IMP/kernel/__init__.py", line 2183, in evaluate return _IMP_kernel.Restraint_evaluate(self, *args) _IMP_base.UsageException: Usage check failure: The point is not part of the grid Context: fit_restraint::evaluate/fit_restraint scoring::evaluate/fit_restraint scoring::do_add_score_and_derivatives/fit_restraint::add_score_and_derivatives/fit_restraint::do_add_score_and_derivatives Can somebody explain me this error? Thank you Karine

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Compiling IMP 2.5.0 on CentOS 7
by Novosielski, Ryan 02 Feb '16

02 Feb '16

Hi there, Having a heck of a time trying to compile IMP 2.5.0 and its dependencies. Hopefully someone can help. Note that below, the ones that do not say (CentOS 7.2) are in non-standard locations under /opt because we have to keep multiple versions of a lot of this stuff due to other software depending on it. I’m using: * GCC 4.8.5 (CentOS 7.2) * CMake 2.8.11 * Boost 1.60.00 * HDF5 1.8.16 (--with-parallel) * Python 2.7.11 * SWIG 2.0.10 (CentOS 7.2) * Modeller 9.16 * GSL 1.15 (CentOS 7.2) * OpenCV 2.3.1 * FFTW 3.3.3 (CentOS 7.2) * MVAPICH 2.1 * NumPy: 1.10.4, SciPy: 0.16.1, matplotlib: 1.5.1, biopython 1.66 First I had a very difficult time getting it to even detect OpenCV. My final solution was to set $PKG_CONFIG_PATH to include the pkgconfig directory for OpenCV 2.3.1 and to symlink opencv.pc (which was created by the build) to opencv22.pc (which is what IMP looks for for some reason). Note that the documentation mentions that 2.1-2.3 works, but it isn’t clear whether that’s actually true when a build failure claims 2.2 is not detected and that is the reason it won’t build em2d. OpenCV 2.2 doesn’t build properly on this environment, for a reason that I’m not quite sure of. As an aside, OpenCV 2.3.1 seems to require a very old version of CUDA that most people would not have, so one has to turn off CUDA support or get that very old version (which doesn’t support our hardware anyway). I then had difficulty with HDF5 not finding mpi.h. Apparently this is a common problem if you’ve built HDF5 parallel. My solution was setting the compilers to be mpicc/mpic++. At this point, I have to say I’m lost. Here is my cmake command line: cmake ../imp-2.5.0 -DCMAKE_BUILD_TYPE=Release -DPYTHON_LIBRARY=/opt/sw/packages/gcc-4.8.3/python/2.7.11/lib -DPYTHON_INCLUDE_DIR=/opt/sw/packages/gcc-4.8.3/python/2.7.11/include -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpic++ -DCMAKE_INSTALL_PREFIX=/opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost-1.60.0/imp/2.5.0 Doing a make with a high parallel number (eg. 24, 32) got me to a place where there were a number of errors on RMF/SWIG relating to not being able to find Python.h. It’s not clear whether that blocks the build, but it’s probably not good. The CMake command at the beginning reports that it found the expected version of Python (which didn’t work right unless I manually supplied it on the command line). It eventually fails for what I suspect is some other reason. Doing just a make fails on what looks like a problem with Boost. Perhaps Boost 1.60.0 isn’t supported? I don’t know what version to use instead, other than to assume 1.40.0 works since 1.40.0 or newer is required. Output as follows; your help is appreciated! Scanning dependencies of target IMP.statistics-lib [ 18%] Building CXX object modules/statistics/src/CMakeFiles/IMP.statistics-lib.dir/__/__/__/src/statistics_all.cpp.o In file included from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/functional/hash/extensions.hpp:24:0, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/functional/hash/hash.hpp:558, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/functional/hash.hpp:6, from /usr/src/imp-2.5.0-build/include/IMP/hash.h:17, from /usr/src/imp-2.5.0-build/include/IMP/statistics/statistics_config.h:162, from /usr/src/imp-2.5.0-build/include/IMP/statistics/ChiSquareMetric.h:11, from /usr/src/imp-2.5.0/modules/statistics/src/ChiSquareMetric.cpp:8, from /usr/src/imp-2.5.0-build/src/statistics_all.cpp:4: /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/graph/adjacency_matrix.hpp:446:25: error: ^Xice_not^Y is not a member of ^Xboost::type_traits^Y BOOST_STATIC_ASSERT(type_traits::ice_not<(is_same<Directed, bidirectionalS>::value)>::value); ^ /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/static_assert.hpp:70:55: note: in definition of macro ^XBOOST_STATIC_ASSERT^Y # define BOOST_STATIC_ASSERT( ... ) static_assert(__VA_ARGS__, #__VA_ARGS__) ^ /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/graph/adjacency_matrix.hpp:446:89: error: ^X::value^Y has not been declared BOOST_STATIC_ASSERT(type_traits::ice_not<(is_same<Directed, bidirectionalS>::value)>::value); ^ /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/static_assert.hpp:70:55: note: in definition of macro ^XBOOST_STATIC_ASSERT^Y # define BOOST_STATIC_ASSERT( ... ) static_assert(__VA_ARGS__, #__VA_ARGS__) ^ /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/graph/adjacency_matrix.hpp:446:89: note: suggested alternatives: BOOST_STATIC_ASSERT(type_traits::ice_not<(is_same<Directed, bidirectionalS>::value)>::value); ^ /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/static_assert.hpp:70:55: note: in definition of macro ^XBOOST_STATIC_ASSERT^Y # define BOOST_STATIC_ASSERT( ... ) static_assert(__VA_ARGS__, #__VA_ARGS__) ^ In file included from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/program_options/value_semantic.hpp:432:0, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/program_options/options_description.hpp:13, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/program_options.hpp:15, from /usr/src/imp-2.5.0-build/include/IMP/internal/Flag.h:13, from /usr/src/imp-2.5.0-build/include/IMP/Flag.h:13, from /usr/src/imp-2.5.0-build/include/IMP/internal/base_static.h:13, from /usr/src/imp-2.5.0-build/include/IMP/exception.h:16, from /usr/src/imp-2.5.0-build/include/IMP/Object.h:14, from /usr/src/imp-2.5.0-build/include/IMP/statistics/Metric.h:13, from /usr/src/imp-2.5.0-build/include/IMP/statistics/ChiSquareMetric.h:12, from /usr/src/imp-2.5.0/modules/statistics/src/ChiSquareMetric.cpp:8, from /usr/src/imp-2.5.0-build/src/statistics_all.cpp:4: /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/program_options/detail/value_semantic.hpp:180:5: note: ^Xboost::program_options::value^Y value(T* v) ^ In file included from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/detail/core/access.hpp:18:0, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/detail/core/state.hpp:18, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/detail/core/matcher/alternate_end_matcher.hpp:20, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/detail/core/matchers.hpp:17, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/regex_primitives.hpp:22, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/xpressive_static.hpp:24, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/graph/graphviz.hpp:34, from /usr/src/imp-2.5.0-build/include/IMP/internal/base_graph_utility.h:16, from /usr/src/imp-2.5.0-build/include/IMP/graph_macros.h:14, from /usr/src/imp-2.5.0-build/include/IMP/base_macros.h:24, from /usr/src/imp-2.5.0-build/include/IMP/base_utility.h:15, from /usr/src/imp-2.5.0-build/include/IMP/utility.h:13, from /usr/src/imp-2.5.0-build/include/IMP/algebra/VectorBaseD.h:16, from /usr/src/imp-2.5.0-build/include/IMP/algebra/VectorD.h:12, from /usr/src/imp-2.5.0-build/include/IMP/algebra/BoundingBoxD.h:12, from /usr/src/imp-2.5.0-build/include/IMP/algebra.h:10, from /usr/src/imp-2.5.0/modules/statistics/src/ChiSquareMetric.cpp:9, from /usr/src/imp-2.5.0-build/src/statistics_all.cpp:4: /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/proto/traits.hpp:1161:5: note: ^Xboost::proto::value^Y value(Expr const &e) ^ In file included from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/detail/core/access.hpp:18:0, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/detail/core/state.hpp:18, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/detail/core/matcher/alternate_end_matcher.hpp:20, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/detail/core/matchers.hpp:17, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/regex_primitives.hpp:22, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/xpressive_static.hpp:24, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/graph/graphviz.hpp:34, from /usr/src/imp-2.5.0-build/include/IMP/internal/base_graph_utility.h:16, from /usr/src/imp-2.5.0-build/include/IMP/graph_macros.h:14, from /usr/src/imp-2.5.0-build/include/IMP/base_macros.h:24, from /usr/src/imp-2.5.0-build/include/IMP/base_utility.h:15, from /usr/src/imp-2.5.0-build/include/IMP/utility.h:13, from /usr/src/imp-2.5.0-build/include/IMP/algebra/VectorBaseD.h:16, from /usr/src/imp-2.5.0-build/include/IMP/algebra/VectorD.h:12, from /usr/src/imp-2.5.0-build/include/IMP/algebra/BoundingBoxD.h:12, from /usr/src/imp-2.5.0-build/include/IMP/algebra.h:10, from /usr/src/imp-2.5.0/modules/statistics/src/ChiSquareMetric.cpp:9, from /usr/src/imp-2.5.0-build/src/statistics_all.cpp:4: /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/proto/traits.hpp:294:16: note: ^Xboost::proto::result_of::value^Y struct value ^ In file included from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/detail/core/access.hpp:18:0, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/detail/core/state.hpp:18, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/detail/core/matcher/alternate_end_matcher.hpp:20, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/detail/core/matchers.hpp:17, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/regex_primitives.hpp:22, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/xpressive_static.hpp:24, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/graph/graphviz.hpp:34, from /usr/src/imp-2.5.0-build/include/IMP/internal/base_graph_utility.h:16, from /usr/src/imp-2.5.0-build/include/IMP/graph_macros.h:14, from /usr/src/imp-2.5.0-build/include/IMP/base_macros.h:24, from /usr/src/imp-2.5.0-build/include/IMP/base_utility.h:15, from /usr/src/imp-2.5.0-build/include/IMP/utility.h:13, from /usr/src/imp-2.5.0-build/include/IMP/algebra/VectorBaseD.h:16, from /usr/src/imp-2.5.0-build/include/IMP/algebra/VectorD.h:12, from /usr/src/imp-2.5.0-build/include/IMP/algebra/BoundingBoxD.h:12, from /usr/src/imp-2.5.0-build/include/IMP/algebra.h:10, from /usr/src/imp-2.5.0/modules/statistics/src/ChiSquareMetric.cpp:9, from /usr/src/imp-2.5.0-build/src/statistics_all.cpp:4: /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/proto/traits.hpp:824:16: note: ^Xboost::proto::functional::value^Y struct value ^ In file included from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/detail/detail_fwd.hpp:24:0, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/regex_primitives.hpp:21, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/xpressive_static.hpp:24, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/graph/graphviz.hpp:34, from /usr/src/imp-2.5.0-build/include/IMP/internal/base_graph_utility.h:16, from /usr/src/imp-2.5.0-build/include/IMP/graph_macros.h:14, from /usr/src/imp-2.5.0-build/include/IMP/base_macros.h:24, from /usr/src/imp-2.5.0-build/include/IMP/base_utility.h:15, from /usr/src/imp-2.5.0-build/include/IMP/utility.h:13, from /usr/src/imp-2.5.0-build/include/IMP/algebra/VectorBaseD.h:16, from /usr/src/imp-2.5.0-build/include/IMP/algebra/VectorD.h:12, from /usr/src/imp-2.5.0-build/include/IMP/algebra/BoundingBoxD.h:12, from /usr/src/imp-2.5.0-build/include/IMP/algebra.h:10, from /usr/src/imp-2.5.0/modules/statistics/src/ChiSquareMetric.cpp:9, from /usr/src/imp-2.5.0-build/src/statistics_all.cpp:4: /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/xpressive_fwd.hpp:134:12: note: ^Xboost::xpressive::value^Y struct value; ^ In file included from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/bind.hpp:22:0, from /usr/src/imp-2.5.0-build/include/IMP/internal/container_helpers.h:19, from /usr/src/imp-2.5.0-build/include/IMP/internal/TupleRestraint.h:14, from /usr/src/imp-2.5.0-build/include/IMP/singleton_macros.h:15, from /usr/src/imp-2.5.0-build/include/IMP/macros.h:13, from /usr/src/imp-2.5.0-build/include/IMP/statistics/PartitionalClustering.h:13, from /usr/src/imp-2.5.0/modules/statistics/src/PartitionalClustering.cpp:7, from /usr/src/imp-2.5.0-build/src/statistics_all.cpp:8: /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/bind/bind.hpp:118:25: note: ^Xboost::_bi::value^Y template<class T> class value ^ In file included from /usr/src/imp-2.5.0-build/include/IMP/statistics/internal/TrivialPartitionalClustering.h:14:0, from /usr/src/imp-2.5.0/modules/statistics/src/RecursivePartitionalClusteringEmbedding.cpp:9, from /usr/src/imp-2.5.0-build/src/statistics_all.cpp:10: /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/graph/adjacency_matrix.hpp: In instantiation of ^Xstatic boost::adj_mat_pm_helper<D, VP, EP, GP, A, Tag, boost::edge_property_tag>::type boost::adj_mat_pm_helper<D, VP, EP, GP, A, Tag, boost::edge_property_tag>::get_nonconst(boost::adjacency_matrix<D , VP, EP, GP, A>&, Tag) [with D = boost::undirectedS; VP = boost::no_property; EP = boost::property<boost::edge_weight_t, double, boost::property<boost::edge_ centrality_t, double> >; GP = boost::no_property; A = std::allocator<bool>; Tag = boost::edge_centrality_t; boost::adj_mat_pm_helper<D, VP, EP, GP, A, Tag, bo ost::edge_property_tag>::type = boost::function_property_map<boost::adj_mat_pm_helper<boost::undirectedS, boost::no_property, boost::property<boost::edge_weig ht_t, double, boost::property<boost::edge_centrality_t, double> >, boost::no_property, std::allocator<bool>, boost::edge_centrality_t, boost::edge_property_ta g>::lookup_property_from_edge<mpl_::bool_<false> >, boost::detail::matrix_edge_desc_impl<boost::undirected_tag, long unsigned int>, double&>; typename boost:: result_of<const boost::adj_mat_pm_helper<D, VP, EP, GP, A, Tag, boost::edge_property_tag>::lookup_property_from_edge<mpl_::bool_<false> >(const typename boost ::graph_traits<boost::adjacency_matrix<D, VP, EP, GP, A> >::edge_descriptor&)>::type = double&; typename boost::graph_traits<boost::adjacency_matrix<D, VP, EP , GP, A> >::edge_descriptor = boost::detail::matrix_edge_desc_impl<boost::undirected_tag, long unsigned int>]^Y: /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/graph/adjacency_matrix.hpp:1119:86: required from ^Xtypename boost::property_map<boost::ad jacency_matrix<D, VP, EP, GP, A>, Tag>::type boost::get(Tag, boost::adjacency_matrix<D, VP, EP, GP, A>&) [with D = boost::undirectedS; VP = boost::no_property ; EP = boost::property<boost::edge_weight_t, double, boost::property<boost::edge_centrality_t, double> >; GP = boost::no_property; A = std::allocator<bool>; T ag = boost::edge_centrality_t; typename boost::property_map<boost::adjacency_matrix<D, VP, EP, GP, A>, Tag>::type = boost::function_property_map<boost::adj_ma t_pm_helper<boost::undirectedS, boost::no_property, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_centrality_t, double> >, boost:: no_property, std::allocator<bool>, boost::edge_centrality_t, boost::edge_property_tag>::lookup_property_from_edge<mpl_::bool_<false> >, boost::detail::matrix_ edge_desc_impl<boost::undirected_tag, long unsigned int>, double&>]^Y /usr/src/imp-2.5.0/modules/statistics/src/internal/centrality_clustering.cpp:74:43: required from here /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/graph/adjacency_matrix.hpp:1092:17: warning: unused parameter ^Xg^Y [-Wunused-parameter] static type get_nonconst(adjacency_matrix<D, VP, EP, GP, A>& g, Tag tag) { ^ /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/graph/adjacency_matrix.hpp: In instantiation of ^Xstatic boost::adj_mat_pm_helper<D, VP, EP, GP, A, Tag, boost::edge_property_tag>::type boost::adj_mat_pm_helper<D, VP, EP, GP, A, Tag, boost::edge_property_tag>::get_nonconst(boost::adjacency_matrix<D , VP, EP, GP, A>&, Tag) [with D = boost::undirectedS; VP = boost::no_property; EP = boost::property<boost::edge_weight_t, double, boost::property<boost::edge_ centrality_t, double> >; GP = boost::no_property; A = std::allocator<bool>; Tag = boost::edge_weight_t; boost::adj_mat_pm_helper<D, VP, EP, GP, A, Tag, boost: :edge_property_tag>::type = boost::function_property_map<boost::adj_mat_pm_helper<boost::undirectedS, boost::no_property, boost::property<boost::edge_weight_t , double, boost::property<boost::edge_centrality_t, double> >, boost::no_property, std::allocator<bool>, boost::edge_weight_t, boost::edge_property_tag>::look up_property_from_edge<mpl_::bool_<false> >, boost::detail::matrix_edge_desc_impl<boost::undirected_tag, long unsigned int>, double&>; typename boost::result_o f<const boost::adj_mat_pm_helper<D, VP, EP, GP, A, Tag, boost::edge_property_tag>::lookup_property_from_edge<mpl_::bool_<false> >(const typename boost::graph_ traits<boost::adjacency_matrix<D, VP, EP, GP, A> >::edge_descriptor&)>::type = double&; typename boost::graph_traits<boost::adjacency_matrix<D, VP, EP, GP, A> > ::edge_descriptor = boost::detail::matrix_edge_desc_impl<boost::undirected_tag, long unsigned int>]^Y: /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/graph/adjacency_matrix.hpp:1119:86: required from ^Xtypename boost::property_map<boost::ad jacency_matrix<D, VP, EP, GP, A>, Tag>::type boost::get(Tag, boost::adjacency_matrix<D, VP, EP, GP, A>&) [with D = boost::undirectedS; VP = boost::no_property ; EP = boost::property<boost::edge_weight_t, double, boost::property<boost::edge_centrality_t, double> >; GP = boost::no_property; A = std::allocator<bool>; T ag = boost::edge_weight_t; typename boost::property_map<boost::adjacency_matrix<D, VP, EP, GP, A>, Tag>::type = boost::function_property_map<boost::adj_mat_pm _helper<boost::undirectedS, boost::no_property, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_centrality_t, double> >, boost::no_p roperty, std::allocator<bool>, boost::edge_weight_t, boost::edge_property_tag>::lookup_property_from_edge<mpl_::bool_<false> >, boost::detail::matrix_edge_des c_impl<boost::undirected_tag, long unsigned int>, double&>]^Y /usr/src/imp-2.5.0/modules/statistics/src/metric_clustering.cpp:25:39: required from here /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/graph/adjacency_matrix.hpp:1092:17: warning: unused parameter ^Xg^Y [-Wunused-parameter] make[2]: *** [modules/statistics/src/CMakeFiles/IMP.statistics-lib.dir/__/__/__/src/statistics_all.cpp.o] Error 1 ake[1]: *** [modules/statistics/src/CMakeFiles/IMP.statistics-lib.dir/all] Error 2 make: *** [all] Error 2 -- ____ *Note: UMDNJ is now Rutgers-Biomedical and Health Sciences* || \\UTGERS |---------------------*O*--------------------- ||_// Biomedical | Ryan Novosielski - Senior Technologist || \\ and Health | novosirj(a)rutgers.edu - 973/972.0922 (2x0922) || \\ Sciences | OIRT/High Perf & Res Comp - MSB C630, Newark `'

2 8

em.MapDistanceTransform class
by Karine VOLTZ 07 Jan '16

07 Jan '16

Dear IMP-users, I would like to use the em.MapDistanceTransform functionality of IMP but this class does not seem to be recognized as belonging to the em module. Can somebody give me information on the way to use this class? With my best wishes for 2016, Karine

2 1

error during installation
by ashutosh srivastava 04 Jan '16

04 Jan '16

Dear IMP users I am trying to install IMP but I keep getting following error CMake Error at modules/atom/bin/cmake_install.cmake:42 (file): file INSTALL cannot find "/home/ashutosh/softwares/imp/bin/ligand_score". Call Stack (most recent call first): modules/atom/cmake_install.cmake:45 (include) cmake_install.cmake:8645 (include) I am installing imp-2.5.0 from source to local user (I dont have root permissions). I have installed SWIG and HDF5 also locally and passed their paths as environment variables. What could be the source of this error? Kindly let me know if any other detail is required. Thank you Best Regards Ashutosh

2 2

Failed to build 1e6v example with multifit
by Mateusz Koryciński 02 Dec '15

02 Dec '15

Dear All, Was anyone able to build 1e6v example? I was trying to model complex I am currently working on, however with no luck. To test the software I've tried to model example 1e6v, provided along with the source code. Multifit align step produced asmb.combinations file with "NO SOLUTIONS FOUND". Shouldn't example produce results? I was following the same instructions as in the 3sfd tutorial, which works. Looking forward to hearing from you. Best regards, Mateusz Korycinski

3 3

installation issue: cgal version 10.dylib missing
by John Robinson 13 Nov '15

13 Nov '15

After installation of IMP via homebrew, 'import IMP' fails because it can’t find /usr/local/lib/libCGAL.10.dylib I have verison 11.dylib installed. ls /usr/local/lib/libCGAL* produces /usr/local/lib/libCGAL.11.0.0.dylib /usr/local/lib/libCGAL.11.dylib /usr/local/lib/libCGAL.dylib /usr/local/lib/libCGAL_Core.11.0.0.dylib /usr/local/lib/libCGAL_Core.11.dylib /usr/local/lib/libCGAL_Core.dylib And suggestions would be helpful. Thanks, ~John Robinson

2 2

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