January 2011 - IMP-users

restraint set
by Keren Lasker 24 Jan '11

24 Jan '11

thought its relevant for all: if i create a RestraintSet rs and a restraint r that is added to the model and to rs if then i add rs to the model is r added twice to the model? keren.

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calculating chi squared
by Robert Brynmor Fenwick 24 Jan '11

24 Jan '11

Hi I have a script that calculates and fits saxs profiles and have observed that the fits are worse than previously calculated. I have a test case that now fits much worse than before. I guess that there is something wrong. Any help would be appreciated. I have attached the two output files and the saxs input files. If you look at the two output files to see that they give slightly different results. Another problem that I have is that I can not calculate the chi square value that is in the output file from the data. Is this the expected behavior? Bryn -- R. Bryn Fenwick robert.fenwick(a)irbbarcelona.org Post-doctoral fellow Chemistry and Molecular Pharmacology Programme Institute for Research in Biomedicine (IRB Barcelona) Parc Científic de Barcelona Baldiri Reixac 10, 08028 Barcelona, SPAIN Tel. (+34) 9340 20460

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compilation bus error
by Robert Brynmor Fenwick 24 Jan '11

24 Jan '11

Hi, I've just checked out this: svn co http://svn.salilab.org/imp/branches/stable imp .... Checked out revision 8381. and tried to compile it, I am using the same compiler that compiles the imp 1.0 version so I don't think it is a compiler problem Install file: "modules/cgal/include/internal/knn.h" as "build/include/IMP/cgal/internal/knn.h" g++ -o modules/cgal/src/internal/knn.os -c -Os -Wno-long-double -no-cpp-precomp -mno-fused-madd -fno-common -Wall -Wno-deprecated -Woverloaded-virtual -O2 -fno-finite-math-only -ftrapping-math -fsignaling-nans -fno-float-store -frounding-math -fno-strict-aliasing -DCGAL_DISABLE_ROUNDING_MATH_CHECK -fvisibility=hidden -fPIC -DIMPCGAL_EXPORTS -DGCC_VISIBILITY -Ibuild/include -I/sw/include modules/cgal/src/internal/knn.cpp modules/cgal/src/internal/knn.cpp: In member function 'void IMP::cgal::internal::KNNData2::fill_nearest_neighbors_v(const IMP::algebra::VectorD<2u>&, unsigned int, double, IMP::Ints&) const': modules/cgal/src/internal/knn.cpp:122: warning: passing negative value '-0x00000000000000001' for argument 1 to 'IMP::cgal::internal::VectorWithIndex<D>::VectorWithIndex(unsigned int, const IMP::algebra::VectorD<D>&) [with unsigned int D = 2u]' modules/cgal/src/internal/knn.cpp: In member function 'void IMP::cgal::internal::KNNData2::fill_nearest_neighbors_v(const IMP::algebra::VectorD<2u>&, double, double, IMP::Ints&) const': modules/cgal/src/internal/knn.cpp:122: warning: passing negative value '-0x00000000000000001' for argument 1 to 'IMP::cgal::internal::VectorWithIndex<D>::VectorWithIndex(unsigned int, const IMP::algebra::VectorD<D>&) [with unsigned int D = 2u]' modules/cgal/src/internal/knn.cpp: In member function 'void IMP::cgal::internal::KNNData3::fill_nearest_neighbors_v(const IMP::algebra::VectorD<3u>&, unsigned int, double, IMP::Ints&) const': modules/cgal/src/internal/knn.cpp:123: warning: passing negative value '-0x00000000000000001' for argument 1 to 'IMP::cgal::internal::VectorWithIndex<D>::VectorWithIndex(unsigned int, const IMP::algebra::VectorD<D>&) [with unsigned int D = 3u]' modules/cgal/src/internal/knn.cpp: In member function 'void IMP::cgal::internal::KNNData3::fill_nearest_neighbors_v(const IMP::algebra::VectorD<3u>&, double, double, IMP::Ints&) const': modules/cgal/src/internal/knn.cpp:123: warning: passing negative value '-0x00000000000000001' for argument 1 to 'IMP::cgal::internal::VectorWithIndex<D>::VectorWithIndex(unsigned int, const IMP::algebra::VectorD<D>&) [with unsigned int D = 3u]' modules/cgal/src/internal/knn.cpp: In member function 'void IMP::cgal::internal::KNNData4::fill_nearest_neighbors_v(const IMP::algebra::VectorD<4u>&, unsigned int, double, IMP::Ints&) const': modules/cgal/src/internal/knn.cpp:124: warning: passing negative value '-0x00000000000000001' for argument 1 to 'IMP::cgal::internal::VectorWithIndex<D>::VectorWithIndex(unsigned int, const IMP::algebra::VectorD<D>&) [with unsigned int D = 4u]' modules/cgal/src/internal/knn.cpp: In member function 'void IMP::cgal::internal::KNNData4::fill_nearest_neighbors_v(const IMP::algebra::VectorD<4u>&, double, double, IMP::Ints&) const': modules/cgal/src/internal/knn.cpp:124: warning: passing negative value '-0x00000000000000001' for argument 1 to 'IMP::cgal::internal::VectorWithIndex<D>::VectorWithIndex(unsigned int, const IMP::algebra::VectorD<D>&) [with unsigned int D = 4u]' Install file: "modules/cgal/include/internal/polygons.h" as "build/include/IMP/cgal/internal/polygons.h" g++ -o modules/cgal/src/internal/polygons.os -c -Os -Wno-long-double -no-cpp-precomp -mno-fused-madd -fno-common -Wall -Wno-deprecated -Woverloaded-virtual -O2 -fno-finite-math-only -ftrapping-math -fsignaling-nans -fno-float-store -frounding-math -fno-strict-aliasing -DCGAL_DISABLE_ROUNDING_MATH_CHECK -fvisibility=hidden -fPIC -DIMPCGAL_EXPORTS -DGCC_VISIBILITY -Ibuild/include -I/sw/include modules/cgal/src/internal/polygons.cpp Install file: "modules/cgal/include/internal/polyhedrons.h" as "build/include/IMP/cgal/internal/polyhedrons.h" Install file: "modules/algebra/include/Plane3D.h" as "build/include/IMP/algebra/Plane3D.h" g++ -o modules/cgal/src/internal/polyhedrons.os -c -Os -Wno-long-double -no-cpp-precomp -mno-fused-madd -fno-common -Wall -Wno-deprecated -Woverloaded-virtual -O2 -fno-finite-math-only -ftrapping-math -fsignaling-nans -fno-float-store -frounding-math -fno-strict-aliasing -DCGAL_DISABLE_ROUNDING_MATH_CHECK -fvisibility=hidden -fPIC -DIMPCGAL_EXPORTS -DGCC_VISIBILITY -Ibuild/include -I/sw/include modules/cgal/src/internal/polyhedrons.cpp modules/cgal/src/internal/polyhedrons.cpp: In function 'std::vector<std::vector<IMP::algebra::VectorD<3u>, std::allocator<IMP::algebra::VectorD<3u> > >, std::allocator<std::vector<IMP::algebra::VectorD<3u>, std::allocator<IMP::algebra::VectorD<3u> > > > > IMP::cgal::internal::<unnamed>::get_facets(CGAL::Nef_polyhedron_3<K, typename CGAL::Default_items<Kernel>::Items, bool>&)': modules/cgal/src/internal/polyhedrons.cpp:99: internal compiler error: Bus error Please submit a full bug report, with preprocessed source if appropriate. See <URL:http://developer.apple.com/bugreporter> for instructions. scons: *** [modules/cgal/src/internal/polyhedrons.os] Error 1 scons: building terminated because of errors. Enabled dependencies: python, NetCDF, FFTW3, CGAL, Boost.FileSystem, Boost.ProgramOptions Disabled/unfound optional dependencies: ANN, ExampleLib, GSL, OpenCV, Bullet, OpenMM Enabled modules: kernel, cgal, algebra, core, container, atom, display, domino, em, example, misc, saxs, helper, statistics, restrainer, domino2, multifit, benchmark Disabled modules: gsl, modeller, em2d, bullet, openmm Errors building: modules/cgal/src/internal/polyhedrons.os -- R. Bryn Fenwick robert.fenwick(a)irbbarcelona.org Post-doctoral fellow Chemistry and Molecular Pharmacology Programme Institute for Research in Biomedicine (IRB Barcelona) Parc Científic de Barcelona Baldiri Reixac 10, 08028 Barcelona, SPAIN Tel. (+34) 9340 20460

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stable nightly build
by Robert Brynmor Fenwick 21 Jan '11

21 Jan '11

Hi, I am a bit new to svn and am trying get the most up to date version of the code that is available on the nightly builds. Any advice would be appreciated. Bryn -- R. Bryn Fenwick robert.fenwick(a)irbbarcelona.org Post-doctoral fellow Chemistry and Molecular Pharmacology Programme Institute for Research in Biomedicine (IRB Barcelona) Parc Científic de Barcelona Baldiri Reixac 10, 08028 Barcelona, SPAIN Tel. (+34) 9340 20460

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add_partial_profiles
by Robert Fenwick 21 Jan '11

21 Jan '11

Hi, I am having a bit of a tough time with writing a script and wondered if someone could help. I have installed the latest nightly builds and am trying to write the following: I wish to loop over n structures, calculate the summed partial saxs profile. I hope to achieve this using the attached code and example structures. I think that I should use the add_partial_profiles function, however I can not get it to work the way that I would like. Is there a way to access the values in the predicted saxs profiles using the python interface? Here is my current code, but it does not work as I would expect. Bryn R. Bryn Fenwick robert.fenwick(a)irbbarcelona.org Post-doctoral fellow Chemistry and Molecular Pharmacology Programme Institute for Research in Biomedicine (IRB Barcelona) Parc Científic de Barcelona Baldiri Reixac 10, 08028 Barcelona, SPAIN Tel. (+34) 9340 20460

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running error
by Robert Fenwick 20 Jan '11

20 Jan '11

Hi, I have installed IMP with the minimal requirements that I think that it needs and everything seems to compile without problems. However when I try to import the python modules I get some nasty import errors. Any help greatly appreciated. >>> import IMP.core >>> import IMP.atom Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/fenwick/opt/lib64/python2.5/site-packages/IMP/atom/__init__.py", line 28, in <module> import _IMP_atom ImportError: /home/fenwick/opt/lib64/python2.5/site-packages/_IMP_atom.so: undefined symbol: _ZN3IMP4atom14CHARMMTopology32CHARMMSegmentTopologyDataWrapperD1Ev >>> import IMP.saxs Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/fenwick/opt/lib64/python2.5/site-packages/IMP/saxs/__init__.py", line 163, in <module> import IMP.atom File "/home/fenwick/opt/lib64/python2.5/site-packages/IMP/atom/__init__.py", line 28, in <module> import _IMP_atom ImportError: /home/fenwick/opt/lib64/python2.5/site-packages/_IMP_atom.so: undefined symbol: _ZN3IMP4atom14CHARMMTopology32CHARMMSegmentTopologyDataWrapperD1Ev Here is the end of teh build process that appears to have worked. scons: done building targets. Enabled dependencies: Boost.FileSystem, Boost.ProgramOptions Disabled dependencies: OpenMM, Bullet, CGAL, ANN, OpenCV, NetCDF, modeller, FFTW3, GSL Enabled modules: em, kernel, domino, misc, statistics, container, display, saxs, system, core, algebra, restrainer, benchmark, atom, example Disabled modules: openmm, cgal, bullet, multifit, gsl, modeller, em2d Enabled applications: foxs, ligand_score, saxs_tools, em_tools Enabled systems: Groel, example_system R. Bryn Fenwick robert.fenwick(a)irbbarcelona.org Post-doctoral fellow Chemistry and Molecular Pharmacology Programme Institute for Research in Biomedicine (IRB Barcelona) Parc Científic de Barcelona Baldiri Reixac 10, 08028 Barcelona, SPAIN Tel. (+34) 9340 20460

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good coding habits
by Benjamin SCHWARZ 13 Jan '11

13 Jan '11

Hi list Trying to acquire good coding habits, I started a new personal module, now 1. I wonder if there is an IMP_WARN macro that would output some message under some condition, just like IMP_USAGE_CHECK() does but without aborting the application 2. I would like to write test case functions a. Is there a doc on how to write good test functions ? b. Where can I find the IMP.test.TestCase class, so that I can dissect it at will ? --Ben

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