June 2013 - IMP-users

Is ConnectivityRestraint really deprecated? What to use instead?
by Jan Kosinski 27 Jun '13

27 Jun '13

Dear all, When running several examples like connectivity_restraint.py from core/examples or nup84_complex_in_bead_representation.py from restrainer examples I see warnings like: WARNING: Restraint is deprecated. Is this restraint really deprecated? What do you recommend to use instead? Thanks in advance, Jan -- Jan Kosinski, PhD Structural and Computational Biology Unit European Molecular Biology Laboratory (EMBL) Meyerhofstrasse 1 69117 Heidelberg Germany

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problem with compiling IMP after a commit "add adaptors for taking particles to reduce need for typemaps"
by Jan Kosinski 26 Jun '13

26 Jun '13

I have problems with compiling recent dev versions of IMP. The last version I can build successfully is 2.0.0-544-gb4dfefb. The version 2.0.0-545-ga3aaf4a is the first that crashes (it is the version after commit a3aaf4a5a9983d7b68ba3d5709b12ff3ad1bcd65 - "add adaptors for taking particles to reduce need for typemaps" https://github.com/salilab/imp/commit/a3aaf4a5a9983d7b68ba3d5709b12ff3ad1bc…) The error is: /home/kosinski/software/test_older_imp_a3aaf4a5a9983d7b68ba3d5709b12ff3ad1bcd65/imp_dev/include/IMP/kernel/internal/../Particle.h: In constructor 'IMP::kernel::ParticleAdaptor::ParticleAdaptor(const IMP::kernel::Decorator&)': /home/kosinski/software/test_older_imp_a3aaf4a5a9983d7b68ba3d5709b12ff3ad1bcd65/imp_dev/include/IMP/kernel/internal/../Particle.h:94: error: invalid use of incomplete type 'const struct IMP::kernel::Decorator' /struct/cmueller/kosinski/software/test_older_imp_a3aaf4a5a9983d7b68ba3d5709b12ff3ad1bcd65/imp_dev/include/IMP/kernel/internal/../particle_index.h:18: error: forward declaration of 'const struct IMP::kernel::Decorator' /home/kosinski/software/test_older_imp_a3aaf4a5a9983d7b68ba3d5709b12ff3ad1bcd65/imp_dev/include/IMP/kernel/internal/../Particle.h:95: error: invalid use of incomplete type 'const struct IMP::kernel::Decorator' /home/kosinski/software/test_older_imp_a3aaf4a5a9983d7b68ba3d5709b12ff3ad1bcd65/imp_dev/include/IMP/kernel/internal/../particle_index.h:18: error: forward declaration of 'const struct IMP::kernel::Decorator' make[2]: *** [modules/container/benchmark/CMakeFiles/container.benchmark_evaluate.dir/benchmark_evaluate.cpp.o] Error 1 make[1]: *** [modules/container/benchmark/CMakeFiles/container.benchmark_evaluate.dir/all] Error 2 My builds always worked with a commands like: $cmake_bin ../src/imp -DCMAKE_BUILD_TYPE=Release \ -DCGAL_DIR=$root_dir/lib/CGAL \ -DEIGEN3_INCLUDE_DIR=$src_dir/eigen-v3.1.3 \ -DCMAKE_INSTALL_PREFIX=$root_dir make -j 8 Is it a bug? The dev logs from http://salilab.org/imp/nightly/logs/develop/20130625/x86_64-intel8/ seem ok. So maybe I build IMP wrong way? Thanks in advance, Jan -- Jan Kosinski, PhD Structural and Computational Biology Unit European Molecular Biology Laboratory (EMBL) Meyerhofstrasse 1 69117 Heidelberg Germany

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how to integrate RMF with IMP.restrainer?
by Jan Kosinski 26 Jun '13

26 Jun '13

Dear all, What are the methods to log the simulation frames to RMF format instead of old Chimera style? I have managed to integrate RMF with IMP.restrainer but not everything works. It seems to work with restraints like ExcludedVolume, Distance or EM but not Y2H or PullDown - virtually all that internally are translated to connectivity restraint make a script crashing. For example if I modify the restrainer/nup84_complex_in_bead_representation.py to: import IMP import IMP.restrainer IMP.base.set_log_level(IMP.base.VERBOSE) # Create restrainer object restrainer = IMP.restrainer.Main() # Add representation, restraint, optimization and display to restrainer rep = restrainer.add_representation(IMP.restrainer.get_example_path('input/nup84_representation.xml')) rsr = restrainer.add_restraint(IMP.restrainer.get_example_path('input/nup84_restraint.xml')) #BEGIN ADDED PART import IMP.rmf import RMF rmf= RMF.create_rmf_file('nup84_simulation.rmf') rmf.set_description("Simulate nup84.\n") model = restrainer.get_model() root_hierarchy = rep.get_root_imp_hierarchy() IMP.rmf.add_hierarchy(rmf, root_hierarchy) IMP.rmf.add_restraints(rmf, model.get_restraints()) IMP.rmf.save_frame(rmf, 0) os= IMP.rmf.SaveOptimizerState(rmf) os.update_always("initial conformation") restrainer.log = os #END ADDED PART opt = restrainer.add_optimization(IMP.restrainer.get_example_path('input/nup84_optimization.xml')) disp = restrainer.add_display(IMP.restrainer.get_example_path('input/nup84_display.xml'), 'some_log_name') ###=======================================================================### # At this point all data from XML files have been placed into the model. # Now it is possible to perform various operations on the IMP model. ###=======================================================================### # Save the initial state in Chimera format # restrainer.log.write('initial.py') # Perform optimization restrainer.optimize() # Save the optimized state in Chimera format # restrainer.log.write('optimized.py') (note added lines and old-style Chimera stuff commented out) I get the following error: Traceback (most recent call last): File "nup84_complex_in_bead_representation.py", line 50, in <module> IMP.rmf.save_frame(rmf, 0) File "/home/user/software/imp_dev/lib/IMP/rmf/__init__.py", line 875, in save_frame return _IMP_rmf.save_frame(*args) _IMP_base.IOException: UsageError: "Cannot write sentry value to an RMF file." processing decorator of type Score WARNING No frames were saved to file "RestraintSaveLink0" even though objects were added. If however I change <Y2H> node to <Distance> in input/nup84_restraint.xml everything runs correctly and I can enjoy a working RMF file. Would you have any suggestions how to make RMF logging working properly? BTW. I am using the current dev version of IMP and RMF. Thank you in advance for help, Jan

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