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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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Help-symmetry operation
by Joseph Eschweiler 24 May '13

24 May '13

Hello, I'm trying to implement a symmetry restraint into my python script. I would like to define a C3 symmetry between 3 of my subunits. I've looked into the TransformedDistancePairScore function and the PairsRestraint container, but I have no programming experience and am not sure how to implement these. Does anyone have a simple code for this type of restraint? Thanks, Joseph Eschweiler

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restrainer representation problem
by Ibai Irastorza 14 May '13

14 May '13

Hi IMP users, I have a fully functional script that works with IMP 1.0 libraries. When I run the same script in IMP 2.0.1 in the same computer, it throws this error: Traceback (most recent call last): File "exocyst_prt_March2013_app1.py", line 10, in <module> rep = restrainer.add_representation('input/repr_rdm_app1.xml') File "/home/ibai/imp2/lib/IMP/restrainer/__init__.py", line 464, in add_representation return _main.Main.add_representation(self, fname) File "/home/ibai/imp2/lib/IMP/restrainer/_main.py", line 17, in add_representation self.representation = XMLRepresentation(fname).run() File "/home/ibai/imp2/lib/IMP/restrainer/_xml_parser.py", line 94, in run r = self._handle_node(node) File "/home/ibai/imp2/lib/IMP/restrainer/_xml_parser.py", line 102, in _handle_node return handler(node) File "/home/ibai/imp2/lib/IMP/restrainer/_xml_parser.py", line 198, in _handle_protein r = self._handle_node(child) File "/home/ibai/imp2/lib/IMP/restrainer/_xml_parser.py", line 102, in _handle_node return handler(node) File "/home/ibai/imp2/lib/IMP/restrainer/_xml_parser.py", line 220, in _handle_chain result = _RepChain(attrs) File "/home/ibai/imp2/lib/IMP/restrainer/_representation.py", line 204, in __init__ self.topology_file = attributes.get('topology_filename', IMP.atom.get_data_path('top_heav.lib')) File "/home/ibai/imp2/lib/IMP/atom/__init__.py", line 10284, in get_data_path return _IMP_atom.get_data_path(*args) _IMP_base.IOException: Unable to find data file top_heav.lib in [/usr/local/share/IMP]. IMP is not installed or set up correctly. And the missing data file is here: /$ sudo find -name "top_heav.lib" ./home/damien/impJune/share/imp/atom/top_heav.lib ./home/ibai/imp2/data/atom/top_heav.lib ./usr/share/imp/atom/top_heav.lib ./usr/lib/modeller9.10/modlib/top_heav.lib I don't think the code is wrong. Is the installation of imp 2.0.1 wrong? I have just installed in another laptop a fresh new IMP 2.0.1 and neither works the code. I have not read any changes about the representation module and I know the xml file is well because it works in the same computer with the IMP 1.0. Thanks in advance, ibai

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Re: [IMP-users] building error linux 64 bits
by Ben Webb 13 May '13

13 May '13

On 5/13/13 12:57 AM, Ibai Irastorza wrote: > bioinfo@bioinfo:~$ ldd Programs/Imp/lib/libimp_base.so > linux-vdso.so.1 => (0x00007fff4b1ff000) > libboost_program_options.so.1.46.1 => > /usr/lib/libboost_program_options.so.1.46.1 (0x00007f1cb65d4000) > libboost_system.so.1.46.1 => /usr/lib/libboost_system.so.1.46.1 > (0x00007f1cb63d0000) > libboost_random.so.1.53.0 => /usr/local/lib/libboost_random.so.1.53.0 > (0x00007f1cb61cc000) OK, something isn't right here. Looks like you have an incomplete copy of boost in /usr/local/lib, so it picked up boost_random from there but couldn't find boost_system, so the linker pulled in the older version in /usr/lib/. This mix of boost versions is the cause of your problem later on. You'll need to either remove the partial copy of boost 1.53 from /usr/local, or install a full copy there. 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] building error linux 64 bits
by Ben Webb 10 May '13

10 May '13

On 05/10/2013 12:06 AM, Ibai Irastorza wrote: > I did what you say but nothing changed. I send you the failes attached. > I don write the log in the email because of its length. Is libimp_base.so linked to libboost_filesystem? (Run 'ldd' on it.) What is Boost_FILESYSTEM_LIBRARY set to in CMakeCache.txt? Can you run 'rm lib/libimp_base.so; make VERBOSE=1 IMP.base' and show me the command it's running to build libimp_base.so? What version of IMP are you building? 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] building error linux 64 bits
by Ben Webb 08 May '13

08 May '13

On 05/08/2013 09:03 AM, Ibai Irastorza wrote: > it does work fine now the "cmake" line, I guess i fixed it without > noticing, but thats not the problem now, I still can't "make -j 4" In that case I suggest that in order to eliminate the "fixed it without noticing" issue, you make a fresh build directory, and run cmake && make in that directory. If it still doesn't work, send the complete output of both commands. 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] building error linux 64 bits
by Ben Webb 08 May '13

08 May '13

On 5/8/13 8:54 AM, Ibai Irastorza wrote: > the cmake code line fails when I try to build the "imp-2.0.0" folder > cloned from git. Fails how? 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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building error linux 64 bits
by Ibai Irastorza 08 May '13

08 May '13

Hi, I have a problem installing IMP in mu 64bits ubuntu laptop. I had no problem installing in a ubuntu 32 bits. Here are all the steps, I know some of then are redundant but wanna make sure: sudo apt-get install cmake sudo apt-get install libboost-all-dev sudo apt-get install libbz2-dev sudo apt-get install libboost-dev sudo apt-get install build-essential g++ sudo apt-get install build-essential sudo apt-get install python-dev sudo apt-get install autotools-dev sudo apt-get install swig sudo apt-get install libhdf5-serial-dev sudo apt-get install hdf5-tools sudo apt-get install zlib1g sudo apt-get install libhdf5-serial-1.8.4 sudo apt-get install libc6 git clone git://github.com/salilab/imp.git then created a folder and from there: cmake ../imp -DCMAKE_BUILD_TYPE=Release make -j 4 what am I missing?? thanks a lot! Ibai

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