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274 discussions

Conjugate Gradient optimizer with rigid bodies
by Karine VOLTZ 10 Nov '15

10 Nov '15

Dear all, I have a system consisting of several sub-units all represented as rigid bodies (even sub-units containing only one domain). I have tried a MC sampling with a simple set of restraints on the system and it's working fine. Now I would like to use the IMP.core.MonteCarloWithLocalOptimization() using a CG optimizer but it does not seem to work: monitoring the energies at each MC step shows always the same energy. I wanted to know if it's actually possible to use the function IMP.core.MonteCarloWithLocalOptimization() with rigid bodies? Thank you in advance for your help, Karine

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question about PMI included.None.xl.db file
by Jason Schmidberger 02 Nov '15

02 Nov '15

Hello, I have been running IMP::pmi with a protein complex we are working on in our lab. I have managed to adapt the PMI online example (RNA pol) to work for my example. A series of files are output in the execution directory: included.None.xl.db, excluded.None.xl.db, missing.None.xl.db In my "included.None.xl.db file" I only have the following two lines; {'res2': '155', 'prot1': 'mol3', 'prot2': 'mol5', 'res1': '160'} {'res2': '155', 'prot1': 'mol3', 'prot2': 'mol5', 'res1': '154'} I include more than 30 x-link restraints in my set up. When I compare this to the same file as output with the worked RNA pol example, that file has many more entries. QUESTION: what is the meaning behind this file? Does it mean most of my x-link restraints were thrown out? Cheers, Jason

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restraint based on pre-calculated scores
by Jan Kosinski 28 Oct '15

28 Oct '15

Hi, I have a custom MonteCarlo mover that randomly samples positions of a rigid body from predefined list of transformations. Each transformation corresponds to some position, and for each position I have precalculated a score. Now I would like to have a restraint that scores the positions generated by the mover according to these precalculated scores. The restraint would have to find out which transformation was used for the move, get the index of the transformation in the list and then get the score. Would you have a suggestion how to implement this? I can store the current index in the mover object but then I don't know how to access the movers from the restraint object. Thanks in advance, Jan

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question about running PMI
by Jason Schmidberger 27 Oct '15

27 Oct '15

Hello, I am new to the imp-users mailing list. I am having trouble running PMI. I am following the online RNA Polymerase example (http://integrativemodeling.org/2.5.0/doc/manual/rnapolii_stalk.html) and adapting it to suit my own protein complex. When I run the modeling.py script, I seem to get as far as defining my x-links, then the program optimizes floppy bodies, lists all my proteins, then crashes. The crash takes place with the following error; (after x-linking information) Generating a NEW crosslink restraint with an uniqueID 45 -------------- ISDCrossLinkMS: generating cross-link restraint between ISDCrossLinkMS: residue 89 of chain mol1d and residue 559 of chain mol2c ISDCrossLinkMS: with sigma1 1.000000 sigma2 1.000000 psi 0.05 ISDCrossLinkMS: between particles mol1d_89_pdb and mol2c_536-585_bead_floppy_body_rigid_body_member ========================================== optimize_floppy_bodies: optimizing 49 floppy bodies mol2a_1 mol2a_2 mol2a_3 mol2a_4 mol1b_1 mol2c_1 mol2c_2 mol2c_3 mol2c_4 mol1d_1 mol3_1 mol3_2 mol4f mol4g mol4h mol4i mol4j mol4k mol4l mol4m will scale target mass by 454684.664 mass_scale=target_mass_scale) File "/usr/local/lib/IMP-python/IMP/isd/gmm_tools.py", line 29, in decorate_gmm_from_text weight=float(fields[2]) IndexError: list index out of range WARNING Object "linker_restraints" was never used. See the IMP::Object documentation for an explanation. Can anyone advise me what the issue here is? Does it relate to my target GMM file? I am at a loss. Yours, Jason

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Visualizing entire scoring function (Optimization)
by Hughes, Katelyn Jean 31 Aug '15

31 Aug '15

Hello, Is there currently a way to return every score generated by the scoring function (or the function itself) during the optimization stage? From what I've tried, I can only retrieve an object or a number with the final score/best score. I'm currently using Conjugate Gradients. If not, is there a way to do this with MC? I would like to use a package like matplotlib (or gnuplot, if that's easier, as I see that your Replica Exchange feature uses gnuplot) to generate a plot for all of the scores from the scoring function. Thank you, Katie Worcester Polytechnic Institute Korkin Lab kjhughes(a)wpi.edu

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IMP 2.5.0 release
by Ben Webb 01 Jul '15

01 Jul '15

IMP 2.5.0 is now available. This is a bugfix and minor update release. Most notably the documentation has been revised and updated; we now provide binary packages for Ubuntu 12.04 (Precise Pangolin) in addition to 14.04 (Trusty Tahr); a lot of obsolete and deprecated functionality has been removed; support for OpenMP and MPI is improved; and the IMP::base and IMP::kernel namespaces are now deprecated in favor of the top-level "IMP" namespace. See the http://integrativemodeling.org/2.5.0/doc/manual/changelog.html for the full change log. Check it out at http://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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Problems with installing IMP on Ubuntu 15.04
by Dennis FoxLetterman 03 Jun '15

03 Jun '15

Hi all, I have installed all prerequisites for IMP (even libTAU and openCV which IMP cannot find, but that problem can I deal with later) but IMP won't install. In brief, I obtain following error message: Makefile:127: recipe for target 'all' failed make: *** [all] Error 2 All details of output from cmake and installation can be found in the attached log file. Could someone help me with this? Also, as you can see in the log file, I have received many warnings concerning PyObject.. Am I using a wrong version of swig? I have swig 2.0.12. Could someone please help me out here? Warm regards Dennis

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Re: [IMP-users] IMP-CGAL4.5.2-Surface_mesh_simplification’ is not a namespace-name
by Ben Webb 16 Mar '15

16 Mar '15

On 03/14/2015 01:50 AM, 陈同 wrote: > I have to add the following lines to CMakeLists.txt. (Listing here for > newbies like me.) While that (in principle) should work, you don't need to edit CMakeLists.txt. Either run ccmake (rather than cmake) and edit the variables in the CMake cache, or you can specify them on the command line when you run cmake. e.g. this is how we run cmake on a 64-bit RHEL5 system (which is too old to have recent enough Boost or HDF5 libraries): cmake28 .. -DCMAKE_INCLUDE_PATH=/usr/include/boost141;/usr/include/hdf518/ -DCMAKE_LIBRARY_PATH=/usr/lib64/boost141;/usr/lib64/hdf518 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] IMP-CGAL4.5.2-Surface_mesh_simplification’ is not a namespace-name
by Ben Webb 13 Mar '15

13 Mar '15

On 3/12/15 11:26 PM, 陈同 wrote: > This software recommends install IMP: *IMP version 2.0.1* and *IMP > version 2.1.1.* Ah, looks like they didn't test it with any newer versions of IMP. Well, a newer version of IMP might work. Or you can just apply the patch from my previous email to IMP 2.1.1 - that part of the code hasn't changed for a while. 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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IMP-CGAL4.5.2-Surface_mesh_simplification’ is not a namespace-name
by 陈同 12 Mar '15

12 Mar '15

Hi, all, when installing IMP (2.1.1), I met following errors, Built target RMF-rmf_slice [ 34%] Built target RMF-rmf_pdb [ 34%] Built target RMF-rmf_transform [ 34%] Built target RMF-rmf_validate [ 35%] Built target RMF-rmf_xml [ 35%] Built target RMF-rmf_update [ 35%] Building CXX object modules/cgal/src/CMakeFiles/IMP.cgal-lib.dir/__/__/__/src/cgal_all.cpp.o [ 37%] [ 37%] [ 37%] Built target _RMF_HDF5 Built target RMF-test_associations Built target _RMF [ 37%] Built target RMF-test_buffer [ 37%] Built target RMF-test_fill [ 38%] Built target IMP.benchmark-doc [ 38%] [ 38%] Built target RMF-test_json_encode_decode Built target RMF.benchmark_rmf [ 38%] Built target IMP.kmeans-doc [ 38%] [ 38%] Built target IMP.mpi-doc Built target IMP.test-doc [ 39%] Built target RMF.benchmark_size In file included from /imp5/imp/src/cgal_all.cpp:5: imp-2.1.1/modules/cgal/src/internal/polyhedrons.cpp: In function ‘std::pair<IMP::base::Vector<IMP::algebra::VectorD<3> >, IMP::base::Vector<int> > IMP::cgal::internal::get_skin_surface(const IMP::algebra::Sphere3Ds&)’: imp5/imp-2.1.1/modules/cgal/src/internal/polyhedrons.cpp:275: error: ‘Surface_mesh_simplification’ is not a namespace-name imp5/imp-2.1.1/modules/cgal/src/internal/polyhedrons.cpp:275: error: expected namespace-name before ‘;’ token make[2]: *** [modules/cgal/src/CMakeFiles/IMP.cgal-lib.dir/__/__/__/src/cgal_all.cpp.o] Error 1 make[1]: *** [modules/cgal/src/CMakeFiles/IMP.cgal-lib.dir/all] Error 2 make: *** [all] Error 2 I am using CGAL-4.5.2 and mpfr-3.1.1, could anybody tell me what is wrong? Thanks! Best, Tong Chen

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