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273 discussions

RRT Sample with DNA
by John Stiller 01 Mar '21

01 Mar '21

Hello All, Does the rrt sample module support DNA? It seems to not be dividing the molecule into rigid bodies like it does for proteins. I assume I just need to tell it that it's DNA and not protein, but I can't figure out how... Thank you in advance. Best, John *My attempt: * rrt_sample Test_DNA.pdb Linker.txt *Result:* Starting reading pdb file Test_DNA.pdb WARNING Could not determine CHARMM atom type for atom "O2'" in residue #2 "DG" WARNING Could not determine CHARMM atom type for atom "O2'" in residue #3 "DT" WARNING Could not determine CHARMM atom type for atom "O2'" in residue #5 "DC" 2 residues 0 bonds were read from file Linker.txt # atoms 83 # bonds 87 # angles 131 # dihedrals 172 4 bonds were added # atoms 83 # bonds 91 # angles 131 # dihedrals 172 begin ForceFieldParameters0::get_force_field_atom_type: WARNING Atom #9 "O2'" (O) does not have a known CHARMM type end ForceFieldParameters0::get_force_field_atom_type *Rb 0 created with 83 atoms* *1 rigid bodies were created * rb order 0 --> 0 parent 0 0 joints were constructed ProteinKinematics done Init RRT Start RRT run *ERROR: No degrees of freedom to sample!* DNA Molecule Example: ATOM 1 P DG 2 120.209 118.900 144.134 1.00210.77 A P ATOM 2 C5' DG 2 117.681 119.487 143.764 1.00210.77 A C ... Linker.txt: 3 4

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Specification of symmetry groups file for imp_sampcon --ambiguity option
by Jan Kosinski 25 Feb '21

25 Feb '21

Hi guys, What is the specification of the symmetry groups file for imp_sampcon --ambiguity option? Best, Jan

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PMI crosslinks and state ambiguity
by Andrea Graziadei 23 Feb '21

23 Feb '21

Hello, I am building a system using topolgyReader in PMI in imp-2.13. I have built a 2-state system by bm = IMP.pmi.macros.BuildSystem(m, force_create_gmm_files=False) bm.add_state(topology) bm.add_state(topology2) I then add crosslinks to the system with IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint How does the system handle the state ambiguity? If a crosslink is satisfied at a particular frame only in state1, it should count overall as satisfied (given crosslinks are measured on in solution ensembles), also when for example analysing %ge violations with imp-sampcon or similar modules... >From what I understand, It looks to me like this is handled correctly in the sampling, but imp-sampcon and pmi_analysis are not yet equipped to deal with this (slicing on %ge over length does not report crosslinks as satisfied if they are under maximum distance in one of the states only). Is this correct? Many thanks, Andrea

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Missing frame during imp_sampcon
by Gorbea, Jose 27 Jan '21

27 Jan '21

Hi all, I am having a bit of an issue during analysis using imp_sampcon on IMP 2.13.0. Here is the error message: OSError: UsageError: "Trying to load a frame that isn't there" while void RMF::FileConstHandle::set_current_frame(FrameID) const in file "../modeling/run1/output/rmfs/2.rmf3" at frame f46 I suspect this may have something to do with a file becoming "broken" or "corrupted" because of abrupt program termination. Our cluster allows a maximum amount of time per calculation and will shut down a process if time exceeds, which was the case here. I wonder if somebody has dealt with this type of error before and could confirm whether termination may be the root of this issue. Additionally, is there a way one could "continue" a job in case this happens again? Any suggestions would be much appreciated. All the best, Jose Gorbea

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Setting coordinates from RMF
by Altair Hernández 13 Dec '20

13 Dec '20

Hi there, I'm trying to use the *IMP.pmi.tools.set_coordinates_from_rmf *to start modelling a complex from a previous modelled frame. In a first step, I set the whole structure as a single rigid body and perform 100 rex frames. In the second step I want to use the frame 99 of this modelling as starting point, but now I want to divide the structure into several rigid parts and super rigid bodies. However, the first frame has not the exact same coordinates as in the 99th from the first step using the method mentioned above. I'm using two different topology files: For instance: topology1.txt |molecule_name ... |chain|residue_range ... |rigid_body |super_rigid_body subunit1 A 1,10 1 1 subunit1 A 11,20 1 1 subunit2 B 1,15 1 1 subunit2 B 6,25 1 1 ... topology2.txt |molecule_name ... |chain|residue_range ... |rigid_body |super_rigid_body subunit1 A 1,10 1 1 subunit1 A 11,20 2 1 subunit2 B 1,15 3 2 subunit2 B 6,25 4 2 .... I tried also by not shuffling the system in case that was the error, but the same output was obtained. What may be wrong? Thanks in advance! Altair

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Problem with IMP.core.TransformationSymmetry
by Jan Kosinski 07 Dec '20

07 Dec '20

Hi Ben, I tried to test sth related to the TransformationSymmetry on rigid bodies and I fail to get it work properly in the below simple example. In the example I create four copies of a chain, create four-fold symmetry constraints and try to generate the updated configuration using model.update(). In the resulting model.rmf, three chain copies are fine and follow the symmetry but one copy of the chains is weirdly rotated. What do I do wrong? import IMP import IMP.core import IMP.atom import IMP.container import IMP.rmf import RMF import sys IMP.setup_from_argv(sys.argv, "rigid bodies") m = IMP.Model() rbs = [] hs = [] for i in range(4): mp1 = IMP.atom.read_pdb(IMP.core.get_example_path('example_protein.pdb'), m) chains = IMP.atom.get_by_type(mp1, IMP.atom.CHAIN_TYPE) hs.append(IMP.atom.Hierarchy(chains[0])) rbs.append(IMP.atom.create_rigid_body(chains[0])) for i, rb in enumerate(rbs[1:]): # the other 3 particles are all symmetric copies of the first IMP.core.Reference.setup_particle(rb, rbs[0]) # the symmetry operation is rotation around the z axis tr = IMP.algebra.Transformation3D( IMP.algebra.get_rotation_about_axis(IMP.algebra.get_basis_vector_3d(2), 2 * 3.14 / len(rbs) * (i + 1)), IMP.algebra.Vector3D(0, 0, 0)) sm = IMP.core.TransformationSymmetry(tr) c = IMP.core.SingletonConstraint(sm, None, m, rb) m.add_score_state(c) m.update() modelrmf = RMF.create_rmf_file('model.rmf') IMP.rmf.add_hierarchies(modelrmf, hs) IMP.rmf.save_frame(modelrmf) Using IMP 2.13.0. Best, Jan

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IMP 2.14.0 release
by Ben Webb 02 Dec '20

02 Dec '20

IMP 2.14.0 is now available. This is contains minor updates, most notably an overhaul of the IMP::kinematics and IMP::parallel modules, and support for Python 3.9. See https://integrativemodeling.org/2.14.0/doc/manual/changelog.html for the full change log. Check it out at https://integrativemodeling.org/ Ben -- ben(a)salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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Large spheres in output rmf3 files
by Gorbea, Jose 30 Nov '20

30 Nov '20

Hi all, Upon displaying an output rmf3 file on Chimera, I am getting a number of large, radially distributed spheres as part of the model. Within the rmf3 file hierarchy, they are not part of the System or States within (meaning I can exclude these spheres from visualization by showing only "System" in the rmf3 file hierarchy panel). I wonder exactly what they mean. If anyone has experienced these before I'd appreciate any help interpreting and/or addressing this issue. Best, Jose Gorbea

2 1

Making restraints
by SoltaniKazemi, Elham 18 Nov '20

18 Nov '20

Hello, When I had the exact distance between two residues, I used something like the following to add restraints: dist_close_restraints.append(forms.gaussian(group=physical.xy_distance, feature=features.distance(modeller_atoms[res1_pos], modeller_atoms[res2_pos]), mean=re_value, stdev=distdev)) re_value is the exact distance, and I set stdev to one. Now, my problem is that I don't have the exact distance. I have something like the following: 1- The distance between (for example) residue1 and residue2 is 4.0857 with a probability of 0.66. 2- The distance between residue1 and residue2 is between 0 and 6 with a probability of 0.78 (just as an example). Does anyone know how can I add restraints when I have probability (I want to use probabilities in my restraints)?

1 0

imp_sampcon pyRMSD installation issue
by Gorbea, Jose 18 Nov '20

18 Nov '20

Hi all, I am trying to run imp_sampcon exhaust from the actin tutorial and pyRMSD is required. I tried pip installation and git cloned the repository but got the following issue on installation. """ /cm/shared/apps/python-3.7.7/lib/python3.7/distutils/dist.py:274: UserWarning: Unknown distribution option: 'install_requires' warnings.warn(msg) running install running build running build_py running build_ext building 'pyRMSD.pdbReader' extension gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/cm/shared/apps/python-3.7.7/lib/python3.7/site-packages/numpy/core/include -I/cm/shared/apps/python-3.7.7/include/python3.7m -I/cm/shared/apps/python-3.7.7/include/python3.7m -c src/pdbreaderlite/PDBReader.cpp -o build/temp.linux-x86_64-3.7/src/pdbreaderlite/PDBReader.o gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/cm/shared/apps/python-3.7.7/lib/python3.7/site-packages/numpy/core/include -I/cm/shared/apps/python-3.7.7/include/python3.7m -I/cm/shared/apps/python-3.7.7/include/python3.7m -c src/pdbreaderlite/PDBReaderObject.cpp -o build/temp.linux-x86_64-3.7/src/pdbreaderlite/PDBReaderObject.o In file included from /cm/shared/apps/python-3.7.7/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832:0, from /cm/shared/apps/python-3.7.7/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /cm/shared/apps/python-3.7.7/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from src/pdbreaderlite/PDBReaderObject.cpp:3: /cm/shared/apps/python-3.7.7/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" -Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ src/pdbreaderlite/PDBReaderObject.cpp: In function ‘PyObject* pdbreader_read(pdbreader*, PyObject*)’: src/pdbreaderlite/PDBReaderObject.cpp:87:55: warning: narrowing conversion of ‘self->pdbreader::reader->PDBReader::all_coordinates.std::vector<_Tp, _Alloc>::size<double, std::allocator<double> >()’ from ‘std::vector<double>::size_type {aka long unsigned int}’ to ‘npy_intp {aka long int}’ inside { } [-Wnarrowing] npy_intp dims[] = {self->reader->all_coordinates.size()}; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ src/pdbreaderlite/PDBReaderObject.cpp: At global scope: src/pdbreaderlite/PDBReaderObject.cpp:142:1: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t {aka long int}’ [-fpermissive] }; ^ src/pdbreaderlite/PDBReaderObject.cpp:108:5: error: invalid conversion from ‘destructor {aka void (*)(_object*)}’ to ‘printfunc {aka int (*)(_object*, _IO_FILE*, int)}’ [-fpermissive] (destructor)pdbreader_dealloc, /*tp_dealloc*/ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/pdbreaderlite/PDBReaderObject.cpp:123:23: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] Py_TPFLAGS_DEFAULT| Py_TPFLAGS_BASETYPE , /*tp_flags*/ src/pdbreaderlite/PDBReaderObject.cpp:142:1: error: cannot convert ‘const char*’ to ‘traverseproc {aka int (*)(_object*, int (*)(_object*, void*), void*)}’ in initialization }; ^ src/pdbreaderlite/PDBReaderObject.cpp:142:1: error: cannot convert ‘PyMethodDef*’ to ‘PyMemberDef*’ in initialization src/pdbreaderlite/PDBReaderObject.cpp:142:1: error: cannot convert ‘PyMemberDef*’ to ‘PyGetSetDef*’ in initialization src/pdbreaderlite/PDBReaderObject.cpp:139:2: error: invalid conversion from ‘initproc {aka int (*)(_object*, _object*, _object*)}’ to ‘allocfunc {aka _object* (*)(_typeobject*, long int)}’ [-fpermissive] (initproc)pdbreader_init, /* tp_init */ ^~~~~~~~~~~~~~~~~~~~~~~~ src/pdbreaderlite/PDBReaderObject.cpp:142:1: error: invalid conversion from ‘PyObject* (*)(PyTypeObject*, PyObject*, PyObject*) {aka _object* (*)(_typeobject*, _object*, _object*)}’ to ‘freefunc {aka void (*)(void*)}’ [-fpermissiv] }; ^ src/pdbreaderlite/PDBReaderObject.cpp: In function ‘PyObject* initpdbReader()’: src/pdbreaderlite/PDBReaderObject.cpp:153:9: error: return-statement with no value, in function returning ‘PyObject* {aka _object*}’ [-fpermissive] return; ^~~~~~ src/pdbreaderlite/PDBReaderObject.cpp:155:67: error: ‘Py_InitModule3’ was not declared in this scope module = Py_InitModule3("pdbReader", NULL,"Simple pdb reading"); ^ src/pdbreaderlite/PDBReaderObject.cpp:157:11: error: return-statement with no value, in function returning ‘PyObject* {aka _object*}’ [-fpermissive] return; ^~~~~~ src/pdbreaderlite/PDBReaderObject.cpp:163:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ error: command 'gcc' failed with exit status 1 """ Has anyone encountered this error before? Any help would be greatly appreciated. All the best, Jose Gorbea

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