November 2020 - IMP-users

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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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

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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)?

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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

2 2

Defining rigid bodies
by Altair Hernández 16 Nov '20

16 Nov '20

Hi, I would like to know the appropìate way to define rigid bodies with PMI. Let's say I am working with a multimeric complex of 8 chains, grouped in 2 subcomplex of 4 chains each (subcpx1 "ABCD" and subcpx2 "EFGH"). At the same time, each subcomplex is bound in a coiled coil region, which is fixed, and I name it CorEX (coiled coils of chains "ABCD" and coiled coils of chains "EFGH"). I would like to explore different conformations of this protein complex by allowing each chain to move in the space, but imposing that coiled coil regions must be rigid (coiled coils of chain "ABCD" must move together and cannot break, e.g). My doubt is how to define this behaviour: 1- Define 3 rigid regions per chain (N-ter; CoiledCoil; C-ter) plus define each CorEX as another rigid body. 2- Define 2 rigid regions per chain (N-ter and C-ter) and then define the 2 CorEX regions. It seems that IMP.pmi does not allow to define it as in 1, some errors occur. I guess I cannot define two times a given region as a rigid body if it is already defined. I hope it is well explained :) Thanks! Altair

2 1

Suffle before sampling: fixed parts
by Altair Hernández 04 Nov '20

04 Nov '20

Hi, I am trying to sample a PDB with different restraints. I would like to shuffle only some molecules, in order to have some of them in a fixed position (the coordinates should not change after sampling). I define these rigid particles as rigid bodies before shuffling, and suffling as: IMP.pmi.tools.shuffle_configuration(root_hierarchy, excluded_rigid_bodies=fixed_particles, max_translation=50, verbose=True, cutoff=5.0, niterations=100) - Fixed particles change their coordinates after shuffling. - In the PDB (4 chains "ABCD"), the chains appear disconnected, even if I apply connectivity restraint. I may do something wrong, any help would be appreciated! Thanks! Altair

2 1

PMI with multiple PDBs
by Altair Hernández 04 Nov '20

04 Nov '20

Hi, I am trying to use multiple PDB files using the PMI multiscale modelling protocol. I'm doing it by creating different PMI.states within the main system. Is this the IMP.pmi way to do it? My script: data_directory = "../input/" pict_pdb = data_directory + "path/to/pdb1" hg_pdb_model = data_directory + "path/to/pdb2" hg_fasta = data_directory + "path/to/pdb2.fasta" # Initialize model m = IMP.Model() # HEMOGLOBIN hg_fasta_seqs = IMP.pmi.topology.Sequences(hg_fasta) hg_pdb_seqs = IMP.pmi.topology.PDBSequences(m, hg_pdb_model) # PICT PDB pict_pdb_seqs = IMP.pmi.topology.PDBSequences(m, pict_pdb) # Create System and State s = IMP.pmi.topology.System(m) # defining the root of a hierarchy st_1 = s.create_state() st_2 = s.create_state() Thanks! Best, Altair

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