IMP-users December 2020

imp-users@salilab.org

4 participants
3 discussions

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 03 Dec '20

03 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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IMP-users December 2020