IMP-users September 2020

imp-users@salilab.org

3 participants
4 discussions

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

3 14

Precision for systems with fixed bodies
by Atefeh Rafiei 13 Oct '20

13 Oct '20

Hi there, I have a question regarding the interpretation of the last step of integrative modeling. I am wondering if the precision calculations (for structural clusters) presented in the analysis workflow (from PMI analysis repository on GitHub), will calculate precision for all components of the modeling system including the fixed rigid bodies? I am asking this as I have a good portion of my protein system being fixed in the modeling (for specific reasons), so I am not sure if that will impact the precision I get. Thanks, Atefeh

2 1

Different initial model
by SoltaniKazemi, Elham 22 Sep '20

22 Sep '20

Hello, I have a code like the following: e = modeller.environ(rand_seed=-4000) e.edat.dynamic_sphere = False e.libs.topology.read('${LIB}/top_heav.lib') e.libs.parameters.read('${LIB}/par.lib') modmodel = modeller.model(e) modmodel.build_sequence(sequence) I want it to produce a different initial model each time. Because I'm using gradient descent and I don't want gradient descent to start with the same model each time. What should I do to randomize the initial model? Thank you

1 0

anaconda package update
by Andrea Graziadei 01 Sep '20

01 Sep '20

Hello, A;though I see from here https://anaconda.org/salilab/imp that the anaconda package is at version 2.13 , when I try to install imp with conda install imp I get: The following NEW packages will be INSTALLED: imp salilab/linux-64::imp-2.12.0-py37hf484d3e_1 I have installed it, and indeed the tools seem to be the version 2.12, not 2.13. This happens also if I remove the current imp installation, or remove the channel salilab and add it back. Any idea what may be causing this? Many thanks! Andrea

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IMP-users September 2020