Hello IMP users, My pair restraints aren’t behaving as they should. I have a system with multiple domains which I want to move as rigid bodies while having a pair restraint between the end of the first domain and the beginning of the next. My input .pdb files are coarse-grained using IMP.atom.create_simplified_along_backbone. My approach was to take the coordinates of the alpha carbons I want to restrain, add the two points into my coarse-grained RigidBody objects, and add a pair restraint between them, see the following code. The funny thing is, as my initial .pdb files satisfy this restraint, an initial energy evaluation comes out as zero, as it should do. However, if I perturb the system and minimise with the MC mover, the energy starts high and reduces down to almost zero, as it should, but the distances between adjacent domains of the final structure are much higher than they should be – often over 20A away from the HarmonicUpperBound. I have set my_MC_optimiser.set_return_best(True), so this isn’t the reason. Does anyone have any idea what is wrong?
Many thanks, Iain Moal
Hingedata = [[9,0,34.885,-57.443,9.494,23.464,-48.297,6.885],… and so on] rigbods=[] for abcd in IMP.atom.get_by_type(all, IMP.atom.CHAIN_TYPE): rigbods.append(IMP.core.RigidBody(IMP.Decorator.get_particle(IMP.atom.Hierarchy.get_as_chain(abcd)))) for x in hingedata: p1 = IMP.Particle(m) p2 = IMP.Particle(m) XYZ_a= IMP.core.XYZR.setup_particle(p1,IMP.algebra.Sphere3D(IMP.algebra.Vector3D(x[2],x[3],x[4]),0.01)) XYZ_b= IMP.core.XYZR.setup_particle(p2,IMP.algebra.Sphere3D(IMP.algebra.Vector3D(x[5],x[6],x[7]),0.01)) #NB) THIS DOESN’T WORK HERE: XYZ_a= IMP.core.XYZ.setup_particle(p1,IMP.algebra.Vector3D(x[2],x[3],x[4])) # NB) THIS DOESN’T WORK HERE:XYZ_b= IMP.core.XYZ.setup_particle(p2,IMP.algebra.Vector3D(x[5],x[6],x[7])) rigbods[x[0]].add_member(XYZ_a) rigbods[x[1]].add_member(XYZ_b) r= IMP.core.PairRestraint(IMP.core.DistancePairScore(IMP.core.HarmonicUpperBound(20,5.0)),IMP.ParticlePair(p1,p2)) m.add_restraint(r)
I read my .pdb files using this: all.add_child(create_from_pdb(“filename”))
def create_from_pdb(file): t=IMP.atom.read_pdb(file, m, IMP.atom.ATOMPDBSelector()) IMP.atom.add_radii(t) c=IMP.atom.Chain( IMP.Decorator.get_particle(IMP.atom.Hierarchy.get_as_chain(IMP.atom.get_by_type(t, IMP.atom.CHAIN_TYPE)[0] ))) s=IMP.atom.create_simplified_along_backbone(c,4) IMP.atom.destroy(t) IMP.Decorator.get_particle(IMP.atom.Hierarchy.get_as_chain(IMP.atom.get_by_type(s, IMP.atom.CHAIN_TYPE)[0] )) rb=IMP.atom.setup_as_rigid_body(s) rb.set_coordinates_are_optimized(True) return s
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