one correlation -
> Frido - this is how it should look like: > > #create the two proteins > prot_ps=IMP.Particles() > prot_ps.append(IMP.Particle(m)) > prot_ps.append(IMP.Particle(m)) > prot1= > IMP > .atom.Hierarchy.setup_particle(prot_ps[0],IMP.atom.Hierarchy.PROTEIN) > prot2= > IMP > .atom.Hierarchy.setup_particle(prot_ps[1],IMP.atom.Hierarchy.PROTEIN) > #make the parts fragments and add to the molecules > for e in [part1,part2,part3]: > fh= IMP.atom.Hierarchy.setup_particle(e,IMP.atom.Hierarchy.FRAGMENT) > #also make sure the part has radius > prot1.add_child(fh) > for e in [part4,part5,part6]: > fh= IMP.atom.Hierarchy.setup_particle(e,IMP.atom.Hierarchy.FRAGMENT) > #also make sure the part has radius > prot2.add_child(fh) > > #create the restraint > ufu = IMP.core.TruncatedHarmonicUpperBound( span, k, stddev, 2.) > cps= IMP.core.ChildrenRefiner(IMP.atom.Hierarchy.get_traits()) > lrps = IMP.misc.LowestRefinedPairScore(cps,ufu) > connrest = IMP.core.ConnectivityRestraint(lrps) > connrest.set_particles(prot_ps) > m.add_restraint(connrest) > > > On Sep 21, 2009, at 6:54 AM, Daniel Russel wrote: > >> I think the problem is that the list of particles the connectivity >> restraint ends up with is [p0,p1...p5]. You should just give it two >> particles, one for each protein (with radius and center computed >> from a sphere cover, or with the distance computed using a particle >> refiner). I doubt the code below ever really did what you wanted >> (although it might have happened to agree:-) >> >> I can explain better once I'm back in the US in two days. >> >> >> On Sep 21, 2009, at 2:30 PM, Friedrich Foerster <foerster@biochem.mpg.de >> > wrote: >> >>> hi all, >>> >>> i noticed that the connectivity restraint must have changed at >>> some point: >>> i want to impose a restraint on two proteins, each consisting of >>> several particles. thus, i am interested in restraining the closest >>> pair between the two proteins. whereas the following code did what i >>> need previously it now calculates all against all distances >>> (including >>> intra-protein distances) - which is not what i want. >>> i'd be grateful if anyone could tell me how i need to change my >>> pseudo code: >>> >>> >>> prot1 = [part1,part2,part3] >>> prot2 = [part4,part5,part6] >>> ufu = IMP.core.TruncatedHarmonicUpperBound( span, k, stddev, 2.) >>> pairsc = IMP.core.SphereDistancePairScore(ufu, IRAD_KEY) >>> connrest = IMP.core.ConnectivityRestraint(pairsc) >>> for pps in [prot1,prot2]: >>> connrest.add_particles(pps) >>> >>> to be explicit: the code now restrains distances in prot1 and prot2, >>> which is what i do not want. i only want the inter-protein distances >>> to be considered... >>> >>> thanks >>> >>> frido >>> >>> >>> -- >>> >>> Dr. Friedrich Foerster >>> Max-Planck Institut fuer Biochemie >>> Am Klopferspitz 18 >>> D-82152 Martinsried >>> >>> Tel: +49 89 8578 2651 >>> Fax: +49 89 8578 2641 >>> >>> foerster@biochem.mpg.de >>> >>> www.tomotronic.org >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev >