thanks. but the functionality is not sufficient for my needs as it is: i do not see any way to specify parts of a protein involved in an interaction. e.g., my proteins a and b each consist of 10 fragments. i have an interaction between A and B that involves the first 3 fragments of protein A and fragments 3,5,7 of protein B. how can i specify that restraint currently (it used to work previously ...). so i am not convinced why the old syntax had to go ...
thanks
frido
On Mon, Sep 21, 2009 at 6:37 PM, Keren Lasker kerenl@salilab.org wrote: > 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 > > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev > >