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