On Sep 21, 2009, at 3:54 PM, 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).could you give an example, please? i have no clue what a refiner does. the doc says it returns particles. no clue which ones ... what'd happen if i have different granularities in one protein (atoms and fragments).
I doubt the code below ever really did what you wanted (although it might have happened to agree:-)
yes, it did work fine. probably going back to brad, the syntax was simply to specify each protein as a list. pretty convenient ... at some point in the recent months, it started being ignored which particles are put into IMP.Particles. they seem to be just thrown into one basket, which they were not before. needless to say i'd prefer that simple syntax compared dealing with hyper-abstract classes etc unless someone convinces me of the necessity of those. anyway, help with getting that functionality would be greatly appreciated.
cheers frido
I can explain better once I'm back in the US in two days.On Sep 21, 2009, at 2:30 PM, Friedrich Foerster < > 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 ineed previously it now calculates all against all distances (includingintra-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 www.tomotronic.org _______________________________________________ IMP-dev mailing list https://salilab.org/mailman/listinfo/imp-dev_______________________________________________ IMP-dev mailing list https://salilab.org/mailman/listinfo/imp-dev
-- Friedrich Foerster Max-Planck Institut fuer Biochemie Am Klopferspitz 18 D-82152 Martinsried Tel: +49 89 8578 2651 Fax: +49 89 8578 2641 www.biochem.mpg.de/foerster