thanks.
currently, i do not use the top hierarchy layer. personally, i find it cumbersome to tie everything to a hierarchy on the representation level. every time i want to incorporate a new type of experimental data, i discover that it requires a new hierarchy level, which i haven't imagined before. but changing the representation hierarchy always involves so many changes so that i try to keep away from tying the restraints to a fixed hierarchy. for example, in this case i might discover that i require a sub-complex and a sub-sub-complex hierarchy level and so forth. thus, i'd appreciate some way of incorporating such a restraint without a fixed representation hierarchy, which i would need to fix constantly... any other opinions?
thanks
frido
On Dec 18, 2008, at 2:59 PM, Daniel Russel wrote:
> See the "connectivity restraint" example (under simple examples) to > get started. To replicate Frank's restraint you need another layer > of conditionality which can be done by chaining the > LowerRefinedPairScores something like > > ps= IMP.core.SphereDistancePairScore(IMP.core.HarmonicUpperBound(0,1)) > cps= IMP.core.ChildrenParticleRefiner() > # find the closest pair connecting two instances of two proteins > ilrps = IMP.misc.LowestRefinedPairScore(cps,ps) > # find the closest instances of two proteins > lrps = IMP.misc.LowestRefinedPairScore(cps,lrps) > cr = IMP.core.ConnectivityRestraint(lrps) > cr.set_particles(hs) > m.add_restraint(cr) > > and ensuring that your molecular hierarchy looks like > - all proteins of type a > - first protein of type a > - leaf representations of first protein of type a > ... > - second protein of type a > ... > - third protein of type a > ... > - all proteins of type b > - first protein of type b > ... > - all proteins of type c > ... > > And putting the "all proteins of type x" particles in the > ConnectivityRestraint. > > If such a hierarchy organization is problematic than we should talk > some more. At the moment there is a shortage of other > ParticleRefiners so you have little choice on your organization > scheme. I have a table based particle refiner somewhere (so you > could replace the first level of ChildrenParticleRefiner with a non- > MolecularHierarchy based approach), but it never got committed > during the reorg. > > The other thing to be aware of is that, if you are using a > derivative-based optimizer, the evaluation is not very efficient (in > that the closest pair is found twice). Let me know if it becomes too > slow and I'll put some effort into figuring out a way to avoid this > problem. > > Does this all make sense? > > > On Dec 18, 2008, at 12:14 AM, Friedrich Foerster wrote: > >> hi there, >> >> is there any example for generating ambiguous restraints in imp? >> i want to deal with a 'frank classic': multiple copies of a >> specific protein exist in an assembly and only one instance >> interacts with another protein (the one that is closer to its >> putative partner). i guess npc people need it every day. >> >> thanks >> >> frido >> >> -- >> >> 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 >
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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