Do you guys know frido is now a real group leader, the only one, in wolfgang's group? :)
Andrej (Sent from my iPhone)
On Sep 23, 2009, at 10:06 AM, Friedrich Foerster <foerster@biochem.mpg.de > wrote:
> On Wed, Sep 23, 2009 at 4:42 PM, Daniel Russel drussel@gmail.com > wrote: >> >> On Sep 23, 2009, at 7:31 AM, Friedrich Foerster wrote: >> >>> On Wed, Sep 23, 2009 at 5:14 AM, Daniel Russel drussel@gmail.com >>> wrote: >>>> >>>> On Sep 22, 2009, at 6:55 PM, Keren Lasker wrote: >>>> >>>>> Daniel - >>>>> 1. does this solution means that f3-f5-f7 (and f0-f1-f2) are >>>>> simplified >>>>> to >>>>> a single sphere ? >>> >>> so i implemented option 1, which seems to do what i want (the >>> restraint acting closest two spheres). >>> to check that the code actually does the right thing (score the >>> single >>> shortest distance between (f3,f5,f7) and (f0,f1,f2)) i tried to >>> return >>> the connected pairs (=ONE pair for my desired restraint, not FIVE >>> restraints for the undesired behavior). sadly, >>> connrest.get_connected_pairs() returns my newly generated particles, >>> which specify the interacting fragments. is there any way to return >>> the actually interacting LowestRefined particles? otherwise, i >>> cannot >>> check that the code does the right thing (and the information is >>> useful for me)... >> >> Good point. The easiest way around is for me to add add a method to >> the >> LowestRefinedPairScore that returns the actual pair given an input >> pair. >> Makes the verification two steps, but it is just verification, so >> being >> slightly annoying seems fine to me. I'll do that later today. > > thanks. that'd be ver useful for me. > >> >> BTW, if you really only have an interaction between two sets of >> particles, >> you might as well skip the connectivityrestraint and just use a >> pairrestraint. > > ? > I need the msp functionality, i.e., the restraint should only use the > shortest inter-fragment distance for scoring. i thought the > ConnectivityRestraint is the appropriate restraint type. if > PairRestraint does the same i could also use that - however, i have > sometimes >2 fragments involved, so anyways, i'll need the > ConnectivityRestraint, i guess. > i'd encourage another thing for the documentation: it'd be useful to > have a somewhat more informative short description (one sentence) for > each class/function in IMP. for example, if PairRestraint calculates > the msp between input particles if they have children, it'd be nice to > tell that explicitly. even better would be to link to > ConnectivityRestraint and highlight similarities/differences. > > thanks > > frido > > _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev >> >> > > > > -- > -- > > 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