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 <> 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 <>
> 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
>
>
>
> www.tomotronic.org
>
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--
--
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