Re: [IMP-dev] connectivity restraints

Frido - this is how it should look like:

#create the two proteins

prot_ps=IMP.Particles()

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

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www.tomotronic.org
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