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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