Hello Vitaly--
>
> I am assembling a structure of a homopentamer using XPLOR-NIH. There
> are several ambiguous distance restraints that I would like to
> implement, but I am not sure if it is possible to group the
> restraints using "and" and "or" logic. As an example, suppose there
> is a residue "B" in one monomer that has an NOE contact with either
> residue "A" or residue "C" of an adjacent monomer. I would like a
> statement something among the lines of:
>
> assign [((MON1 B) (MON2 A)) AND ((MON2 B) (MON3 A)) AND ... ] OR
> [((MON1 B) (MON2 C)) AND ((MON2 B) (MON3 C)) AND ... ]
>
> Is this something that can be done? Or do I have to specify this for
> only one protomer and the symmetry restraints will take care of the
> rest?
You could write a separate table for each subunit, or you can use a
single segid-less table and specify the nMono parameter using the
pot.setNMono(5)
accessor.
Of course symmetry restraints should be used as well. In your case
these are ``ncs'' and distance symmetry. These should look something
like:
from selectTools import getSegsResidues
segsResidues=getSegsResidues("name CA")
segids=sorted(segidsResidues.keys())
resids=segidsResidues[segids[0]]
from posDiffPotTools import create_PosDiffPot
ncs = PotList('ncs')
for (i,a) in enumerate(AtomSel("(not segid A) and resid %d" % resids[0])):
segid=a.segmentName()
ncs.append( create_PosDiffPot('ncs%d'%i,
"segid A",
"segid %s" % segid) )
pass
ncs.setScale(50)
potList.append(ncs)
from distSymmTools import create_DistSymmPot, genPolyRestraints
dSymm = create_DistSymmPot('dSymm)
for (i,a) in enumerate(segids):
j= (i+1) % len(segids)
K= (i+2) % len(segids)
dSymm.addRestraints(
genPolyRestraints(resids=range(resids[0],resids[:-1]+1,5),
segids=(segids[i],segids[j],segids[k])))
pass
dSymm.setScale(50)
potList.append(dSymm)
best regards--
Charles
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--
Charles Schwieters email: Charles at Schwieters.org
www: http://schwieters.org/cds
phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt
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