As Tsjerk pointed out, there was a mistake in the code. Just for the
record this is the right function:
pdb2entry = { "1ONE": "1ONE_A", "2ONE": "2ONE_A" }
# a function to measure Ca distances of oposite pairs of superimpossed
chains (the proteins must have the same aa composition)
def check_for_symmetry(tstruct, qstruct):
# align the pair
cmd.fetch(tstruct)
cmd.extract(pdb2entry[tstruct]+"1", tstruct + " and chain "+
pdb2entry[tstruct][-1:] + " and not hetatm")
cmd.fetch(qstruct)
cmd.extract(pdb2entry[qstruct]+"1", qstruct +" and chain "+
pdb2entry[qstruct][-1:] + " and not hetatm")
cmd.delete(tstruct)
cmd.delete(qstruct)
print "Aligning "+pdb2entry[tstruct]+"1"+" with "+pdb2entry[qstruct]+"1"
cmd.align(pdb2entry[tstruct]+"1", pdb2entry[qstruct]+"1")
#cmd.do("cealign "+pdb2entry[qstruct]+"1, "+pdb2entry[tstruct]+"1")
# align the symmetric pair
cmd.fetch(tstruct)
cmd.extract(pdb2entry[tstruct]+"2", tstruct + " and chain "+
pdb2entry[tstruct][-1:] + " and not hetatm")
cmd.fetch(qstruct)
cmd.extract(pdb2entry[qstruct]+"2", qstruct +" and chain "+
pdb2entry[qstruct][-1:] + " and not hetatm")
print "Aligning "+pdb2entry[qstruct]+"1"+" with "+pdb2entry[tstruct]+"1"
cmd.align(pdb2entry[qstruct]+"2", pdb2entry[tstruct]+"2")
#cmd.do("cealign "+pdb2entry[qstruct]+"2, "+pdb2entry[tstruct]+"2")
# measure distances
pymol.stored.protein_dict = {}
cmd.iterate(pdb2entry[tstruct]+"1", "stored.protein_dict[(chain,resi)]=1")
Residues = pymol.stored.protein_dict.keys()
Residues.sort()
RMSD = 0
for res in Residues:
chain = res[0]
resi = res[1]
dist1 = cmd.distance('tmp',pdb2entry[tstruct]+"1 and chain
"+chain+" and resi "+resi+" and name ca",pdb2entry[qstruct]+"1 and
chain "+chain+" and resi "+resi+" and name ca")
dist2 = cmd.distance('tmp',pdb2entry[tstruct]+"2 and chain
"+chain+" and resi "+resi+" and name ca",pdb2entry[qstruct]+"2 and
chain "+chain+" and resi "+resi+" and name ca")
print "The difference in distance betweem residue IDs ",
resi," is : ",dist1, "-",dist2," = ",dist1-dist2
RMSD += (dist1-dist2)**2
RMSD = sqrt(RMSD/len(Residues))
print "RMSD of distances between identical residues in 1ONE x
2ONE and this in 2ONE x 1ONE: ", RMSD
check_for_symmetry("1ONE", "2ONE")
After this correction the RMSD falls to 2.06853295972e-06, which a
reasonably good number.
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