def displacementUpdateB(objA, alnAri, objB, alnBri):
    ### If residue is unassigned in one of the pdb files, we reset its value
    for x in range(len(alnAri)):
        s1 = objA + " and name CA and resi " + alnAri[x]
 	cmd.alter( s1, "b = " + str(-0.01))
    for x in range(len(alnBri)):
	s2 = objB + " and name CA and resi " + alnBri[x]
        cmd.alter( s2, "b = " + str(-0.01))
    cmd.sort(objA); cmd.sort(objB)
    for x in range(len(alnAri)):
        s1 = objA + " and name CA and resi " + alnAri[x]
	s2 = objB + " and name CA and resi " + alnAri[x]
	### Names starting with __ (underscores) are normally hidden by PyMOL
	tempObject = "__tempObject"
	Displacement = cmd.distance(tempObject, s1, s2)
 	cmd.alter( s1, "b = " + str(Displacement))
        cmd.alter( s2, "b = " + str(Displacement))
	cmd.delete(tempObject)
    cmd.sort(objA); cmd.sort(objB)
def displacementUpdateBAll(objA, alnAri, objB, alnBri):
    print "This will take a while to go through the for loops. Give me around 3-5 minutes..."
    ### If residue is unassigned in one of the pdb files, we reset its value
    for x in range(len(alnAri)):
        s1 = objA + " and resi " + alnAri[x][0] + " and name " + str(alnAri[x][1])
 	cmd.alter( s1, "b = " + str(-0.01))
    for x in range(len(alnBri)):
	s2 = objB + " and resi " + alnBri[x][0] + " and name " + alnBri[x][1]
        cmd.alter( s2, "b = " + str(-0.01))
    cmd.sort(objA); cmd.sort(objB)
    for x in range(len(alnAri)):
        s1 = objA + " and resi " + alnAri[x][0] + " and name " + alnAri[x][1]
	s2 = objB + " and resi " + alnAri[x][0] + " and name " + alnAri[x][1]
	### Names starting with __ (underscores) are normally hidden by PyMOL
	tempObject = "__tempObject"
	Displacement = cmd.distance(tempObject, s1, s2)
 	cmd.alter( s1, "b = " + str(Displacement))
        cmd.alter( s2, "b = " + str(Displacement))
	cmd.delete(tempObject)
    cmd.sort(objA); cmd.sort(objB)