The Zimm–Bragg model relaxes one of the assumptions used to derive the zipper model. Namely, the helix is now allowed to have multiple nucleation sites, or beginning points, for base-pair association. One constructs the partition function consecutively. The first pair on the end of the chain is either unattached, with partition function qu(T), or attached with partition σqa(T). Hence, the partition function of a chain with one base pair is qa + σqu. It is convenient to write this as the sum of the elements of a column vector:

The second base pair is again either attached or unattached. However, the partition function of the second pair depends on whether or not the first pair is attached. If the second pair is unattached, it has partition function qu. If the second pair is attached and the first pair is attached, the partition function of the second pair is qa. However, if the first pair is unattached, and the second is attached, the partition function of the second pair is σqa. It is convenient, again, to write this as the sum of the column vector Q2,