When building a knowledge-based homology model with Prime, the resulting model's chain ID assignment and residue numbers are not always correct. Why is this?

This can happen when you are building a multi-chain model that has missing terminal residues, where the residue numbers from the terminal of one chain may be associated with the terminal of a second chain. As a simple example, consider building a dimer where each chain is 10 residues. You'd expect the chain name assignment to look like this:

AAAAAAAAAA
BBBBBBBBBB

but instead, it may end up looking like this:

AAAAAAAAAA
AABBBBBBBB

The residue numbers will also probably be out of order, and look something like this on the second chain:

11-12-1-2-3-4-5-6-7-8

If this happens, an easy workaround is to re-assign the residue numbers and chain ID in Maestro, in the Residue Properties tab of the Build panel (Edit → Build → Residue Properties).

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