PrimeX Reserved Residue Names

PrimeX uses residue names to classify residues as protein residues, and hence determine whether chains are protein chains or not. In addition to the standard names for the 20 standard amino acids, the following names are also recognized as protein residues:

You should ensure that these residue names are only used for protein residues. In addition, HOH is recognized as water. Internally, PrimeX uses the names XXX, YYY, and ZZZ, and any other names starting with X. You should therefore ensure that none of these internal names is used in your model.