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CHIMERA_AA is an integrated toolkit that allows researchers to modify and analyze protein structures and their complexes. This toolkit enables users to perform user-specified single or multiple amino acid mutations, as well as class-wise mutations, generating diverse structural combinations for further computational studies and generating initial coordinates of the mutated structures in user-specified formats (PDB, mmCIF, and mol2). The toolkit also generates minimized structures and facilitates the extraction and analysis of structural and physicochemical features of protein structures.