We have found a case where a Build Mutants run failed with the error “handle_seq_indx raise KeyError(indx)”, it was due to the name of the input protein molecule being too long.

For the input molecule name or sequence name, the Modeler program can only handle alphanumeric characters including the underscore. There is also a limitation on the total number of characters a name can have. It's best to use short names (<20 characters) to avoid any problems.