mode res
pdb_res_dict pdb_res_dict.txt
rmsd_threshold 0.7
score_max 16
max_longest_matches 5
def *=CA
The definitions with a "*" are catch-all definitions. Everything that does not have a more specific definition is represented this way. In this case all the residues are represented only by their C-alphas
equiv ALA=ALA
equiv ARG=ARG
equiv ASN=ASN
equiv ASP=ASP
equiv CYS=CYS
equiv GLN=GLN
equiv GLU=GLU
equiv GLY=GLY
equiv HIS=HIS
equiv ILE=ILE
equiv LEU=LEU
equiv LYS=LYS
equiv MET=MET
equiv PHE=PHE
equiv PRO=PRO
equiv SER=SER
equiv THR=THR
equiv TRP=TRP
equiv TYR=TYR
equiv VAL=VAL
equiv ALA=ARG=ASN=ASP=CYS=GLN=GLU=GLY=HIS=ILE=LEU=LYS=MET=PHE=PRO=SER=THR=TRP=TYR=VAL
Equivalent residues can be matched together. The first 20 lines specify that each residue can be matched with itself (identities are not assumed by default!). The last line indicates that all the residues are part of the same equivalence group and therefore all the substitutions are allowed. Please note the differences with the syntax used here. In that case there is a single ‘=' sign per line meaning that the residue on the left on the left of the ‘=' can be matched with any of the residues on the right, but the residues on the right can’t be matched together. Also note that the residues you are equivalencing need to be represented with the same number of points (see the Documentation for details)