mode res
pdb_res_dict pdb_res_dict.txt
rmsd_threshold 0.7
max_longest_matches 5
def *=CA;avg(side_chain):bar
The definitions with a "*" are catch-all definitions. Everything that does not have a more specific definition is represented this way. Here all the residues are represented by the C-alpha together with a point (called “bar” in this case) calculated as the geometric centroid of the side chain atoms. When you use the “avg()" syntax the program will calculate the geometric centroid of the comma-separated list of atoms between the parenthesis. In this case the special keyword “side_chain" has been used. This allows you refer to all the side chain atoms without bothering to enumerate them. When you use the “avg()" syntax is mandatory to include a name for the pseudoatom (i.e. the centroid) you are creating. The “avg()" part and the name (“bar" in this case”) are separated by a “:”. These labels can then be used to refer to the pseudoatoms in the “Equivalences" section (not done here, see the Documentation or the description of the representation focused on specific chemical groups for more details)
equiv ALA=CYS;GLU;GLY;ILE;LYS;LEU;MET;PRO;GLN;ARG;SER;THR;VAL
equiv CYS=ALA;CYS;ILE;LEU;MET;SER;THR;VAL
equiv ASP=ASP;GLU;GLY;HIS;LYS;ASN;PRO;GLN;SER;THR
equiv GLU=ALA;ASP;GLU;HIS;LYS;ASN;PRO;GLN;ARG;SER;THR
equiv PHE=PHE;HIS;ILE;LEU;MET;VAL;TRP;TYR
equiv GLY=ALA;ASP;GLY;ASN;SER
equiv HIS=ASP;GLU;PHE;HIS;LYS;ASN;GLN;ARG;SER;TYR
equiv ILE=ALA;CYS;PHE;ILE;LEU;MET;THR;VAL;TYR
equiv LYS=ALA;ASP;GLU;HIS;LYS;MET;ASN;PRO;GLN;ARG;SER;THR
equiv LEU=ALA;CYS;PHE;ILE;LEU;MET;THR;VAL;TYR
equiv MET=ALA;CYS;PHE;ILE;LYS;LEU;MET;GLN;ARG;SER;THR;VAL;TRP;TYR
equiv ASN=ASP;GLU;GLY;HIS;LYS;ASN;GLN;ARG;SER;THR
equiv PRO=ALA;ASP;GLU;LYS;PRO;GLN;SER;THR
equiv GLN=ALA;ASP;GLU;HIS;LYS;MET;ASN;PRO;GLN;ARG;SER;THR;TYR
equiv ARG=ALA;GLU;HIS;LYS;MET;ASN;GLN;ARG;SER;THR
equiv SER=ALA;CYS;ASP;GLU;GLY;HIS;LYS;MET;ASN;PRO;GLN;ARG;SER;THR
equiv THR=ALA;CYS;ASP;GLU;ILE;LYS;LEU;MET;ASN;PRO;GLN;ARG;SER;THR;VAL
equiv VAL=ALA;CYS;PHE;ILE;LEU;MET;THR;VAL;TYR
equiv TRP=PHE;MET;TRP;TYR
equiv TYR=PHE;HIS;ILE;LEU;MET;GLN;VAL;TRP;TYR
Here only residues that have a score of at least -1 in a BLOSUM62 matrix are allowed to match. Each line means that the first residue (left of the ‘=‘ sign) can be matched with any of the residues in the ';' separated list (right of the ‘=' sign). This syntax is different from the one used here (in that case all the residues were separated by a '=' meaning that they formed a group in which each residue could be matched with any other one) These definitions are symmetric so it isn't strictly necessary to specify ASN=ASP and ASP=ASN; this is only done for clarity. Note that you have to specify identities explicitly (e.g. ASP=ASP) since they are not assumed by default