mode atom
In this mode each one of the point describing a residue is treated independently. Therefore the program may output matches where the same residue is paired with two or more different residues using different points
rmsd_threshold 0.7
pdb_res_dict pdb_res_dict.txt
def ALA=CB:ali
def ARG=avg(CB,CG,CD):ali;NE:don1;NH1:don2;NH2:don3
def ASN=OD1:acc;ND2:don
def ASP=OD1:acc1;OD2:acc2
def CYS=avg(CB,SG):ali
def GLN=OE1:acc;NE2:don
def GLU=OE1:acc1;OE2:acc2
def HIS=avg(CG,ND1,CD2,CE1,NE2):pi;NE1:DONACC1;NE2:DONACC2
def ILE=avg(CB,CG1,CG2,CD1):ali
def LEU=avg(CB,CG,CD1,CD2):ali
def LYS=avg(CB,CG,CD,CE):ali;NZ:don
def MET=avg(CB,CG,SD,CE):ali
def PHE=avg(CG,CD1,CD2,CE1,CE2,CZ):pi
def PRO=avg(CB,CG,CD):ali
def SER=OG:DONACC
def THR=CG2:ali;OG1:DONACC
def TRP=avg(CD,CD1,CD2,NE1,CE2,CE3):pi;avg(CZ1,CZ3,CH,NE1):don
def TYR=avg(CB,CD1,CD2,CE1,CZ):pi;OH:DONACC
def VAL=avg(CB,CG1,CG2):ali
def *=O:acc_O;N:don_N;C:pi_C
These definitions make extensive use of the “avg()" syntax to specify the different chemical groups that constitute each side chain. When you use the “avg()" syntax the program will calculate the geometric centroid of the comma-separated list of atoms between the parenthesis. It is mandatory to include a name for the pseudoatom (i.e. the centroid) you are creating. The “avg()" part and the name (“ali” for instance) are separated by a “:”. These labels can then be used to refer to the pseudoatoms in the “Equivalences" section. See below and refer to the Documentation for more details
equiv *.\don=*.\don=*.\DONACC
equiv *.\ali=*.\ali
equiv *.\acc=*.\acc=*.\DONACC
equiv *.\DONACC=*.\DONACC
equiv *.\pi=*.\pi
These equivalences make heavy use of wildcards. In general the syntax for equivalences is equiv res.atom=res.atom (with the .atom part optional). In this specific case both the residue and the atom part are specified using wildcard. The “*" in the residue name means “any residue for which a more specific equivalence has not been provided”. "\" is used in atom names with the meaning "Any atom whose name contains the string following the backslash”. The string matching is case sensitive so for instance \don won’t match with DONACC. Therefore the above equivalences mean that, irrespectively of the residue, DONACC (hydrogen bond donor and acceptor) can match with either DONACC, don (donor), or acc (acceptor). Aliphatic groups (ali) will match together and pi systems as well