name.txt

# Rename rule file contains rules to format atom names and residue
# names. The purpose is to unify residue names to 3-char mcce names
# and break some big cofactors into small ones.
#
# Each line has two fields separated by at least one space. Each field
# is 14 characters long, matching the atom, residue name, chainID and
# sequence number field of a pdb line. The first string will be
# replaced by the second string.
#
# Symbol "*" in the first string is a wildcard that matchs any character.
# It means "do not replace" in the second string.
#
# The replace is accumulative in the order of appearing in this file.
#
####_###_#_###  ####_###_#_###
*D************  *H************      rename all atom D to H
***** ********  *****_********
****** *******  ******_*******
******* ******  *******_******
*****HEA******  *****HEM******
*****HEC******  *****HEM******
*CAA*HEM******  *****PAA******      extract PAA from heme
*CBA*HEM******  *****PAA******
*CGA*HEM******  *****PAA******
*O1A*HEM******  *****PAA******
*O2A*HEM******  *****PAA******
*HAA*HEM******  *****PAA******
*HBA*HEM******  *****PAA******
*H1A*HEM******  *****PAA******
*H2A*HEM******  *****PAA******
*CAD*HEM******  *****PDD******      extract PDD from heme
*CBD*HEM******  *****PDD******
*CGD*HEM******  *****PDD******
*O1D*HEM******  *****PDD******
*O2D*HEM******  *****PDD******
*HAD*HEM******  *****PDD******
*HBD*HEM******  *****PDD******
*H1D*HEM******  *****PDD******
*H2D*HEM******  *****PDD******
*C11*HEM******  *****FAR******      extract FAR from heme
*C12*HEM******  *****FAR******
*C13*HEM******  *****FAR******
*C14*HEM******  *****FAR******
*C15*HEM******  *****FAR******
*C16*HEM******  *****FAR******
*C17*HEM******  *****FAR******
*C18*HEM******  *****FAR******
*C19*HEM******  *****FAR******
*C20*HEM******  *****FAR******
*C21*HEM******  *****FAR******
*C22*HEM******  *****FAR******
*C23*HEM******  *****FAR******
*C24*HEM******  *****FAR******
*C25*HEM******  *****FAR******
*C26*HEM******  *****FAR******
*C27*HEM******  *****FAR******
*O11*HEM******  *****FAR******
 O **ACT******   O_***********
 C **ACT******   C_***********
 O **CMO******   O_***********
 C **CMO******   C_***********
 O **CSS******   O_***********
 C **CSS******   C_***********
 N **CSS******   N_***********
 O **PCA******   O_***********
 C **PCA******   C_***********
 N **PCA******   N_***********
 O **ACN******   O_***********
 C **ACN******   C_***********
*NA **********  *N A**********     extra space for the NA in bcl, bph
*NB **********  *N B**********
*NC **********  *N C**********
*ND **********  *N D**********