remarks custom patch file
remarks
remarks makes covalent links between pseudoatoms (representing dye centers) and the CA atoms of
remarks the corresponding residues that the dye is connected to. 
remarks

for $id in id (    

                   ( resid 140 and segid S and name CA) 
                or ( resid 154 and segid S and name CA) 
                or ( resid 174 and segid S and name CA)
                or ( resid 189 and segid S and name CA)
                or ( resid 254 and segid S and name CA)
                or ( resid 269 and segid S and name CA)
                or ( resid 350 and segid S and name CA)
                or ( resid 368 and segid S and name CA)
                or ( resid 383 and segid S and name CA)
                or ( resid 396 and segid S and name CA)
                
                or ( resid 61 and ( segid A ) and name CA)
                
                or ( resid 20 and ( segid C or segid D ) and name CA ) 
                or ( resid 139 and ( segid C or segid D ) and name CA ) 
                or ( resid 76 and ( segid C or segid D ) and name CA ) 
                or ( resid 197 and ( segid C or segid D ) and name CA ) 
                
                   ) loop patc

 show elem ( segid ) ( id $id ) 
 evaluate ($segid=$result)

 show elem ( resid ) ( id $id )
 evaluate ($resid=$result) 

 patch pdum
  reference=-=( byresidue ( id $id)  ) 
  reference=+=( resname PSDO and resid $resid and segid $segid ) 
 end

end loop patc

connectivity print=true end