subroutine define_pairs
      implicit real*8 (a-h,o-z)
      include 'DIMENSIONS'
      include 'DIMENSIONS.ZSCOPT'
      include 'DIMENSIONS.COMPAR'
      include 'COMMON.IOUNITS'
      include 'COMMON.TIME1'
      include 'COMMON.SBRIDGE'
      include 'COMMON.CONTROL'
      include 'COMMON.COMPAR'
      include 'COMMON.FRAG'
      include 'COMMON.CHAIN'
      include 'COMMON.HEADER'
      include 'COMMON.GEO'
      include 'COMMON.CONTACTS1'
      include 'COMMON.PEPTCONT'
      do j=1,nfrag(1)
        length_frag = 0
        do k=1,npiece(j,1)
          length_frag=length_frag+ifrag(2,k,j)-ifrag(1,k,j)+1
        enddo
        len_frag(j,1)=length_frag
        write (iout,*) "Fragment",j," length",len_frag(j,1)
      enddo
      nfrag(2)=0
      do i=1,nfrag(1)
        do j=i+1,nfrag(1)
          ind = icant(i,j)
          if (istruct(i).le.1 .or. istruct(j).le.1) then
            if (istruct(i).le.1) then
              ll1=len_frag(i,1)
            else
              ll1=len_frag(i,1)/2
            endif
            if (istruct(j).le.1) then
              ll2=len_frag(j,1)
            else
              ll2=len_frag(j,1)/2
            endif
            len_cut=max0(min0(ll1*2/3,ll2*4/5),3)
          else
            if (istruct(i).eq.2 .or. istruct(i).eq.4) then
              ll1=len_frag(i,1)/2
            else
              ll1=len_frag(i,1) 
            endif
            if (istruct(j).eq.2 .or. istruct(j).eq.4) then
              ll2=len_frag(j,1)/2
            else
              ll2=len_frag(j,1) 
            endif
            len_cut=max0(min0(ll1*4/5,ll2)*4/5,3)
          endif
          write (iout,*) "Fragments",i,j," structure",istruct(i),
     &       istruct(j)," # contacts",
     &       ncont_frag_ref(ind),nsccont_frag_ref(ind),
     &       " lengths",len_frag(i,1),len_frag(j,1),
     &       " ll1",ll1," ll2",ll2," len_cut",len_cut
          if ((istruct(i).eq.1 .or. istruct(j).eq.1) .and.
     &      nsccont_frag_ref(ind).ge.len_cut ) then
            if (istruct(i).eq.1 .and. istruct(j).eq.1) then
              write (iout,*) "Adding pair of helices",i,j,
     &        " based on SC contacts"
            else
              write (iout,*) "Adding helix+strand/sheet pair",i,j,
     &        " based on SC contacts"
            endif
            nfrag(2)=nfrag(2)+1
            if (icont_pair.gt.0) then
              write (iout,*)  "# SC contacts will be used",
     &        " in comparison."
              isccont(nfrag(2),2)=1
            endif
            if (irms_pair.gt.0) then
              write (iout,*)  "Fragment RMSD will be used",
     &        " in comparison."
              irms(nfrag(2),2)=1
            endif
            npiece(nfrag(2),2)=2
            ipiece(1,nfrag(2),2)=i
            ipiece(2,nfrag(2),2)=j
            ielecont(nfrag(2),2)=0
            n_shift(1,nfrag(2),2)=nshift_pair
            n_shift(2,nfrag(2),2)=nshift_pair
            nc_fragm(nfrag(2),2)=ncfrac_pair
            nc_req_setf(nfrag(2),2)=ncreq_pair
          else if ((istruct(i).ge.2 .and. istruct(i).le.4)
     &       .and. (istruct(j).ge.2 .and. istruct(i).le.4)
     &       .and. ncont_frag_ref(ind).ge.len_cut ) then
            nfrag(2)=nfrag(2)+1
            write (iout,*) "Adding pair strands/sheets",i,j,
     &        " based on pp contacts"
            if (icont_pair.gt.0) then
              write (iout,*) "# pp contacts will be used",
     &        " in comparison."
              ielecont(nfrag(2),2)=1
            endif
            if (irms_pair.gt.0) then
              write (iout,*)  "Fragment RMSD will be used",
     &        " in comparison."
              irms(nfrag(2),2)=1
            endif
            npiece(nfrag(2),2)=2
            ipiece(1,nfrag(2),2)=i
            ipiece(2,nfrag(2),2)=j
            ielecont(nfrag(2),2)=1
            isccont(nfrag(2),2)=0
            n_shift(1,nfrag(2),2)=nshift_pair
            n_shift(2,nfrag(2),2)=nshift_pair
            nc_fragm(nfrag(2),2)=ncfrac_bet
            nc_req_setf(nfrag(2),2)=ncreq_bet
          endif
        enddo
      enddo
      write (iout,*) "Pairs found"
      do i=1,nfrag(2)
        write (iout,*) ipiece(1,i,2),ipiece(2,i,2)
      enddo
      return
      end