subroutine define_pairs(iprot)
      implicit none
      include 'DIMENSIONS'
      include 'DIMENSIONS.ZSCOPT'
      include 'DIMENSIONS.COMPAR'
      include 'COMMON.IOUNITS'
      include 'COMMON.TIME1'
      include 'COMMON.SBRIDGE'
      include 'COMMON.COMPAR'
      include 'COMMON.FRAG'
      include 'COMMON.CHAIN'
      include 'COMMON.HEADER'
      include 'COMMON.GEO'
      include 'COMMON.CONTACTS1'
      include 'COMMON.PEPTCONT'
      include 'COMMON.CLASSES'
      integer i,j,k,ind,ll1,ll2,len_cut,length_frag,ib,iprot,icant
#ifdef DEBUG
      write (iout,*) "define_pairs: iprot",iprot," nfrag",nfrag(1,iprot)
#endif
      do ib=1,nclass(iprot)-1
      do j=1,nfrag(1,iprot)
        length_frag = 0
        do k=1,npiece(j,1,ib,iprot)
          length_frag=length_frag+ifrag(2,k,j,ib,iprot)
     &      -ifrag(1,k,j,ib,iprot)+1
        enddo
        len_frag(j,1,ib,iprot)=length_frag
#ifdef DEBUG
        write (iout,*) "Batch",ib," fragment",j,
     &    " length",len_frag(j,1,ib,iprot)
#endif
      enddo
      enddo
      nfrag(2,iprot)=0
      do i=1,nfrag(1,iprot)
        do j=i+1,nfrag(1,iprot)
          ind = icant(i,j)
          if (istruct(i,1,iprot).le.1 .or. istruct(j,1,iprot).le.1) 
     &    then
            if (istruct(i,1,iprot).le.1) then
              ll1=len_frag(i,1,1,iprot)
            else
              ll1=len_frag(i,1,1,iprot)/2
            endif
            if (istruct(j,1,iprot).le.1) then
              ll2=len_frag(j,1,1,iprot)
            else
              ll2=len_frag(j,1,1,iprot)/2
            endif
            len_cut=max0(min0(ll1*2/3,ll2*4/5),3)
          else
            if (istruct(i,1,iprot).eq.2.or.istruct(i,1,iprot).eq.4) 
     &      then
              ll1=len_frag(i,1,1,iprot)/2
            else
              ll1=len_frag(i,1,1,iprot) 
            endif
            if (istruct(j,1,iprot).eq.2 .or. istruct(j,1,iprot).eq.4) 
     &      then
              ll2=len_frag(j,1,1,iprot)/2
            else
              ll2=len_frag(j,1,1,iprot) 
            endif
            len_cut=max0(min0(ll1*4/5,ll2)*4/5,3)
          endif
#ifdef DEBUG
          write (iout,*) "Fragments",i,j," structure",
     &       istruct(i,1,iprot),
     &       istruct(j,1,iprot)," # contacts",
     &       ncont_frag_ref(ind,1,iprot),
     &       nsccont_frag_ref(ind,1,iprot),
     &       " lengths",len_frag(i,1,1,iprot),len_frag(j,1,1,iprot),
     &       " ll1",ll1," ll2",ll2," len_cut",len_cut
#endif
          if ((istruct(i,1,iprot).eq.1 .or. istruct(j,1,iprot).eq.1) 
     &        .and.nsccont_frag_ref(ind,1,iprot).ge.len_cut) then
            if(istruct(i,1,iprot).eq.1 .and. istruct(j,1,iprot).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,iprot)=nfrag(2,iprot)+1
            do ib=1,nclass(iprot)-1
#ifdef DEBUG
            write (iout,*) "Batch",ib
#endif
            if (icont_pair(ib).gt.0 .and. icontp_pair(ib).eq.0) then
#ifdef DEBUG
              write (iout,*)  "# SC contacts will be used",
     &        " in comparison."
#endif
              isccont(nfrag(2,iprot),2,ib,iprot)=1
              ielecont(nfrag(2,iprot),2,ib,iprot)=0
            else if (icontp_pair(ib).gt.0) then
#ifdef DEBUG
              write (iout,*)  "# pp contacts will be used",
     &        " in comparison."
#endif
              ielecont(nfrag(2,iprot),2,ib,iprot)=1
              isccont(nfrag(2,iprot),2,ib,iprot)=0
            else
              ielecont(nfrag(2,iprot),2,ib,iprot)=0
              isccont(nfrag(2,iprot),2,ib,iprot)=0
            endif
            if (irms_pair(ib).gt.0) then
#ifdef DEBUG
              write (iout,*)  "Fragment RMSD will be used",
     &        " in comparison."
#endif
              irms(nfrag(2,iprot),2,ib,iprot)=1
            endif
            if (iqwol_pair(ib).gt.0) then
#ifdef DEBUG
              write (iout,*)  "Fragment Q will be used",
     &        " in comparison."
#endif
              iqwol(nfrag(2,iprot),2,ib,iprot)=1
              qcutfrag(nfrag(2,iprot),2,ib,iprot)=qcut_pair(ib)
            endif
            npiece(nfrag(2,iprot),2,ib,iprot)=2
            ipiece(1,nfrag(2,iprot),2,ib,iprot)=i
            ipiece(2,nfrag(2,iprot),2,ib,iprot)=j
            n_shift(1,nfrag(2,iprot),2,ib,iprot)=nshift_pair(ib)
            n_shift(2,nfrag(2,iprot),2,ib,iprot)=nshift_pair(ib)
            nc_fragm(nfrag(2,iprot),2,ib,iprot)=ncfrac_pair(ib)
            nc_req_setf(nfrag(2,iprot),2,ib,iprot)=ncreq_pair(ib)
            enddo
          else if ((istruct(i,1,iprot).ge.2 
     &       .and. istruct(i,1,iprot).le.4)
     &       .and. (istruct(j,1,iprot).ge.2 
     &       .and. istruct(i,1,iprot).le.4)
     &       .and. ncont_frag_ref(ind,1,iprot).ge.len_cut ) then
            nfrag(2,iprot)=nfrag(2,iprot)+1
            write (iout,*) "Adding pair strands/sheets",i,j,
     &        " based on pp contacts"
            do ib=1,nclass(iprot)-1
#ifdef DEBUG
            write (iout,*) "Batch",ib
#endif
            if (icont_pair(ib).gt.0 .and. icontsc_pair(ib).eq.0) then
#ifdef DEBUG
              write (iout,*) "# pp contacts will be used",
     &        " in comparison."
#endif
              ielecont(nfrag(2,iprot),2,ib,iprot)=1
              isccont(nfrag(2,iprot),2,ib,iprot)=0
            else if (icontsc_pair(ib).eq.1) then
#ifdef DEBUG
              write (iout,*) "# sc contacts will be used",
     &        " in comparison."
#endif
              ielecont(nfrag(2,iprot),2,ib,iprot)=0
              isccont(nfrag(2,iprot),2,ib,iprot)=1
              write (iout,*) nfrag(2,iprot),2,ib,iprot,
     &          isccont(nfrag(2,iprot),2,ib,iprot)
            else
              ielecont(nfrag(2,iprot),2,ib,iprot)=0
              isccont(nfrag(2,iprot),2,ib,iprot)=0
            endif
            if (irms_pair(ib).gt.0) then
#ifdef DEBUG
              write (iout,*)  "Fragment RMSD will be used",
     &        " in comparison."
#endif
              irms(nfrag(2,iprot),2,ib,iprot)=1
            else
              irms(nfrag(2,iprot),2,ib,iprot)=0
            endif
            if (iqwol_pair(ib).gt.0) then
#ifdef DEBUG
              write (iout,*)  "Fragment Q will be used",
     &        " in comparison."
#endif
              iqwol(nfrag(2,iprot),2,ib,iprot)=1
              qcutfrag(nfrag(2,iprot),2,ib,iprot)=qcut_pair(ib)
            endif
            npiece(nfrag(2,iprot),2,ib,iprot)=2
            ipiece(1,nfrag(2,iprot),2,ib,iprot)=i
            ipiece(2,nfrag(2,iprot),2,ib,iprot)=j
            n_shift(1,nfrag(2,iprot),2,ib,iprot)=nshift_pair(ib)
            n_shift(2,nfrag(2,iprot),2,ib,iprot)=nshift_pair(ib)
            nc_fragm(nfrag(2,iprot),2,ib,iprot)=ncfrac_bet(ib)
            nc_req_setf(nfrag(2,iprot),2,ib,iprot)=ncreq_bet(ib)
            enddo
          endif
        enddo
      enddo
#ifdef DEBUG
      write (iout,*) "Pairs found"
      do i=1,nfrag(2,iprot)
        write (iout,*) ipiece(1,i,2,1,iprot),ipiece(2,i,2,1,iprot)
      enddo
      write (iout,*) "ielecont"
      do ib=1,nclass(iprot)-1
        write (iout,*) "structural level",ib
        do i=1,iabs(nlevel(iprot))
          write (iout,*) "Level",i
          write (iout,*) (ielecont(j,i,ib,iprot),j=1,nfrag(i,iprot))
        enddo
      enddo
      write (iout,*) "isccont"
      do ib=1,nclass(iprot)-1
        write (iout,*) "structural level",ib
        do i=1,iabs(nlevel(iprot))
          write (iout,*) "Level",i
          write (iout,*) (isccont(j,i,ib,iprot),j=1,nfrag(i,iprot))
        enddo
      enddo
#endif
      return
      end