!
! setup.tbl
! Sets up the selections for the various database energies
! Works with all.tbl
!
! WARNING: this script overwrites the store7, store8, and store9 arrays
!
! by John Kuszewski 6/19/96
! modified from earlier version for PROCHECK database energy
!
! modified 11/17/96 JJK for new phi/psi/chi1 dists
!

set message off echo off end

!
! need to select all the residues that immediately preceed a proline
! in order to designate them "xpr"
!
! xpr residues are stored in the store6 array
!

 do (store6 = 0) (all)

for $count in id (name ca and resn pro) loop database
    show elem (segid) (id $count)
   eval ($curSeg = $result)
    show elem (resid) (id $count)
   eval ($curRes = decode($result))
   eval ($prevRes = $curRes - 1)
    identify (store6) (store6 or (resid $prevRes and segid $curSeg))
end loop database


!
! get selections for N and C termini
! 
! atoms that are in N terminal residues are selected in store7
! atoms that are in C terminal residues are selected in store8
! 

 do (store7 = 0) (all)
 do (store8 = 0) (all)

for $count in id (name ca) loop database
    show elem (segid) (id $count)
   eval ($curSeg = $result)
    show elem (resid) (id $count)
   eval ($curRes = decode($result))
   eval ($nextRes = $curRes + 1)
   eval ($prevRes = $curRes - 1)
    do (store9 = 1) (all)
    show sum (store9) (resid $nextRes and segid $curSeg)
   eval ($nextResExists = $result)
    show sum (store9) (resid $prevRes and segid $curSeg)
   eval ($prevResExists = $result)
   if ($nextResExists = 0) then
       identify (store7) (store7 or (resid $curRes and segid $curSeg))
   end if
   if ($prevResExists = 0) then
       identity (store8) (store8 or (resid $curRes and segid $curSeg))
   end if
end loop database

!
! ala
!

for $count in id (name ca and resn ala and not store6) loop database

    show elem (segid) (id $count)
   eval ($curSeg = $result)
    show elem (resid) (id $count)
   eval ($curRes = $result)
   eval ($nextRes = encode(decode ($curRes) + 1))
   eval ($prevRes = encode(decode ($curRes) - 1))

   !
   ! now deal with BB selections -- 
   ! phi not defined for N terminal resids, 
   ! psi not defined for C terminal resids,
   ! omega not defined for C terminal resids
   !
    do (x = x) (segid $curSeg and resid $curRes and (store7 or store8))
   if ($select < 1) then
      RAMA 
      class phi_psi_rest
      assign 
         (segid $curSeg and resid $prevRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $nextRes and name n)
      end
   end if

end loop database


!
! arg
!

for $count in id (name ca and resn arg and not store6) loop database

    show elem (segid) (id $count)
   eval ($curSeg = $result)
    show elem (resid) (id $count)
   eval ($curRes = $result)
   eval ($nextRes = encode(decode ($curRes) + 1))
   eval ($prevRes = encode(decode ($curRes) - 1))

   !
   ! now deal with BB selections -- 
   ! phi not defined for N terminal resids, 
   ! psi not defined for C terminal resids,
   ! omega not defined for C terminal resids
   !
    do (x = x) (segid $curSeg and resid $curRes and (store7 or store8))
   if ($select < 1) then
      RAMA
      class phi_psi_rest
      assign
         (segid $curSeg and resid $prevRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $nextRes and name n)
      end
      RAMA 
      class phi_psi_chi1_arg_lys_met_gln_glu
      assign 
         (segid $curSeg and resid $prevRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $nextRes and name n)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name cb)
         (segid $curSeg and resid $curRes and name cg)
      end
   end if

   RAMA
   class chi1_chi2_arg_lys_met
   assign 
      (segid $curSeg and resid $curRes and name n)
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name cd)
   end   

   RAMA
   class chi2_chi3_arg
   assign 
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name cd)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name cd)
      (segid $curSeg and resid $curRes and name ne)
   end

   !
   ! chi1/chi2/chi3
   !
   RAMA
   class chi1_chi2_chi3_arg
   assign 
      (segid $curSeg and resid $curRes and name n)
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name cd)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name cd)
      (segid $curSeg and resid $curRes and name ne)
   end 

   !
   ! chi4
   !
   RAMA
   class chi4_arg
   assign
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name cd)
      (segid $curSeg and resid $curRes and name ne)
      (segid $curSeg and resid $curRes and name cz)
   end

end loop database


!
! asn
!

for $count in id (name ca and resn asn and not store6) loop database

    show elem (segid) (id $count)
   eval ($curSeg = $result)
    show elem (resid) (id $count)
   eval ($curRes = $result)
   eval ($nextRes = encode(decode ($curRes) + 1))
   eval ($prevRes = encode(decode ($curRes) - 1))

   !
   ! now deal with BB selections -- 
   ! phi not defined for N terminal resids, 
   ! psi not defined for C terminal resids,
   ! omega not defined for C terminal resids
   !
    do (x = x) (segid $curSeg and resid $curRes and (store7 or store8))
   if ($select < 1) then
      RAMA
      class phi_psi_hbonding
      assign
         (segid $curSeg and resid $prevRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $nextRes and name n)
      end
      RAMA 
      class phi_psi_chi1_cysred_his_asp_asn
      assign 
         (segid $curSeg and resid $prevRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $nextRes and name n)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name cb)
         (segid $curSeg and resid $curRes and name cg)
      end
   end if

   !
   ! chi1/chi2
   !
   RAMA
   class chi1_chi2_asn 
   assign 
      (segid $curSeg and resid $curRes and name n)
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
! is this right?
      (segid $curSeg and resid $curRes and name od1)
   end

end loop database


!
! asp
!

for $count in id (name ca and resn asp and not store6) loop database

    show elem (segid) (id $count)
   eval ($curSeg = $result)
    show elem (resid) (id $count)
   eval ($curRes = $result)
   eval ($nextRes = encode(decode ($curRes) + 1))
   eval ($prevRes = encode(decode ($curRes) - 1))

   !
   ! now deal with BB selections -- 
   ! phi not defined for N terminal resids, 
   ! psi not defined for C terminal resids,
   ! omega not defined for C terminal resids
   !
    do (x = x) (segid $curSeg and resid $curRes and (store7 or store8))
   if ($select < 1) then
      RAMA
      class phi_psi_hbonding
      assign
         (segid $curSeg and resid $prevRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $nextRes and name n)
      end
      RAMA 
      class phi_psi_chi1_cysred_his_asp_asn
      assign 
         (segid $curSeg and resid $prevRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $nextRes and name n)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name cb)
         (segid $curSeg and resid $curRes and name cg)
      end
   end if

   !
   ! chi1/chi2
   !
   RAMA
   class chi1_chi2_asp 
   assign 
      (segid $curSeg and resid $curRes and name n)
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
! is this right?
      (segid $curSeg and resid $curRes and name od1)
   end

end loop database


!
! cysox
!

for $count in id (name ca and resn cys and not store6) loop database
 show sum (x) (byresidue id $count and name hg)
if ($select = 0) then
    show elem (segid) (id $count)
   eval ($curSeg = $result)
    show elem (resid) (id $count)
   eval ($curRes = $result)
   eval ($nextRes = encode(decode ($curRes) + 1))
   eval ($prevRes = encode(decode ($curRes) - 1))

   !
   ! now deal with BB selections -- 
   ! phi not defined for N terminal resids, 
   ! psi not defined for C terminal resids,
   ! omega not defined for C terminal resids
   !
    do (x = x) (segid $curSeg and resid $curRes and (store7 or store8))
   if ($select < 1) then
      RAMA
      class phi_psi_rest
      assign
         (segid $curSeg and resid $prevRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $nextRes and name n)
      end
      RAMA 
      class phi_psi_chi1_cysox
      assign 
         (segid $curSeg and resid $prevRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $nextRes and name n)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name cb)
         (segid $curSeg and resid $curRes and name sg)
      end
   end if

   !
   ! chi1/chi2
   !
   RAMA
   class chi1_chi2_cysox
   assign 
      (segid $curSeg and resid $curRes and name n)
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name sg)
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name sg)
      (segid $curSeg and resid $curRes and name hg)
   end
end if
end loop database

!
! cysred
!

for $count in id (name ca and resn cys and not store6) loop database
 show sum (x) (byresidue id $count and name hg)
if ($select = 1) then
    show elem (segid) (id $count)
   eval ($curSeg = $result)
    show elem (resid) (id $count)
   eval ($curRes = $result)
   eval ($nextRes = encode(decode ($curRes) + 1))
   eval ($prevRes = encode(decode ($curRes) - 1))

   !
   ! now deal with BB selections -- 
   ! phi not defined for N terminal resids, 
   ! psi not defined for C terminal resids,
   ! omega not defined for C terminal resids
   !
    do (x = x) (segid $curSeg and resid $curRes and (store7 or store8))
   if ($select < 1) then
      RAMA 
      class phi_psi_hbonding
      assign 
         (segid $curSeg and resid $prevRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $nextRes and name n)
      end

      RAMA
      class phi_psi_chi1_cysred_his_asp_asn
      assign
         (segid $curSeg and resid $prevRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $nextRes and name n)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name cb)
         (segid $curSeg and resid $curRes and name sg)
      end
   end if
end if
end loop database


!
! gln
!

for $count in id (name ca and resn gln and not store6) loop database

    show elem (segid) (id $count)
   eval ($curSeg = $result)
    show elem (resid) (id $count)
   eval ($curRes = $result)
   eval ($nextRes = encode(decode ($curRes) + 1))
   eval ($prevRes = encode(decode ($curRes) - 1))

   !
   ! now deal with BB selections -- 
   ! phi not defined for N terminal resids, 
   ! psi not defined for C terminal resids,
   ! omega not defined for C terminal resids
   !
    do (x = x) (segid $curSeg and resid $curRes and (store7 or store8))
   if ($select < 1) then
      RAMA 
      class phi_psi_rest
      assign 
         (segid $curSeg and resid $prevRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $nextRes and name n)
      end

      RAMA
      class phi_psi_chi1_arg_lys_met_gln_glu
      assign
         (segid $curSeg and resid $prevRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $nextRes and name n)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name cb)
         (segid $curSeg and resid $curRes and name cg)
      end
   end if

   !
   ! chi1/chi2
   !
   RAMA
   class chi1_chi2_gln_glu
   assign 
      (segid $curSeg and resid $curRes and name n)
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name cd)
   end

   !
   ! chi2/chi3
   !
   RAMA
   class chi2_chi3_gln
   assign 
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name cd)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name cd)
! is this right?
      (segid $curSeg and resid $curRes and name oe1)
   end

   !
   ! chi1/chi2/chi3
   !
   RAMA
   class chi1_chi2_chi3_gln
   assign
      (segid $curSeg and resid $curRes and name n)
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name cd)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name cd)
! is this right?
      (segid $curSeg and resid $curRes and name oe1)
   end

end loop database



!
! glu
!

for $count in id (name ca and resn glu and not store6) loop database

    show elem (segid) (id $count)
   eval ($curSeg = $result)
    show elem (resid) (id $count)
   eval ($curRes = $result)
   eval ($nextRes = encode(decode ($curRes) + 1))
   eval ($prevRes = encode(decode ($curRes) - 1))

   !
   ! now deal with BB selections -- 
   ! phi not defined for N terminal resids, 
   ! psi not defined for C terminal resids,
   ! omega not defined for C terminal resids
   !
    do (x = x) (segid $curSeg and resid $curRes and (store7 or store8))
   if ($select < 1) then
      RAMA 
      class phi_psi_rest
      assign 
         (segid $curSeg and resid $prevRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $nextRes and name n)
      end

      RAMA
      class phi_psi_chi1_arg_lys_met_gln_glu
      assign
         (segid $curSeg and resid $prevRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $nextRes and name n)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name cb)
         (segid $curSeg and resid $curRes and name cg)
      end
   end if


   !
   ! chi1/chi2
   !
   RAMA
   class chi1_chi2_gln_glu
   assign 
      (segid $curSeg and resid $curRes and name n)
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name cd)
   end

   !
   ! chi2/chi3
   !
   RAMA
   class chi2_chi3_glu
   assign 
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name cd)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name cd)
! is this right?
      (segid $curSeg and resid $curRes and name oe1)
   end

   !
   ! chi1/chi2/chi3
   !
   RAMA
   class chi1_chi2_chi3_glu
   assign 
      (segid $curSeg and resid $curRes and name n)
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name cd)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name cd)
! is this right?
      (segid $curSeg and resid $curRes and name oe1)
   end

end loop database


!
! gly
!

for $count in id (name ca and resn gly and not store6) loop database

    show elem (segid) (id $count)
   eval ($curSeg = $result)
    show elem (resid) (id $count)
   eval ($curRes = $result)
   eval ($nextRes = encode(decode ($curRes) + 1))
   eval ($prevRes = encode(decode ($curRes) - 1))

   !
   ! now deal with BB selections -- 
   ! phi not defined for N terminal resids, 
   ! psi not defined for C terminal resids,
   ! omega not defined for C terminal resids
   !
    do (x = x) (segid $curSeg and resid $curRes and (store7 or store8))
   if ($select < 1) then
      RAMA 
      class phi_psi_gly
      assign 
         (segid $curSeg and resid $prevRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $nextRes and name n)
      end
   end if

end loop database


!
! his
!

for $count in id (name ca and resn his and not store6) loop database

    show elem (segid) (id $count)
   eval ($curSeg = $result)
    show elem (resid) (id $count)
   eval ($curRes = $result)
   eval ($nextRes = encode(decode ($curRes) + 1))
   eval ($prevRes = encode(decode ($curRes) - 1))

   !
   ! now deal with BB selections -- 
   ! phi not defined for N terminal resids, 
   ! psi not defined for C terminal resids,
   ! omega not defined for C terminal resids
   !
    do (x = x) (segid $curSeg and resid $curRes and (store7 or store8))
   if ($select < 1) then
      RAMA 
      class phi_psi_hbonding
      assign 
         (segid $curSeg and resid $prevRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $nextRes and name n)
      end

      RAMA
      class phi_psi_chi1_cysred_his_asp_asn
      assign
         (segid $curSeg and resid $prevRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $nextRes and name n)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name cb)
         (segid $curSeg and resid $curRes and name cg)
      end
   end if


   !
   ! chi1/chi2
   !
   RAMA
   class chi1_chi2_his
   assign 
      (segid $curSeg and resid $curRes and name n)
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
! is this right?
      (segid $curSeg and resid $curRes and name nd1)
   end

end loop database


!
! ile
!

for $count in id (name ca and resn ile and not store6) loop database

    show elem (segid) (id $count)
   eval ($curSeg = $result)
    show elem (resid) (id $count)
   eval ($curRes = $result)
   eval ($nextRes = encode(decode ($curRes) + 1))
   eval ($prevRes = encode(decode ($curRes) - 1))

   !
   ! now deal with BB selections -- 
   ! phi not defined for N terminal resids, 
   ! psi not defined for C terminal resids,
   ! omega not defined for C terminal resids
   !
    do (x = x) (segid $curSeg and resid $curRes and (store7 or store8))
   if ($select < 1) then
      RAMA 
      class phi_psi_val_ile
      assign 
         (segid $curSeg and resid $prevRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $nextRes and name n)
      end

      RAMA
      class phi_psi_chi1_ile
      assign
         (segid $curSeg and resid $prevRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $nextRes and name n)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name cb)
! is this right?
         (segid $curSeg and resid $curRes and name cg1)
      end
   end if


   !
   ! chi1/chi2
   !
   RAMA
   class chi1_chi2_ile
   assign 
      (segid $curSeg and resid $curRes and name n)
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
! is this right?
      (segid $curSeg and resid $curRes and name cg1)
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
! is this right?
      (segid $curSeg and resid $curRes and name cg1)
      (segid $curSeg and resid $curRes and (name cd1 or name cd))
   end

end loop database


!
! leu
!

for $count in id (name ca and resn leu and not store6) loop database

    show elem (segid) (id $count)
   eval ($curSeg = $result)
    show elem (resid) (id $count)
   eval ($curRes = $result)
   eval ($nextRes = encode(decode ($curRes) + 1))
   eval ($prevRes = encode(decode ($curRes) - 1))

   !
   ! now deal with BB selections -- 
   ! phi not defined for N terminal resids, 
   ! psi not defined for C terminal resids,
   ! omega not defined for C terminal resids
   !
    do (x = x) (segid $curSeg and resid $curRes and (store7 or store8))
   if ($select < 1) then
      RAMA 
      class phi_psi_rest
      assign 
         (segid $curSeg and resid $prevRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $nextRes and name n)
      end

      RAMA
      class phi_psi_chi1_leu
      assign 
         (segid $curSeg and resid $prevRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $nextRes and name n)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name cb)
         (segid $curSeg and resid $curRes and name cg)
      end
   end if


   !
   ! chi1/chi2
   !
   RAMA
   class chi1_chi2_leu
   assign 
      (segid $curSeg and resid $curRes and name n)
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
! is this right?
      (segid $curSeg and resid $curRes and name cd1)
   end

end loop database


!
! lys
!

for $count in id (name ca and resn lys and not store6) loop database

    show elem (segid) (id $count)
   eval ($curSeg = $result)
    show elem (resid) (id $count)
   eval ($curRes = $result)
   eval ($nextRes = encode(decode ($curRes) + 1))
   eval ($prevRes = encode(decode ($curRes) - 1))

   !
   ! now deal with BB selections -- 
   ! phi not defined for N terminal resids, 
   ! psi not defined for C terminal resids,
   ! omega not defined for C terminal resids
   !
    do (x = x) (segid $curSeg and resid $curRes and (store7 or store8))
   if ($select < 1) then
      RAMA 
      class phi_psi_rest
      assign 
         (segid $curSeg and resid $prevRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $nextRes and name n)
      end

      RAMA
      class phi_psi_chi1_arg_lys_met_gln_glu
      assign 
         (segid $curSeg and resid $prevRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $nextRes and name n)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name cb)
         (segid $curSeg and resid $curRes and name cg)
      end
   end if


   !
   ! chi1/chi2
   !
   RAMA
   class chi1_chi2_arg_lys_met
   assign 
      (segid $curSeg and resid $curRes and name n)
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name cd)
   end

   !
   ! chi2/chi3
   !
   RAMA
   class chi2_chi3_lys
   assign 
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name cd)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name cd)
      (segid $curSeg and resid $curRes and name ce)
   end

   !
   ! chi1/chi2/chi3
   !
   RAMA
   class chi1_chi2_chi3_lys
   assign 
      (segid $curSeg and resid $curRes and name n)
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name cd)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name cd)
      (segid $curSeg and resid $curRes and name ce)
   end

   !
   ! chi4
   !
   RAMA
   class chi4_lys
   assign
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name cd)
      (segid $curSeg and resid $curRes and name ce)
      (segid $curSeg and resid $curRes and name nz)
   end

end loop database

!
! met
!

for $count in id (name ca and resn met and not store6) loop database

    show elem (segid) (id $count)
   eval ($curSeg = $result)
    show elem (resid) (id $count)
   eval ($curRes = $result)
   eval ($nextRes = encode(decode ($curRes) + 1))
   eval ($prevRes = encode(decode ($curRes) - 1))

   !
   ! now deal with BB selections -- 
   ! phi not defined for N terminal resids, 
   ! psi not defined for C terminal resids,
   ! omega not defined for C terminal resids
   !
    do (x = x) (segid $curSeg and resid $curRes and (store7 or store8))
   if ($select < 1) then
      RAMA 
      class phi_psi_rest
      assign 
         (segid $curSeg and resid $prevRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $nextRes and name n)
      end

      RAMA
      class phi_psi_chi1_arg_lys_met_gln_glu
      assign 
         (segid $curSeg and resid $prevRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $nextRes and name n)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name cb)
         (segid $curSeg and resid $curRes and name cg)
      end
   end if


   !
   ! chi1/chi2
   !
   RAMA
   class chi1_chi2_arg_lys_met 
   assign 
      (segid $curSeg and resid $curRes and name n)
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name sd)
   end

   !
   ! chi2/chi3
   !
   RAMA
   class chi2_chi3_met 
   assign 
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name sd)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name sd)
      (segid $curSeg and resid $curRes and name ce)
   end

   !
   ! chi1/chi2/chi3
   !
   RAMA
   class chi1_chi2_chi3_met
   assign 
      (segid $curSeg and resid $curRes and name n)
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name sd)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name sd)
      (segid $curSeg and resid $curRes and name ce)
   end

end loop database


!
! phe
!

for $count in id (name ca and resn phe and not store6) loop database

    show elem (segid) (id $count)
   eval ($curSeg = $result)
    show elem (resid) (id $count)
   eval ($curRes = $result)
   eval ($nextRes = encode(decode ($curRes) + 1))
   eval ($prevRes = encode(decode ($curRes) - 1))

   !
   ! now deal with BB selections -- 
   ! phi not defined for N terminal resids, 
   ! psi not defined for C terminal resids,
   ! omega not defined for C terminal resids
   !
    do (x = x) (segid $curSeg and resid $curRes and (store7 or store8))
   if ($select < 1) then
      RAMA 
      class phi_psi_rest
      assign 
         (segid $curSeg and resid $prevRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $nextRes and name n)
      end

      RAMA
      class phi_psi_chi1_phe_tyr_trp
      assign 
         (segid $curSeg and resid $prevRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $nextRes and name n)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name cb)
         (segid $curSeg and resid $curRes and name cg)
      end
   end if


   !
   ! chi1/chi2
   !
   RAMA
   class chi1_chi2_phe_tyr_trp
   assign 
      (segid $curSeg and resid $curRes and name n)
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
! is this right?
      (segid $curSeg and resid $curRes and name cd1)
   end

end loop database



!
! pro
!

for $count in id (name ca and resn pro and not store6 and not store5) loop database

    show elem (segid) (id $count)
   eval ($curSeg = $result)
    show elem (resid) (id $count)
   eval ($curRes = $result)
   eval ($nextRes = encode(decode ($curRes) + 1))
   eval ($prevRes = encode(decode ($curRes) - 1))

   !
   ! now deal with BB selections -- 
   ! phi not defined for N terminal resids, 
   ! psi not defined for C terminal resids,
   ! omega not defined for C terminal resids
   !
    do (x = x) (segid $curSeg and resid $curRes and (store7 or store8))
   if ($select < 1) then
      RAMA 
      class phi_psi_pro
      assign 
         (segid $curSeg and resid $prevRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $nextRes and name n)
      end

      RAMA
      class phi_psi_chi1_pro
      assign 
         (segid $curSeg and resid $prevRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $nextRes and name n)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name cb)
         (segid $curSeg and resid $curRes and name cg)
      end
   end if


end loop database


!
! ser
!

for $count in id (name ca and resn ser and not store6) loop database

    show elem (segid) (id $count)
   eval ($curSeg = $result)
    show elem (resid) (id $count)
   eval ($curRes = $result)
   eval ($nextRes = encode(decode ($curRes) + 1))
   eval ($prevRes = encode(decode ($curRes) - 1))

   !
   ! now deal with BB selections -- 
   ! phi not defined for N terminal resids, 
   ! psi not defined for C terminal resids,
   ! omega not defined for C terminal resids
   !
    do (x = x) (segid $curSeg and resid $curRes and (store7 or store8))
   if ($select < 1) then
      RAMA 
      class phi_psi_hbonding
      assign 
         (segid $curSeg and resid $prevRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $nextRes and name n)
      end

      RAMA
      class phi_psi_chi1_ser
      assign 
         (segid $curSeg and resid $prevRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $nextRes and name n)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name cb)
! is this the right name?
         (segid $curSeg and resid $curRes and name og)
      end
   end if

end loop database


!
! thr
!

for $count in id (name ca and resn thr and not store6) loop database

    show elem (segid) (id $count)
   eval ($curSeg = $result)
    show elem (resid) (id $count)
   eval ($curRes = $result)
   eval ($nextRes = encode(decode ($curRes) + 1))
   eval ($prevRes = encode(decode ($curRes) - 1))

   !
   ! now deal with BB selections -- 
   ! phi not defined for N terminal resids, 
   ! psi not defined for C terminal resids,
   ! omega not defined for C terminal resids
   !
    do (x = x) (segid $curSeg and resid $curRes and (store7 or store8))
   if ($select < 1) then
      RAMA 
      class phi_psi_hbonding
      assign 
         (segid $curSeg and resid $prevRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $nextRes and name n)
      end

      RAMA
      class phi_psi_chi1_thr
      assign
         (segid $curSeg and resid $prevRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $nextRes and name n)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name cb)
! is this the right name?
         (segid $curSeg and resid $curRes and name og1)
      end
   end if

end loop database



!
! trp
!

for $count in id (name ca and resn trp and not store6) loop database

    show elem (segid) (id $count)
   eval ($curSeg = $result)
    show elem (resid) (id $count)
   eval ($curRes = $result)
   eval ($nextRes = encode(decode ($curRes) + 1))
   eval ($prevRes = encode(decode ($curRes) - 1))

   !
   ! now deal with BB selections -- 
   ! phi not defined for N terminal resids, 
   ! psi not defined for C terminal resids,
   ! omega not defined for C terminal resids
   !
    do (x = x) (segid $curSeg and resid $curRes and (store7 or store8))
   if ($select < 1) then
      RAMA 
      class phi_psi_rest
      assign 
         (segid $curSeg and resid $prevRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $nextRes and name n)
      end

      RAMA
      class phi_psi_chi1_phe_tyr_trp
      assign 
         (segid $curSeg and resid $prevRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $nextRes and name n)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name cb)
         (segid $curSeg and resid $curRes and name cg)
      end
   end if


   !
   ! chi1/chi2
   !
   RAMA
   class chi1_chi2_trp
   assign 
      (segid $curSeg and resid $curRes and name n)
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
! is this right?
      (segid $curSeg and resid $curRes and name cd1)
   end

end loop database



!
! tyr
!

for $count in id (name ca and resn tyr and not store6) loop database

    show elem (segid) (id $count)
   eval ($curSeg = $result)
    show elem (resid) (id $count)
   eval ($curRes = $result)
   eval ($nextRes = encode(decode ($curRes) + 1))
   eval ($prevRes = encode(decode ($curRes) - 1))

   !
   ! now deal with BB selections -- 
   ! phi not defined for N terminal resids, 
   ! psi not defined for C terminal resids,
   ! omega not defined for C terminal resids
   !
    do (x = x) (segid $curSeg and resid $curRes and (store7 or store8))
   if ($select < 1) then
      RAMA 
      class phi_psi_rest
      assign 
         (segid $curSeg and resid $prevRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $nextRes and name n)
      end

      RAMA
      class phi_psi_chi1_phe_tyr_trp
      assign
         (segid $curSeg and resid $prevRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $nextRes and name n)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name cb)
         (segid $curSeg and resid $curRes and name cg)
      end
   end if


   !
   ! chi1/chi2
   !
   RAMA
   class chi1_chi2_phe_tyr_trp
   assign 
      (segid $curSeg and resid $curRes and name n)
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
      (segid $curSeg and resid $curRes and name ca)
      (segid $curSeg and resid $curRes and name cb)
      (segid $curSeg and resid $curRes and name cg)
! is this right?
      (segid $curSeg and resid $curRes and name cd1)
   end

end loop database



!
! val
!

for $count in id (name ca and resn val and not store6) loop database

    show elem (segid) (id $count)
   eval ($curSeg = $result)
    show elem (resid) (id $count)
   eval ($curRes = $result)
   eval ($nextRes = encode(decode ($curRes) + 1))
   eval ($prevRes = encode(decode ($curRes) - 1))

   !
   ! now deal with BB selections -- 
   ! phi not defined for N terminal resids, 
   ! psi not defined for C terminal resids,
   ! omega not defined for C terminal resids
   !
    do (x = x) (segid $curSeg and resid $curRes and (store7 or store8))
   if ($select < 1) then
      RAMA 
      class phi_psi_val_ile
      assign 
         (segid $curSeg and resid $prevRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $nextRes and name n)
      end

      RAMA
      class phi_psi_chi1_val
      assign 
         (segid $curSeg and resid $prevRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $nextRes and name n)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name cb)
! is this right?
         (segid $curSeg and resid $curRes and name cg1)
      end
   end if

end loop database

!
! Xpr--residues that are followed by a proline
! stored in store6, at the top of this file
!

for $count in id (name ca and store6) loop database

    show elem (segid) (id $count)
   eval ($curSeg = $result)
    show elem (resid) (id $count)
   eval ($curRes = $result)
   eval ($nextRes = encode(decode ($curRes) + 1))
   eval ($prevRes = encode(decode ($curRes) - 1))

   !
   ! now deal with BB selections -- 
   ! phi not defined for N terminal resids, 
   ! psi not defined for C terminal resids,
   ! omega not defined for C terminal resids
   !
    do (x = x) (segid $curSeg and resid $curRes and (store7 or store8))
   if ($select < 1) then
      RAMA 
      class phi_psi_xpr
      assign 
         (segid $curSeg and resid $prevRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $nextRes and name n)
      end

      RAMA
      class phi_psi_chi1_xpr
      assign 
         (segid $curSeg and resid $prevRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name c)
         (segid $curSeg and resid $nextRes and name n)
         (segid $curSeg and resid $curRes and name n)
         (segid $curSeg and resid $curRes and name ca)
         (segid $curSeg and resid $curRes and name cb)
! this should allow any of the chi1 selections
         (segid $curSeg and resid $curRes and 
            (name cg1 or name cg or name sg or name og or name og1))
      end
   end if

end loop database

set message on echo on end