!
! Protons_setup.tbl
!
! Setup for proton chemical shift refinement 
! 
! starts by doing selections for electric field stuff,
! then magnetic anisotropy,
! then ring currents,
! and finally random coil shifts.
!
! Random coil shifts are from Williamson's file random.dat
!
! by John Kuszewski Dec 1994
!

set message off echo off end

checkversion 1.2

!
! select all the alpha and amide protons, the amides alone,
! the carbons, the nitrogens, and the oxygens
!

prot

     alphasandamides (name ha or name hn)

     amides (name hn)

     carbons (name c)

     nitrogens (name n)

     oxygens (name o)

end

!
! set up the CaC=O bonds from the backbone
!

for $count in id (name ca) loop anis
     identify (store1) ((byresidue id $count) and (name ca))
     if ($select=1) then
        identify (store2) ((byresidue id $count) and (name c))
        if ($select=1) then
           identify (store3) ((byresidue id $count) and (name o))
              if ($select=1) then
                 prot anis (store1) (store2) (store3) CO notCOOH BB end
              end if
        end if
     end if
end loop anis

!
! set up the backbone C-N bonds
! (apparently, sidechain C-N bonds are ignored)
! produces an error on the last time through
!
!
! need a loop that goes thru all residues except the first one,
! getting the current residue's O and C atoms and the next residue's
! N atom into store1, 2, and 3, respectively.
!

for $count in id (name ca) loop anis
    show elem (segid) (id $count)
    eval ($curseg = $result)
    show elem (resid) (id $count)
    eval ($curres = $result)
    eval ($nextres = decode($curres) + 1)
    do (store9 = 1) (all)
   show sum (store9)((resid $nextres) and (segid $curseg) and (name n))
    if ($result # 0) then
        identify (store1) ((byresidue id $count) and (name o))
        identify (store2) ((byresidue id $count) and (name c))
        identify (store3) ((resid $nextres) and (segid $curseg) 
                                                   and (name n))
        prot anis (store1) (store2) (store3) CN notCOOH BB end
    end if
end loop anis

!
! set up the CC=O bonds for the sidechains
!

for $count in id (name ca and resn asp) loop anis
     identify (store1) ((byresidue id $count) and (name cb))
     identify (store2) ((byresidue id $count) and (name cg))
     identify (store3) ((byresidue id $count) and (name od1))
     identify (store4) ((byresidue id $count) and (name od2))
     prot anis (store1) (store2) (store3) CO COOH SC end
     prot anis (store1) (store2) (store4) CO COOH SC end
end loop anis

for $count in id (name ca and resn glu) loop anis
     identify (store1) ((byresidue id $count) and (name cg))
     identify (store2) ((byresidue id $count) and (name cd))
     identify (store3) ((byresidue id $count) and (name oe1))
     identify (store4) ((byresidue id $count) and (name oe2))
     prot anis (store1) (store2) (store3) CO COOH SC end
     prot anis (store1) (store2) (store4) CO COOH SC end
end loop anis

for $count in id (name ca and resn asn) loop anis
     identify (store1) ((byresidue id $count) and (name cb))
     identify (store2) ((byresidue id $count) and (name cg))
     identify (store3) ((byresidue id $count) and (name od1))
     prot anis (store1) (store2) (store3) CO notCOOH SC end
end loop anis

for $count in id (name ca and resn gln) loop anis
     identify (store1) ((byresidue id $count) and (name cg))
     identify (store2) ((byresidue id $count) and (name cd))
     identify (store3) ((byresidue id $count) and (name oe1))
     prot anis (store1) (store2) (store3) CO notCOOH SC end
end loop anis

!
! handle the rings
!

for $count in id (name ca and resn phe) loop ring
     identify (store1) ((byresidue id $count) and (name cg))
     identify (store2) ((byresidue id $count) and (name cd1))
     identify (store3) ((byresidue id $count) and (name ce1))
     identify (store4) ((byresidue id $count) and (name cz))
     identify (store5) ((byresidue id $count) and (name ce2))
     identify (store6) ((byresidue id $count) and (name cd2))
     prot ring PHE (store1) (store2) (store3) (store4) (store5) (store6) end
end loop ring

for $count in id (name ca and resn tyr) loop ring
     identify (store1) ((byresidue id $count) and (name cg))
     identify (store2) ((byresidue id $count) and (name cd1))
     identify (store3) ((byresidue id $count) and (name ce1))
     identify (store4) ((byresidue id $count) and (name cz))
     identify (store5) ((byresidue id $count) and (name ce2))
     identify (store6) ((byresidue id $count) and (name cd2))
     prot ring TYR (store1) (store2) (store3) (store4) (store5) (store6) end
end loop ring

for $count in id (name ca and resn trp) loop ring
     identify (store1) ((byresidue id $count) and (name ce2))
     identify (store2) ((byresidue id $count) and (name cd2))
     identify (store3) ((byresidue id $count) and (name ce3))
     identify (store4) ((byresidue id $count) and (name cz3))
     identify (store5) ((byresidue id $count) and (name ch2))
     identify (store6) ((byresidue id $count) and (name cz2))
     prot ring TRP6 (store1) (store2) (store3) (store4) (store5) (store6) end
end loop ring

for $count in id (name ca and resn his) loop ring
     identify (store1) ((byresidue id $count) and (name cg))
     identify (store2) ((byresidue id $count) and (name cd2))
     identify (store3) ((byresidue id $count) and (name ne2))
     identify (store4) ((byresidue id $count) and (name ce1))
     identify (store5) ((byresidue id $count) and (name nd1))
     prot ring HIS (store1) (store2) (store3) (store4) (store5) end
end loop ring

for $count in id (name ca and resn trp) loop ring
     identify (store1) ((byresidue id $count) and (name cg))
     identify (store2) ((byresidue id $count) and (name cd1))
     identify (store3) ((byresidue id $count) and (name ne1))
     identify (store4) ((byresidue id $count) and (name ce2))
     identify (store5) ((byresidue id $count) and (name cd2))
     prot ring TRP5 (store1) (store2) (store3) (store4) (store5) end
end loop ring

!
! this holds the random coil proton chemical shifts
! from the file random.dat provided with Williamson's
! proton shift program, with his secondary corrections
! of -0.65 ppm to each Ha, -0.20 ppm to each HN, +0.22 ppm
! to each gly Ha*, and a change to 4.45 ppm for each 
! Ha of YFWH.  Original values with the noted changes 
! are commented out.
!

prot

rcoil (hydrogen) 0.00

!rcoil (resn GLY and name HN) 8.39 - 0.20
!rcoil (resn GLY and name HA1) 3.97 - 0.65 + 0.22
!rcoil (resn GLY and name HA2) 3.97 - 0.65 + 0.22

rcoil (resn GLY and name HN) 8.19
rcoil (resn GLY and name HA1) 3.54
rcoil (resn GLY and name HA2) 3.54

!rcoil (resn ALA and name HN) 8.25 - 0.20
!rcoil (resn ALA and name HA) 4.35 - 0.65

rcoil (resn ALA and name HN) 8.05
rcoil (resn ALA and name HA) 3.70
rcoil (resn ALA and name HB1) 1.40
rcoil (resn ALA and name HB2) 1.40
rcoil (resn ALA and name HB3) 1.40

!rcoil (resn VAL and name HN) 8.44 - 0.20
!rcoil (resn VAL and name HA) 4.18 - 0.65

rcoil (resn VAL and name HN) 8.24
rcoil (resn VAL and name HA) 3.53
rcoil (resn VAL and name HB) 2.13
rcoil (resn VAL and name HG11) 0.96
rcoil (resn VAL and name HG12) 0.96
rcoil (resn VAL and name HG13) 0.96
rcoil (resn VAL and name HG21) 0.96
rcoil (resn VAL and name HG22) 0.96
rcoil (resn VAL and name HG23) 0.96

!rcoil (resn ILE and name HN) 8.20 - 0.20
!rcoil (resn ILE and name HA) 4.22 - 0.65

rcoil (resn ILE and name HN) 8.00
rcoil (resn ILE and name HA) 3.57
rcoil (resn ILE and name HB) 1.89
rcoil (resn ILE and name HG21) 0.94
rcoil (resn ILE and name HG22) 0.94
rcoil (resn ILE and name HG23) 0.94
rcoil (resn ILE and name HG11) 1.30
rcoil (resn ILE and name HG12) 1.30
rcoil (resn ILE and name HD11) 0.89
rcoil (resn ILE and name HD12) 0.89
rcoil (resn ILE and name HD13) 0.89

!rcoil (resn LEU and name HN) 8.42 - 0.20
!rcoil (resn LEU and name HA) 4.39 - 0.65

rcoil (resn LEU and name HN) 8.02
rcoil (resn LEU and name HA) 3.74
rcoil (resn LEU and name HB1) 1.65
rcoil (resn LEU and name HB2) 1.65
rcoil (resn LEU and name HG) 1.65
rcoil (resn LEU and name HD11) 0.92
rcoil (resn LEU and name HD12) 0.92
rcoil (resn LEU and name HD13) 0.92
rcoil (resn LEU and name HD21) 0.92
rcoil (resn LEU and name HD22) 0.92
rcoil (resn LEU and name HD23) 0.92

!rcoil (resn SER and name HN) 8.38 - 0.20
!rcoil (resn SER and name HA) 4.50 - 0.65

rcoil (resn SER and name HN) 8.18
rcoil (resn SER and name HA) 3.85
rcoil (resn SER and name HB1) 3.89
rcoil (resn SER and name HB2) 3.89
! no HG?

!rcoil (resn THR and name HN) 8.24 - 0.20
!rcoil (resn THR and name HA) 4.35 - 0.65

rcoil (resn THR and name HN) 8.04
rcoil (resn THR and name HA) 3.70
rcoil (resn THR and name HB) 4.22
rcoil (resn THR and name HG21) 1.23
rcoil (resn THR and name HG22) 1.23
rcoil (resn THR and name HG23) 1.23

!rcoil (resn ASP and name HN) 8.41 - 0.20
!rcoil (resn ASP and name HA) 4.77 - 0.65

rcoil (resn ASP and name HN) 8.21
rcoil (resn ASP and name HA) 4.12
rcoil (resn ASP and name HB1) 2.80
rcoil (resn ASP and name HB2) 2.80

!rcoil (resn GLU and name HN) 8.37 - 0.20
!rcoil (resn GLU and name HA) 4.30 - 0.65

rcoil (resn GLU and name HN) 8.17
rcoil (resn GLU and name HA) 3.65
rcoil (resn GLU and name HB1) 2.03
rcoil (resn GLU and name HB2) 2.03
rcoil (resn GLU and name HG1) 2.30
rcoil (resn GLU and name HG2) 2.30

!rcoil (resn LYS and name HN) 8.41 - 0.20
!rcoil (resn LYS and name HA) 4.36 - 0.65

rcoil (resn LYS and name HN) 8.21
rcoil (resn LYS and name HA) 3.71
rcoil (resn LYS and name HB1) 1.81
rcoil (resn LYS and name HB2) 1.81
rcoil (resn LYS and name HG1) 1.47
rcoil (resn LYS and name HG2) 1.47
rcoil (resn LYS and name HD1) 1.71
rcoil (resn LYS and name HD2) 1.71
rcoil (resn LYS and name HE1) 3.02
rcoil (resn LYS and name HE2) 3.02
! no HZ?

!rcoil (resn ARG and name HN) 8.27 - 0.20
!rcoil (resn ARG and name HA) 4.40 - 0.65

rcoil (resn ARG and name HN) 8.07
rcoil (resn ARG and name HA) 3.75
rcoil (resn ARG and name HB1) 1.85
rcoil (resn ARG and name HB2) 1.85
rcoil (resn ARG and name HG1) 1.72
rcoil (resn ARG and name HG2) 1.72
rcoil (resn ARG and name HD1) 3.31
rcoil (resn ARG and name HD2) 3.31
! no HE, HZ?

!rcoil (resn ASN and name HN) 8.75 - 0.20
!rcoil (resn ASN and name HA) 4.76 - 0.65

rcoil (resn ASN and name HN) 8.55
rcoil (resn ASN and name HA) 4.11
rcoil (resn ASN and name HB1) 2.80
rcoil (resn ASN and name HB2) 2.80
! no HD?

!rcoil (resn GLN and name HN) 8.41 - 0.20
!rcoil (resn GLN and name HA) 4.37 - 0.65

rcoil (resn GLN and name HN) 8.21
rcoil (resn GLN and name HA) 3.72
rcoil (resn GLN and name HB1) 2.08
rcoil (resn GLN and name HB2) 2.08
rcoil (resn GLN and name HG1) 2.38
rcoil (resn GLN and name HG2) 2.38
! no HE?

!rcoil (resn MET and name HN) 8.42 - 0.20
!rcoil (resn MET and name HA) 4.51 - 0.65

rcoil (resn MET and name HN) 8.22
rcoil (resn MET and name HA) 3.86
rcoil (resn MET and name HB1) 2.08
rcoil (resn MET and name HB2) 2.08
rcoil (resn MET and name HG1) 2.63
rcoil (resn MET and name HG2) 2.63
rcoil (resn MET and name HE1) 2.13
rcoil (resn MET and name HE2) 2.13
rcoil (resn MET and name HE3) 2.13

!rcoil (resn CYS and name HN) 8.31 - 0.20
!rcoil (resn CYS and name HA) 4.69 - 0.65

rcoil (resn CYS and name HN) 8.11
rcoil (resn CYS and name HA) 4.04
rcoil (resn CYS and name HB1) 3.16
rcoil (resn CYS and name HB2) 3.16
! no HG?

!rcoil (resn TRP and name HN) 8.09 - 0.20
!rcoil (resn TRP and name HA) 4.70 - 0.65 4.45

rcoil (resn TRP and name HN) 7.89
rcoil (resn TRP and name HA) 4.45
rcoil (resn TRP and name HB1) 3.26
rcoil (resn TRP and name HB2) 3.26
rcoil (resn TRP and name HE1) 9.99
rcoil (resn TRP and name HD1) 7.24
rcoil (resn TRP and name HE3) 7.65
rcoil (resn TRP and name HZ3) 7.17
rcoil (resn TRP and name HH2) 7.24
rcoil (resn TRP and name HZ2) 7.50

!rcoil (resn PHE and name HN) 8.23 - 0.20
!rcoil (resn PHE and name HA) 4.66 - 0.65 4.45

rcoil (resn PHE and name HN) 8.03
rcoil (resn PHE and name HA) 4.45
rcoil (resn PHE and name HB1) 3.11
rcoil (resn PHE and name HB2) 3.11
rcoil (resn PHE and name HD1) 7.34
rcoil (resn PHE and name HD2) 7.34
rcoil (resn PHE and name HE1) 7.34
rcoil (resn PHE and name HE2) 7.34
rcoil (resn PHE and name HZ) 7.34

!rcoil (resn TYR and name HN) 8.18 - 0.20
!rcoil (resn TYR and name HA) 4.60 - 0.65 4.45

rcoil (resn TYR and name HN) 7.98
rcoil (resn TYR and name HA) 4.45
rcoil (resn TYR and name HB1) 3.02
rcoil (resn TYR and name HB2) 3.02
rcoil (resn TYR and name HD1) 7.15
rcoil (resn TYR and name HD2) 7.15
rcoil (resn TYR and name HE1) 6.86
rcoil (resn TYR and name HE2) 6.86
! no HH?

!rcoil (resn HIS and name HN) 8.42 - 0.20
!rcoil (resn HIS and name HA) 4.63 - 0.65 4.45

rcoil (resn HIS and name HN) 8.22
rcoil (resn HIS and name HA) 4.45
rcoil (resn HIS and name HB1) 3.23
rcoil (resn HIS and name HB2) 3.23
rcoil (resn HIS and name HE1) 8.12
rcoil (resn HIS and name HD2) 7.14
! changed prev line to HD2 from HD1 (HD1 is exchangable) JK 1/6/95
! no HD2?

!rcoil (resn PRO and name HA) 4.47 - 0.65

rcoil (resn PRO and name HA) 3.82
rcoil (resn PRO and name HB1) 2.16
rcoil (resn PRO and name HB2) 2.16
rcoil (resn PRO and name HG1) 2.03
rcoil (resn PRO and name HG2) 2.03
rcoil (resn PRO and name HD1) 3.65
rcoil (resn PRO and name HD2) 3.65

end
set message on echo on end