Difference between revisions of "User:Remig/plico/plicoCommonNT"

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(Faster A-B conversion)
(Add support for fold_trna.spt)
Line 3: Line 3:
 
Copy and paste the following into a text editor and save in your scripts folder as plicoNTcommon.spt.
 
Copy and paste the following into a text editor and save in your scripts folder as plicoNTcommon.spt.
 
<pre>#  plicoNTcommon - Jmol script by Ron Mignery
 
<pre>#  plicoNTcommon - Jmol script by Ron Mignery
−
#  v1.7 beta    11/18/2014 -faster A-B conversion
+
#  v1.8 beta    7/13/2015 -suport fold_trna.spt
 
#
 
#
 
#  Routines and values common to Plico suite scripts that work with nucleotides
 
#  Routines and values common to Plico suite scripts that work with nucleotides
 
#  Must be present in the same directory as other Plico scripts that use them
 
#  Must be present in the same directory as other Plico scripts that use them
−
kNTcommon = 4
+
kNTcommon = 5
 
kC5O5PO3B = -71.0
 
kC5O5PO3B = -71.0
 
kO5PO3C3B = -107.0
 
kO5PO3C3B = -107.0
Line 57: Line 57:
  
 
         var selsave = {selected}
 
         var selsave = {selected}
−
         set_distance_atoms(aC5, aO3p, 3.1)
+
         set_distance_atoms(aP3p, aC5, 3.1)
−
 
 
 
         select aO5
 
         select aO5
 
         var dist = distance(aO3p, aO5)
 
         var dist = distance(aO3p, aO5)
Line 88: Line 87:
 
         var ms = minimizationSilent
 
         var ms = minimizationSilent
 
         set minimizationSilent true
 
         set minimizationSilent true
−
         minimize select {(connected(aP) or aP) and not aO3p}
+
         minimize {(connected(aP) or aP) and not aO3p}
 
         set minimizationSilent ms
 
         set minimizationSilent ms
 
         select selsave
 
         select selsave
Line 109: Line 108:
 
     if ((aO3p.size > 0)and (aC4.size > 0)) {
 
     if ((aO3p.size > 0)and (aC4.size > 0)) {
 
         var selsave = {selected}
 
         var selsave = {selected}
 +
        select {aP or aOP1 or aOP2}
 +
        set_angle_atoms(aC3p, aO3p, aP, 109.0)
  
 
         # Twice through
 
         # Twice through
Line 176: Line 177:
 
             aOP1.xyz = get_tet_idx(aO5.atomIndex, aP.atomIndex, aO3p.atomIndex, 1.73)
 
             aOP1.xyz = get_tet_idx(aO5.atomIndex, aP.atomIndex, aO3p.atomIndex, 1.73)
 
             if (force) {
 
             if (force) {
 +
                var savemt = useMinimizationThread
 +
                set useMinimizationThread false
 
                 var ms = minimizationSilent
 
                 var ms = minimizationSilent
 
                 set minimizationSilent true
 
                 set minimizationSilent true
 
                 minimize select {(connected(aP) or aP) and not aO3p}
 
                 minimize select {(connected(aP) or aP) and not aO3p}
 +
                set useMinimizationThread savemt
 
                 set minimizationSilent ms
 
                 set minimizationSilent ms
 
             }
 
             }
Line 186: Line 190:
 
}
 
}
  
 +
function fix_p_res_range(res5, res3, iChain, force) {
 +
    for (var i = res5; i <= res3; i++) {
 +
        fix_p_res(i, iChain, force)
 +
    }
 +
}
 +
 +
function fix_all_nt_collisions( iChain) {
 +
    var selsave = {selected}
 +
    var savemt = useMinimizationThread
 +
    set useMinimizationThread false
 +
    var ms = minimizationSilent
 +
    set minimizationSilent true
 +
    chset = count_collisions(true)
 +
    for (var i = 1; i <= chset.size; i++) {
 +
        c = chset[i]
 +
        cset = (within(kCtolerance, c) and  not c
 +
            and not connected(chset[i]))
 +
        rset = [{resno=@{c.resno}}]
 +
        for (var j = 1; j <= cset.size; j++) {
 +
            rset += {resno=@{cset[j].resno}}
 +
        }
 +
       
 +
        if ({c and cset and not base}.size > 0) {
 +
            select {@{rset} and base}
 +
            minimize {selected}
 +
        }
 +
        else if (c.atomname[1][2] == "OP") {
 +
            fix_p_res(chset[i].resno, iChain, true)
 +
        }
 +
        else {
 +
            select {@{rset}}
 +
            minimize {selected}
 +
        }
 +
    }
 +
    measure off
 +
    set useMinimizationThread savemt
 +
    set minimizationSilent ms
 +
    select selsave
 +
}
 +
 +
# The following functions position one nt relative to another:
 +
# Common positioning functions:
 
function get_rotors_res(res) {
 
function get_rotors_res(res) {
 
     var f = (_frameID/1000000)
 
     var f = (_frameID/1000000)
Line 245: Line 291:
 
}
 
}
  
 +
# ri=moved rj=fixed
 +
function position_nt_by_vs(ri, rj, ares, vs, iChain, jChain) {
 +
    var f = (_frameID/1000000)
 +
    var m = (_frameID%1000000)
 +
    if (ri > rj) {
 +
        var as = gen_as(ri, rj, iChain, jChain)
 +
        select {(resno < ares) and (resno >= ri)
 +
            and (chain=iChain) and (file=f) and (model=m)}
 +
    }
 +
    else {
 +
        var as = gen_as(rj, ri, jChain, iChain)
 +
        select {(resno > ares) and (resno <= ri)
 +
            and (chain=iChain) and (file=f) and (model=m)}
 +
    }
 +
    move_it(as, vs)
 +
}
 +
               
 
# Moved object must be selected, fixed object not
 
# Moved object must be selected, fixed object not
−
# as[6] = fixed[1-3] moved[4-6]
+
# as[6] = fixed[1-3] moved[4-6] chis [7-8]
 
# vs[6] = [distance(as[3-4]), angle(as[2-4]),
 
# vs[6] = [distance(as[3-4]), angle(as[2-4]),
 
#  dihedral(as[1-4]), angle(as[5-3], dihedral(as[6-3],
 
#  dihedral(as[1-4]), angle(as[5-3], dihedral(as[6-3],
Line 267: Line 330:
 
     if (vs.size > 6) {
 
     if (vs.size > 6) {
 
         var sel = {selected}
 
         var sel = {selected}
−
         select {(resno=@{as[1].resno}) and base}
+
         select {(resno=@{as[4].resno}) and base}
−
         set_dihedral_atoms(as[1], as[2], as[3], as[7], vs[7])
+
         set_dihedral_atoms(as[6], as[5], as[4], as[8], vs[8])
−
#echo chi *** = t
 
−
#throw context t       
 
−
        if (vs.size > 7) {
 
−
            select {(resno=@{as[4].resno}) and base}
 
−
            set_dihedral_atoms(as[6], as[5], as[4], as[8], vs[8])
 
−
        }
 
−
        select sel
 
 
     }
 
     }
 
}
 
}
  
−
function gen_as(res5, res3, iChain, jChain) {
+
# ri=moved rj=fixed
 +
function gen_as(ri, rj, iChain, jChain) {
 
     var as = array()
 
     var as = array()
−
     as[1] = get_atom_rcn(res3, jChain, "C4\'")
+
     as[1] = get_atom_rcn(rj, jChain, "C4\'")
−
     as[2] = get_atom_rcn(res3, jChain, "C1\'")
+
     as[2] = get_atom_rcn(rj, jChain, "C1\'")
 
     as[3] = connected(as[2]) and {element="N"}
 
     as[3] = connected(as[2]) and {element="N"}
−
     as[5] = get_atom_rcn(res5, iChain, "C1\'")
+
     as[5] = get_atom_rcn(ri, iChain, "C1\'")
−
     as[6] = get_atom_rcn(res5, iChain, "C4\'")
+
     as[6] = get_atom_rcn(ri, iChain, "C4\'")
 
     as[4] = connected(as[5]) and {element="N"}
 
     as[4] = connected(as[5]) and {element="N"}
 
      
 
      
−
     var isR  = ((as[1] and {purine}).size > 0)
+
     as[7] = get_atom_rcn(rj, jChain,
−
    var a6or8 = (isR ? "C8" : "C6")
+
        (((as[1] and {purine}).size > 0) ? "C8" : "C6"))
−
    as[7] = get_atom_rcn(res3, jChain, a6or8)
+
     as[8] = get_atom_rcn(ri, iChain,
−
    a6or8 = (isR ? "C6" : "C8") # rev
+
        (((as[6] and {purine}).size > 0) ? "C8" : "C6"))
−
     as[8] = get_atom_rcn(res5, iChain, a6or8)
 
−
    as[9] = get_atom_rcn(res3, jChain, (isR ? "N1" : "N3"))
 
−
    as[10] = get_atom_rcn(res5, iChain, (isR ? "N3" : "N1"))
 
 
     return as
 
     return as
 
}
 
}
  
−
# Pair res5 on res3 moving res <= res3
+
# Specific positioning functions:
 +
# Pair res5 on res3 moving res5 <= res3
 
function pair_it_res(res5, res3, ares, iChain, jChain) {
 
function pair_it_res(res5, res3, ares, iChain, jChain) {
 
     var f = (_frameID/1000000)
 
     var f = (_frameID/1000000)
Line 310: Line 365:
 
     vs[4] = 125.32                  # angle res5 C1 N9or1 and res3 N9or1       
 
     vs[4] = 125.32                  # angle res5 C1 N9or1 and res3 N9or1       
 
     vs[5] = (isA ? 160.0 : -141.46) # dihedral res5 C4 N9or1 C1 and res3 N9or1
 
     vs[5] = (isA ? 160.0 : -141.46) # dihedral res5 C4 N9or1 C1 and res3 N9or1
−
     vs[6] = (isA ? -5.0 : -17.87)     # dihedral res5 N9or1 C1 and res3 N9or1 C1
+
     vs[6] = (isA ? -5.0 : -17.87)   # dihedral res5 N9or1 C1 and res3 N9or1 C1
−
     vs[7] = (isA ? -20.0 : 38)     # dihedral chi
+
     vs[7] = (isA ? -20.0 : 38)     # dihedral chi res3
−
     vs[8] = (isA ? -20.0 : 38)     # dihedral chi
+
     vs[8] = (isA ? -20.0 : 38)     # dihedral chi res5
 
     if (ares < 0) {
 
     if (ares < 0) {
 
         select ((resno=res5) and (chain=iChain) and (file=f) and (model=m))
 
         select ((resno=res5) and (chain=iChain) and (file=f) and (model=m))
 
     }
 
     }
−
     else {
+
     else if (ares > 0) {
 
         select ((resno <= ares) and (chain=iChain) and (file=f) and (model=m))
 
         select ((resno <= ares) and (chain=iChain) and (file=f) and (model=m))
 
     }
 
     }
 
     move_it(as, vs)
 
     move_it(as, vs)
−
      
+
     fix_p_res(res5, iChain, true)
−
    # Flatten the pair
+
     fix_p_res(res5+1, iChain, true)
−
    #var isR  = ((as[1] and {purine}).size > 0)
 
−
    #set_angle_atoms((isR ? as[3] : as[7]), as[9], as[10], 180)
 
−
     #set_angle_atoms(as[9], as[10], (isR ? as[8] : as[4]), 180)
 
 
}
 
}
  
Line 370: Line 422:
 
}
 
}
  
−
# Flatstack res3 on res5 moving just res5
+
# Flatstack res5 on res3 moving just res5
−
function single_flatstack_res3_on_res5(res5, res3, iChain, jChain) {
+
function single_flatstack_res5_on_res3(res3, res5, iChain, jChain) {
 
     var f = (_frameID/1000000)
 
     var f = (_frameID/1000000)
 
     var m = (_frameID%1000000)
 
     var m = (_frameID%1000000)
Line 428: Line 480:
 
      
 
      
 
     # Rotate ribose to hbond O2' to res5+1 N7
 
     # Rotate ribose to hbond O2' to res5+1 N7
−
     select {(resno = res5) and not base}
+
     select {(resno = res5) and not base
 +
        and (chain=iChain) and (file=f) and (model=m)}
 
     var aC1 = get_atom_rcn( res5, iChain, "C1\'")
 
     var aC1 = get_atom_rcn( res5, iChain, "C1\'")
 
     var aN9 = get_atom_rcn( res5, iChain, "N9")
 
     var aN9 = get_atom_rcn( res5, iChain, "N9")
Line 435: Line 488:
 
     # Fix up     
 
     # Fix up     
 
     select {((resno=res5) or (resno=@{res5+1}))
 
     select {((resno=res5) or (resno=@{res5+1}))
−
    and (chain=iChain) and (file=f) and (model=m)}
+
        and (chain=iChain) and (file=f) and (model=m)}
 
     minimize {selected}
 
     minimize {selected}
 
     fix_p_res(res5+1, iChain, true)
 
     fix_p_res(res5+1, iChain, true)
Line 461: Line 514:
  
 
     # Rotate 5 end out of the way
 
     # Rotate 5 end out of the way
−
     select {resno < res5}
+
     select {(resno < res5) and (chain=iChain) and (file=f) and (model=m)}
 
     var aC4 = get_atom_rcn( res5, iChain, "C4\'")
 
     var aC4 = get_atom_rcn( res5, iChain, "C4\'")
 
     var aC5 = get_atom_rcn( res5, iChain, "C5\'")
 
     var aC5 = get_atom_rcn( res5, iChain, "C5\'")
Line 557: Line 610:
 
     # Set dihedral of fres C5 N1or9 and mres N1or9 C5 (1tna=20)
 
     # Set dihedral of fres C5 N1or9 and mres N1or9 C5 (1tna=20)
 
     vs[6] = ang
 
     vs[6] = ang
−
#throw context t
 
 
     move_it(as, vs)
 
     move_it(as, vs)
 
     #select {(resno=rMove) or (resno=rFixed)}
 
     #select {(resno=rMove) or (resno=rFixed)}
Line 567: Line 619:
  
 
# Rotate rotor set to move target atom to its proper place
 
# Rotate rotor set to move target atom to its proper place
−
function move_atom_nt(targetIdx, targetPt, ares, iRotors) {
+
# ares is the 5ward res limit exclusive of the mobile
 +
function move_atom_nt(targetIdx, targetPt, ares, rotors, force) {
 +
    var set3
 
     var f = (_frameID/1000000)
 
     var f = (_frameID/1000000)
 
     var m = (_frameID%1000000)
 
     var m = (_frameID%1000000)
 
     var pt = targetPt
 
     var pt = targetPt
−
    var rotors = iRotors
 
 
     var targetNo = {atomIndex=targetIdx}.atomno
 
     var targetNo = {atomIndex=targetIdx}.atomno
 
     var targetRes = {atomIndex=targetIdx}.resno
 
     var targetRes = {atomIndex=targetIdx}.resno
Line 606: Line 659:
 
                         v2 = {atomIndex=i3}.xyz - {atomIndex=i2}.xyz
 
                         v2 = {atomIndex=i3}.xyz - {atomIndex=i2}.xyz
  
−
                         s = sin(abs(angle(v1, {0 0 0}, v2)))
+
                         var s = sin(abs(angle(v1, {0 0 0}, v2)))
 
                         if (s > smax) {
 
                         if (s > smax) {
 
                             smax = s
 
                             smax = s
Line 642: Line 695:
  
 
             # If collisions
 
             # If collisions
−
             var res5 = res3-1
+
             set3 = (within(kCtolerance, {selected}) and not {selected}
−
            var set3 = {(resno=res3) and (atomName!="P") and (atomName!="OP1")
+
            and not connected({selected}))
−
                and (file=f) and (model=m)}
+
             if ((force == false) and (set3.size > 0)) {
−
             var set5 = {(resno=res5) and (atomName!="P") and (atomName!="OP1")
 
−
                and (file=f) and (model=m)}
 
−
            if ((set5 and within(kCtolerance, set3)).size > 0) {
 
 
                 # Binary undo until fixed
 
                 # Binary undo until fixed
 
                 while ((abs(dt) > kDtolerance)
 
                 while ((abs(dt) > kDtolerance)
Line 679: Line 729:
 
         }
 
         }
 
     }  # endfor 20 passes
 
     }  # endfor 20 passes
 +
    return set3
 
}
 
}
  
Line 919: Line 970:
 
         aN1or3 =  get_atom_rcn( iRes, iChain, "N3")
 
         aN1or3 =  get_atom_rcn( iRes, iChain, "N3")
 
     }
 
     }
−
     var near = within(3.1, aN1or3) and {resno!=iRes} and {element="N"}
+
    if (aN1or3.size > 0) {
−
    for (var i = 1; i <= near.size; i++) {
+
     var near = within(3.2, aN1or3) and {resno!=iRes} and {element="N"}
−
         if (angle(near[i], aN1or3, aC4or6) > 150) {
+
        for (var i = 1; i <= near.size; i++) {
−
            return [near[i].resno, near[i].chain]
+
            var dist = distance(near[i], aN1or3)
 +
            var ang = abs(angle(near[i], aN1or3, aC4or6))
 +
            if (ang > 150) {
 +
                return [near[i].resno, near[i].chain, dist, ang]
 +
            }
 +
         }
 +
    }
 +
    return [-1, aC4or6.chain, -1, -1]
 +
}
 +
 
 +
function who_almost_pairs(iRes, iChain) {
 +
    var aC2 =  get_atom_rcn( iRes, iChain, "C2")
 +
    var aC4or6 =  get_atom_rcn( iRes, iChain, "C4")
 +
    var aN1or3 =  get_atom_rcn( iRes, iChain, "N1")
 +
    var pname = "C6"
 +
    if ({aN1or3 and purine}.size = 0) {
 +
        aC4or6 =  get_atom_rcn( iRes, iChain, "C6")
 +
        aN1or3 =  get_atom_rcn( iRes, iChain, "N3")
 +
        pname = "C4"
 +
    }
 +
    if (aN1or3.size > 0) {
 +
        var near = within(3.4, aN1or3) and {resno!=iRes} and {element="N"}
 +
        for (var i = 1; i <= near.size; i++) {
 +
            var aC6or4 = get_atom_rcn(near[i].resno, near[i].chain, pname)
 +
            var aC2p = get_atom_rcn(near[i].resno, near[i].chain, "C2")
 +
            var dist = distance(near[i], aN1or3)
 +
            var puang = abs(angle(near[i], aN1or3, aC4or6))
 +
            var pyang = abs(angle(aC6or4, near[i], aN1or3))
 +
            var dihedral = abs(angle(aC2p, near[i], aN1or3, aC2))
 +
if (x1) print format("%d puang=%f pyang=%f dihedral=%f", near[i].resno, puang, pyang, dihedral)           
 +
            if ((puang > 110) and (pyang > 110) and (dihedral < 40)) {
 +
                return [near[i].resno, near[i].chain, dist, puang]
 +
            }
 
         }
 
         }
 
     }
 
     }
−
     return [-1, aC4or6.chain]
+
     return [-1, aC4or6.chain, -1, -1]
 
}
 
}
  
Line 986: Line 1,069:
 
     case "N":
 
     case "N":
 
         ret = true
 
         ret = true
 +
        break
 +
    case "M":
 +
        ret = ((nt=="A") or (nt=="C"))
 
         break
 
         break
 
     case "Y":
 
     case "Y":
Line 1,003: Line 1,089:
 
         var j = 0
 
         var j = 0
 
         for (; j < seq.size; j++) {
 
         for (; j < seq.size; j++) {
−
            var nt = {(chain=iChain) and (file=f) and (model=m) and (resno=@{i+j})
 
−
                and (atomName="C1\'")}.group[1]
 
 
             if ((gNTres[i+j])[2] >= 0) {
 
             if ((gNTres[i+j])[2] >= 0) {
 
                 break
 
                 break
Line 1,011: Line 1,095:
 
                 break
 
                 break
 
             }
 
             }
−
             if (not match_nt(seq[j+1], nt)) { # CALL
+
             if (not match_nt(seq[j+1], gSeq[i+j])) { # CALL
 
                 break
 
                 break
 
             }
 
             }
 
         }
 
         }
 
         if (j == seq.size) {
 
         if (j == seq.size) {
−
             print format("%s at %d (%s-%s-%s)", seq, i,
+
             print format("%s at %d (%s-%s-%s)%s", seq, i,
 
                 gSeq[i-1],
 
                 gSeq[i-1],
 
                 gSeq[i][i+j-1],
 
                 gSeq[i][i+j-1],
−
                 gSeq[i+j])
+
                 gSeq[i+j], aster)
 
             var rset = {(resno=i) and (chain=iChain) and (file=f) and (model=m)}
 
             var rset = {(resno=i) and (chain=iChain) and (file=f) and (model=m)}
 
             rset.selected = true
 
             rset.selected = true
 +
        }
 +
    }
 +
}
 +
 +
function find_tetras(seq, r5, r3, based) {
 +
    select none
 +
    for (var i = r5; i < r3; i++) {
 +
        var j = 0
 +
        for (; j < seq.size; j++) {
 +
            if ((i+j) >= r3) {
 +
                break
 +
            }
 +
            if (not match_nt(seq[j+1], gSeq[i+j])) { # CALL
 +
                break
 +
            }
 +
        }
 +
        if (j == seq.size) {
 +
            if (based) {
 +
                var ends = gSeq[i-1] + gSeq[i+j]
 +
                var bads = ["AA","GG","AG","GA"]
 +
                if (bads.count(ends) > 0) {
 +
                    continue
 +
                }
 +
            }
 +
            print format("%s at %d (%s-%s-%s)%s", seq, i,
 +
                gSeq[i-1],
 +
                gSeq[i][i+j-1],
 +
                gSeq[i+j], aster)
 
         }
 
         }
 
     }
 
     }
Line 1,037: Line 1,149:
 
             var rset = {(resno=i) and (chain=iChain) and (file=f) and (model=m)}
 
             var rset = {(resno=i) and (chain=iChain) and (file=f) and (model=m)}
 
             rset.selected = true
 
             rset.selected = true
−
        }
 
−
    }
 
−
}
 
−
 
−
# From 2LU0
 
−
function make_uncg_loop(res5, ares, iChain) {
 
−
    to_ab_nt_res(res5+1, ares, iChain, false)
 
−
    to_ab_nt_res(res5+2, ares, iChain, false)
 
−
    var vs = [
 
−
        [144.8,  28.8, 138.6,  140.9, 149.6]
 
−
        [-85.1, -148.4,  56.3, -143.6, 135.7]
 
−
        [-145.9, -25.6, -93.0, -148.1,  49.6]
 
−
        [-84.8,  145.9,  -7.0, -130.0, -176.2]
 
−
        [-133.5,  -78.0, -60.2,  132.6,  99.0]]
 
−
    make_tetra_loop(res5, ares, iChain, vs) # <== external call
 
−
}
 
−
 
−
# From 2LU0
 
−
function make_gnra_loop(res5, ares, iChain) {
 
−
    to_ab_nt_res(res5+1, ares, iChain, false)
 
−
    var vs = [
 
−
        [147.0,  23.9,  144.6,  144.5, 151.0]
 
−
        [-118.2, -90.5,  109.0,  166.6, 100.1]
 
−
        [-155.6, -34.4, -167.7,  115.4, 131.2]
 
−
        [-136.5, -69.9,  -86.8, -170.6,  56.0]
 
−
        [-147.1, -57.5,  -76.8,  147.7,  94.7]]
 
−
    make_tetra_loop(res5, ares, iChain, vs) # <== external call
 
−
}
 
−
 
−
function make_tetra_loop(res5, ares, iChain, vs) {
 
−
    var f = (_frameID/1000000)
 
−
    var m = (_frameID%1000000)
 
−
    for (var i = (res5+4); i >= res5; i--) {
 
−
        var j = i-1
 
−
        var as = array()
 
−
        as += get_atom_rcn( j, iChain, "C4\'")
 
−
        as += get_atom_rcn( j, iChain, "C3\'")
 
−
        as += get_atom_rcn( j, iChain, "O3\'")
 
−
        as += get_atom_rcn( i, iChain, "P")
 
−
        as += get_atom_rcn( i, iChain, "O5\'")
 
−
        as += get_atom_rcn( i, iChain, "C5\'")
 
−
        as += get_atom_rcn( i, iChain, "C4\'")
 
−
        as += get_atom_rcn( i, iChain, "C3\'")
 
−
        as += get_atom_rcn( i, iChain, "OP1")
 
−
        as += get_atom_rcn( i, iChain, "OP2")
 
−
        for (var k = 5; k > 0; k--) {
 
−
            pset = ((k>2) ? (connected(@{as[4]}) or @{as[4]}) : ({}))
 
−
            select {((resno<i) and (resno>ares) and (chain=iChain)
 
−
                and (file=f) and (model=m))
 
−
                or pset}
 
−
            set_dihedral_atoms(as[k+3], as[k+2], as[k+1], as[k],
 
−
                (vs[i-res5+1])[k])
 
 
         }
 
         }
 
     }
 
     }
Line 1,174: Line 1,234:
 
}
 
}
  
−
function move_p_to_close_a03( aP, aO3, ares) {
+
function move_p_to_close_o3( aP, aO3, ares, force) {
 
     var cp = aP.xyz
 
     var cp = aP.xyz
 
     var aC3 = {connected(aO3) and (atomname="C3\'")}
 
     var aC3 = {connected(aO3) and (atomname="C3\'")}
Line 1,183: Line 1,243:
 
     aP.xyz = cp  
 
     aP.xyz = cp  
 
     var rotors = gen_nt_rotors(aP.resno, ares, aP.chain)
 
     var rotors = gen_nt_rotors(aP.resno, ares, aP.chain)
−
     move_atom_nt(aP.atomIndex, pt, aP.resno-1, rotors)
+
     move_atom_nt(aP.atomIndex, pt, aP.resno-1, rotors, force)
 
     ##fix_p_res(aP.resno, aP.chain, true)
 
     ##fix_p_res(aP.resno, aP.chain, true)
 
}
 
}
  
−
function move_ao3_to_close_p( aO3, aP, ares) {
+
function move_o3_to_close_p( aO3, aP, ares, force) {
 
     var cp = aO3.xyz
 
     var cp = aO3.xyz
 
     var aO5 = {connected(aP) and (atomname="O5\'")}
 
     var aO5 = {connected(aP) and (atomname="O5\'")}
Line 1,196: Line 1,256:
 
     aO3.xyz = cp  
 
     aO3.xyz = cp  
 
     var rotors = gen_nt_rotors(ares, aO3.resno, aO3.chain)
 
     var rotors = gen_nt_rotors(ares, aO3.resno, aO3.chain)
−
     move_atom_nt(aO3.atomIndex, pt, aO3.resno+1, rotors)
+
     move_atom_nt(aO3.atomIndex, pt, aO3.resno+1, rotors, force)
 
     ##fix_p_res(aP.resno, aP.chain, true)
 
     ##fix_p_res(aP.resno, aP.chain, true)
 +
}
 +
 +
# Select mobile before calling
 +
function pivot_to_close_atoms( aMov, aStat, aPivot, dist) {
 +
    var axis = cross(aStat.xyz, aMov.xyz) - aPivot.xyz
 +
    var dir = 1
 +
    var d = distance(aMov, aStat)
 +
    if (d > dist) {
 +
        while (d > dist) {
 +
            rotateSelected @aPivot @axis @dir
 +
            var nd = distance(aMov, aStat)
 +
            if (nd > d) {
 +
                rotateSelected @aPivot @axis @{-dir}
 +
                if (dir == 1) {
 +
                    rotateSelected @aPivot @axis @{-dir}
 +
                    dir = -1
 +
                    continue
 +
                }
 +
                else {
 +
                    break
 +
                }
 +
            }
 +
            d = nd
 +
        }
 +
    }
 +
    else {
 +
        while (d < dist) {
 +
            rotateSelected @aPivot @axis @dir
 +
            var nd = distance(aMov, aStat)
 +
            if (nd < d) {
 +
                rotateSelected @aPivot @axis @{-dir}
 +
                if (dir == 1) {
 +
                    rotateSelected @aPivot @axis @{-dir}
 +
                    dir = -1
 +
                    continue
 +
                }
 +
                else {
 +
                    break
 +
                }
 +
            }
 +
            d = nd
 +
        }
 +
    }
 
}
 
}
  
Line 1,256: Line 1,359:
 
}
 
}
  
−
function show_adjacent_vs(i, iChain) {
+
function measure_adjacent_vs(r5, iChain) {
−
     var aC4 = get_atom_rcn(i, iChain, "C4\'")
+
     var aC4 = get_atom_rcn(r5, iChain, "C4\'")
−
     var aC1 = get_atom_rcn(i, iChain, "C1\'")
+
     var aC1 = get_atom_rcn(r5, iChain, "C1\'")
 
     var isR = ({aC1 and purine}.size > 0)
 
     var isR = ({aC1 and purine}.size > 0)
−
     var a1or9 = (isR ? "N9" : "N1")
+
     var aN1or9  = get_atom_rcn(r5, iChain, (isR ? "N9" : "N1"))
−
     var aN = get_atom_rcn(i, iChain, a1or9)
+
     var aC8or6 = get_atom_rcn(r5, iChain, (isR ? "C8" : "C6"))
 
      
 
      
−
     var aC4p = get_atom_rcn(i+1, iChain, "C4\'")
+
     var aC4p = get_atom_rcn(r5+1, iChain, "C4\'")
−
     var aC1p = get_atom_rcn(i+1, iChain, "C1\'")
+
     var aC1p = get_atom_rcn(r5+1, iChain, "C1\'")
 
     isR = ({aC1p and purine}.size > 0)
 
     isR = ({aC1p and purine}.size > 0)
−
     a1or9 = (isR ? "N9" : "N1")
+
     var aN1or9p  = get_atom_rcn(r5+1, iChain, (isR ? "N9" : "N1"))
−
     var aNp = get_atom_rcn(i+1, iChain, a1or9)
+
     var aC8or6p = get_atom_rcn(r5+1, iChain, (isR ? "C8" : "C6"))
  
−
     measure @aN @aNp
+
     measure @aN1or9 @aN1or9p
−
     measure @aC1 @aN @aNp        
+
     measure @aC1 @aN1or9 @aN1or9p        
−
     measure @aC4 @aC1 @aN @aNp        
+
     measure @aC4 @aC1 @aN1or9 @aN1or9p        
−
     measure @aC1p @aNp @aN        
+
     measure @aC1p @aN1or9p @aN1or9        
−
     measure @aC4p @aC1p @aNp @aN        
+
     measure @aC4p @aC1p @aN1or9p @aN1or9        
−
     measure @aC1p @aNp @aN @aC1       
+
     measure @aC1p @aN1or9p @aN1or9 @aC1       
 +
   
 +
    measure @aC4 @aC1 @aN1or9 @aC8or6       
 +
    measure @aC4p @aC1p @aN1or9p @aC8or6p       
 
}
 
}
  
Line 1,347: Line 1,453:
 
}
 
}
  
−
function show_pair_vs(i, j, iChain, jChain) {
+
function measure_pair_vs(i, j, iChain, jChain) {
 
     var aC4 = get_atom_rcn(i, iChain, "C4\'")
 
     var aC4 = get_atom_rcn(i, iChain, "C4\'")
 
     var aC4p = get_atom_rcn(j, jChain, "C4\'")
 
     var aC4p = get_atom_rcn(j, jChain, "C4\'")
Line 1,365: Line 1,471:
 
      
 
      
 
         measure @aN @aNp
 
         measure @aN @aNp
 +
        measure @aC1p @aNp @aN       
 +
        measure @aC4p @aC1p @aNp @aN       
 
         measure @aC1 @aN @aNp         
 
         measure @aC1 @aN @aNp         
 
         measure @aC4 @aC1 @aN @aNp         
 
         measure @aC4 @aC1 @aN @aNp         
−
        measure @aC1p @aNp @aN       
 
−
        measure @aC4p @aC1p @aNp @aN       
 
 
         measure @aC1p @aNp @aN @aC1
 
         measure @aC1p @aNp @aN @aC1
 +
        measure @aC4p @aC1p @aNp @aCp
 
         measure @aC4 @aC1 @aN @aC
 
         measure @aC4 @aC1 @aN @aC
−
        measure @aC4p @aC1p @aNp @aCp
 
 
     }
 
     }
 
     else {
 
     else {
Line 1,377: Line 1,483:
 
     }       
 
     }       
 
}
 
}
 +
 +
function minimize_for_collision( r, iChain) {
 +
    var f = (_frameID/1000000)
 +
    var m = (_frameID%1000000)
 +
    fix_p_res( r, iChain, true)
 +
 +
    # External
 +
    var cset = (within(kCtolerance, {resno=r}) and not {resno=r} and not
 +
        connected({resno=r}) and {(chain=iChain) and (file=f) and (model=m)})
 +
    if (cset.size > 0) {
 +
        var savemt = useMinimizationThread
 +
        set useMinimizationThread false
 +
        var ms = minimizationSilent
 +
        set minimizationSilent true
 +
        for (var i = 0; i < cset.size; i++) {
 +
            minimize {(resno=r) or (resno=@{cset[i].resno})}
 +
        }
 +
        set useMinimizationThread savemt
 +
        set minimizationSilent ms
 +
    }
 +
 +
    # Internal
 +
    cset = (within(kCtolerance, {(resno=r) and (atomName="OP?")}) and not
 +
        {(atomName="OP?") or (atomName="P")}
 +
        and {(chain=iChain) and (file=f) and (model=m)})
 +
    if (cset.size > 0) {
 +
        var savemt = useMinimizationThread
 +
        set useMinimizationThread false
 +
        var ms = minimizationSilent
 +
        set minimizationSilent true
 +
        for (var i = 0; i < cset.size; i++) {
 +
            minimize {(resno=r) or (resno=@{cset[i].resno})}
 +
        }
 +
        set useMinimizationThread savemt
 +
        set minimizationSilent ms
 +
    }
 +
}
 +
 +
function eval_pairing( seq, r5, r3, len) {
 +
    var val = 0
 +
    for (var i = 0; i < len; i++) {
 +
        var c5 = seq[r5+i]
 +
        var c3 = seq[r3-i]
 +
        if ((c5 == "A") and (c3 == "U")) {
 +
            val += 2
 +
        }
 +
        else if ((c5 == "U") and (c3 == "A")) {
 +
            val += 2
 +
        }
 +
        else if ((c5 == "G") and (c3 == "C")) {
 +
            val += 3
 +
        }
 +
        else if ((c5 == "C") and (c3 == "G")) {
 +
            val += 3
 +
        }
 +
        else if ((c5 == "G") and (c3 == "U")) {
 +
            val += 2
 +
        }
 +
        else if ((c5 == "U") and (c3 == "G")) {
 +
            val += 1
 +
        }
 +
        else if ((c5 == "A") and (c3 == "A")) {
 +
            val -= 3
 +
        }
 +
        else if ((c5 == "G") and (c3 == "G")) {
 +
            val -= 3
 +
        }
 +
    }
 +
    return val
 +
}
 +
 +
function update_atomnos(iChain) {
 +
    print "Update atomnos..."
 +
    var f = {chain=iChain}.file
 +
    var m = {chain=iChain}.model
 +
    var minres = {chain=iChain}.resno.min
 +
    var maxres = {chain=iChain}.resno.max
 +
    var b = {(chain=iChain) and (file=f) and (model=m)}.atomno.min
 +
    for (var r = {chain=iChain}.resno.min; r <= {chain=iChain}.resno.max; r++) {
 +
        var rset = {(resno=r) and (chain=iChain) and (file=f) and (model=m)}
 +
        for (var n = rset.atomno.min; n <= rset.atomno.max; n++) {
 +
            var a = {(resno=r) and (chain=iChain) and (file=f)
 +
                and (model=m) and (atomno=n)}
 +
            a.atomno = -b
 +
            b++
 +
        }
 +
    }
 +
    for (var i = -b; i < 0; i++) {
 +
        var a = {(chain=iChain) and (file=f) and (model=m)
 +
            and (atomno=i)}
 +
        a.atomno *= -1
 +
    }
 +
    print "Updated"   
 +
}
 +
 +
function replane_bases(iChain) {
 +
    var savemt = useMinimizationThread
 +
    set useMinimizationThread false
 +
    for (var i = {chain=iChain}.resno.min; i <= {chain=iChain}.resno.max; i++) {
 +
        minimize {resno=i and base}
 +
    }
 +
    set useMinimizationThread savemt
 +
}
 +
 +
function measure_p_dihedrals(i, iChain) {
 +
        var j = i-1
 +
        var as = array()
 +
        as += get_atom_rcn( j, iChain, "C4\'")
 +
        as += get_atom_rcn( j, iChain, "C3\'")
 +
        as += get_atom_rcn( j, iChain, "O3\'")
 +
        as += get_atom_rcn( i, iChain, "P")
 +
        as += get_atom_rcn( i, iChain, "O5\'")
 +
        as += get_atom_rcn( i, iChain, "C5\'")
 +
        as += get_atom_rcn( i, iChain, "C4\'")
 +
        as += get_atom_rcn( i, iChain, "C3\'")
 +
        for (var k = 1; k <= (as.size-3); k++) {
 +
            measure @{as[k+0]} @{as[k+1]} @{as[k+2]} @{as[k+3]}
 +
        }
 +
}
 +
 +
function pair_stem( r5, r3, ar5, iChain) {
 +
 +
    # Pair entire stem
 +
    var c = r3 - r5 + 1
 +
    for (var k = (c\2)-1 ; k >= 0; k--) {
 +
        pair_it_res(r5+k, r3-k, ar5, iChain, iChain) # CALL
 +
    }
 +
}
 +
 +
# From 2LU0
 +
function make_uncg_loop(res5, ares5, iChain) {
 +
    var f = (_frameID/1000000)
 +
    var m = (_frameID%1000000)
 +
    var va = array()
 +
    va[1] = [4.46, 100.5, -83.4, 114.4, 99.8, 39.2, -22.2, -11.8]
 +
    va[2] = [7.89, 93.6, 50.7, 29.7, 75.3, 163.6, 14.2 -22.2]
 +
    va[3] = [7.57, 90.9, -11.9, 59.5, 75.6, 74.1, 33.5, 14.2]
 +
    va[4] = [6.09, 124.9, -5.8, 46.4, -72.6, -27.1, -138.3, 33.5]
 +
    va[5] = [5.1, 64.0, -102.5, 98.2, 87.0, 58.6, -9.2, -138.3]
 +
    for (var i = 1; i <= 5; i++) {
 +
        var as = gen_as(res5+i-2, res5+i-1, iChain, iChain)
 +
   
 +
        var vs = array()
 +
        vs[1] = (va[i])[1]  # distance res5 N9or1 and res3 N9or1     
 +
        vs[2] = (va[i])[2]  # angle res5 N9or1 and res3 N9or1 C1     
 +
        vs[3] = (va[i])[3]  # dihedral res5 N9or1 and res3 N9or1 C1 C4
 +
        vs[4] = (va[i])[4]  # angle res5 C1 N9or1 and res3 N9or1     
 +
        vs[5] = (va[i])[5]  # dihedral res5 C4 N9or1 C1 and res3 N9or1
 +
        vs[6] = (va[i])[6]  # dihedral res5 N9or1 C1 and res3 N9or1 C1
 +
        vs[7] = (va[i])[7]  # dihedral chi res3
 +
        vs[8] = (va[i])[8]  # dihedral chi res5
 +
   
 +
        select {(resno < @{res5+i-1}) and (resno > ares5)
 +
            and (chain=iChain) and (file=f) and (model=m)}
 +
        move_it(as, vs)
 +
        fix_p_res(res5+i-1, iChain, true)
 +
    }
 +
}
 +
 +
# From 2LU0
 +
function make_gnra_loop(res5, ares5, iChain) {
 +
    var f = (_frameID/1000000)
 +
    var m = (_frameID%1000000)
 +
    var va = array()
 +
    va[1] = [4.37, 93.9, -84.9, 117.9, 99.1, 42.0, -19.4, 3.2]
 +
    va[2] = [7.94, 77.5, 47.5, 58.9, 87.1, 179.5, 4.5 -19.4]
 +
    va[3] = [4.9, 102.9, -98.6, 79.2, 112.4, 61.2, -29.6, 4.5]
 +
    va[4] = [4.97, 124.5, -70.0, 99.8, 93.2, 34.0, 2.5, -29.6]
 +
    va[5] = [4.31, 76.0, -98.4, 106.6, 97.2, 45.6, -15.5, 2.5]
 +
    for (var i = 1; i <= 5; i++) {
 +
        var as = gen_as(res5+i-2, res5+i-1, iChain, iChain)
 +
   
 +
        var vs = array()
 +
        vs[1] = (va[i])[1]  # distance res5 N9or1 and res3 N9or1     
 +
        vs[2] = (va[i])[2]  # angle res5 N9or1 and res3 N9or1 C1     
 +
        vs[3] = (va[i])[3]  # dihedral res5 N9or1 and res3 N9or1 C1 C4
 +
        vs[4] = (va[i])[4]  # angle res5 C1 N9or1 and res3 N9or1     
 +
        vs[5] = (va[i])[5]  # dihedral res5 C4 N9or1 C1 and res3 N9or1
 +
        vs[6] = (va[i])[6]  # dihedral res5 N9or1 C1 and res3 N9or1 C1
 +
        vs[7] = (va[i])[7]  # dihedral chi res3
 +
        vs[8] = (va[i])[8]  # dihedral chi res5
 +
   
 +
        select {(resno < @{res5+i-1}) and (resno > ares5)
 +
            and (chain=iChain) and (file=f) and (model=m)}
 +
        move_it(as, vs)
 +
        fix_p_res(res5+i-1, iChain, true)       
 +
    }
 +
}
 +
  
 
# end of plicoNTcommon.spt
 
# end of plicoNTcommon.spt
 
</pre>
 
</pre>

Revision as of 18:35, 13 July 2015

This script contains routines used by some other scripts of the Plico suite involved with polynucleotide manipulation. It must be located in the same directory as any script that uses these routines.

Copy and paste the following into a text editor and save in your scripts folder as plicoNTcommon.spt. 

#   plicoNTcommon - Jmol script by Ron Mignery
#   v1.8 beta    7/13/2015 -suport fold_trna.spt
#
#   Routines and values common to Plico suite scripts that work with nucleotides
#   Must be present in the same directory as other Plico scripts that use them
kNTcommon = 5
kC5O5PO3B = -71.0
kO5PO3C3B = -107.0
kPO3C3C4B = -161.5
kO3C3C4C5B = 140.0
kC3C4C5O5B = 55.65
kC4C5O5PB = 169.0

kO4C4C3C2B = 15.92
kC4O4C1C2B = -19.9 #-41.7 1bna minimized
kC2O4C1NxB = -122.6 #-159.0 1bna minimized
kC5C4O4C1B = 122.2 #146.3 1bna minimized
kC3C1C2O2B = 120.5

kPuB = 59.0
kPyB = 61.0

kC5O5PO3A = -59.3
kO5PO3C3A = -63.1
kPO3C3C4A = -157.4
kO3C3C4C5A = 75.5
kC3C4C5O5A = 49.55
kC4C5O5PA = 169.2

kO4C4C3C2A = -35.55
kC4O4C1C2A = 3.8
kC2O4C1NxA = -131.0
kC5C4O4C1A = 144.85
kC3C1C2O2A = 116.3

kPuA = 13.5
kPyA = 16.5

gChain1 = "A"
gChain2 = ""

# Select before calling
function force_p_res(cres, iChain) {
    var pres = cres-1
    var aP =   get_atom_rcn( cres, iChain, "P")
    var aO5 =  get_atom_rcn( cres, iChain, "O5\'")
    var aC5 =  get_atom_rcn( cres, iChain, "C5\'")
    var aC4 =  get_atom_rcn( cres, iChain, "C4\'")
    var aOP1 = get_atom_rcn( cres, iChain, "OP1")
    var aOP2 = get_atom_rcn( cres, iChain, "OP2")
    var aO3p = get_atom_rcn( pres, iChain, "O3\'")
    var aC3p = get_atom_rcn( pres, iChain, "C3\'")
    if (aO3p.size > 0) {

        var selsave = {selected}
        set_distance_atoms(aP3p, aC5, 3.1)
        select aO5
        var dist = distance(aO3p, aO5)
        var widen = (dist < 2.85)
        var dir = (widen ? -1 : 1)
        var first = true
        while (abs(dist-2.85) > kDtolerance) {
            rotateSelected @aC4 @aC5 @dir
            var newdist = distance(aO3p, aO5)
            if (widen ? (newdist < dist) : (newdist > dist)) {
                if (first) {
                    dir = -dir
                    rotateSelected @aC4 @aC5 @dir
                }
                else {
                    break
                }
            }
            dist=newdist
            first = false
        }
        select aP
        set_distance_atoms(aO5, aP, 1.73)
        set_angle_atoms(aC5, aO5, aP, 110.1)

        #set_dihedral_atoms(aC4, aC5, aO5, aP, 150.3)
        aOP2.xyz = get_tet_idx(aO3p.atomIndex, aP.atomIndex, aO5.atomIndex, 1.73)
        aOP1.xyz = get_tet_idx(aO5.atomIndex, aP.atomIndex, aO3p.atomIndex, 1.73)
        var ms = minimizationSilent
        set minimizationSilent true
        minimize {(connected(aP) or aP) and not aO3p}
        set minimizationSilent ms
        select selsave
    }
}

function fix_p_res(cres, iChain, force) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    var pres = cres-1
    var aP   = get_atom_rcn( cres, iChain, "P")
    var aO5  = get_atom_rcn( cres, iChain, "O5\'")
    var aC5  = get_atom_rcn( cres, iChain, "C5\'")
    var aC4  = get_atom_rcn( cres, iChain, "C4\'")
    var aC1  = get_atom_rcn( cres, iChain, "C1\'")
    var aOP1 = get_atom_rcn( cres, iChain, "OP1")
    var aOP2 = get_atom_rcn( cres, iChain, "OP2")
    var aO3p = get_atom_rcn( pres, iChain, "O3\'")
    var aC3p = get_atom_rcn( pres, iChain, "C3\'")
    if ((aO3p.size > 0)and (aC4.size > 0)) {
        var selsave = {selected}
        select {aP or aOP1 or aOP2}
        set_angle_atoms(aC3p, aO3p, aP, 109.0)

        # Twice through
        for (var i = 0; i < 2; i++) {
        
            # If collision
            if (force and distance(aC3p, aC5) <= kCtolerance) {
                # Push away
                select {(resno <= @{aC5.resno}) and (chain=iChain)
                    and (file=f) and (model=m)}
                set_distance_atoms(aC3p, aC5, kCtolerance)
            }
    
            select aO5
            set_dihedral_atoms(aC1, aC4, aC5, aO5, -40)
            var dist = distance(aO3p, aO5)
            var widen = (dist < 2.85)
            var dir = (widen ? -1 : 1)
            var first = true
            while (abs(dist-2.85) > kDtolerance) {
                rotateSelected @aC4 @aC5 @dir
                var newdist = distance(aO3p, aO5)
                if (widen ? (newdist < dist) : (newdist > dist)) {
                    if (first) {
                        dir = -dir
                        rotateSelected @aC4 @aC5 @dir
                    }
                    else {
                        break
                    }
                }
                dist=newdist
                first = false
            }
            if (force and (abs(distance(aO3p, aC5)-4.11) < kDtolerance)) {
                # Push away
                select {(resno <= @{aC5.resno}) and (chain=iChain)
                    and (file=f) and (model=m)}
                set_distance_atoms(aO3p, aC5, 4.11)
            }
            select aP
            set_distance_atoms(aO5, aP, 1.73)
            set_angle_atoms(aC5, aO5, aP, 110.1)
    
            dist = distance(aO3p, aP)
            widen = (dist < 1.73)
            dir = (widen ? -1 : 1)
            first = true
            while (abs(dist-1.73) > kDtolerance) {
                rotateSelected @aC5 @aO5 @dir
                var newdist = distance(aO3p, aP)
                if (widen ? (newdist < dist) : (newdist > dist)) {
                    if (first) {
                        dir = -dir
                        rotateSelected @aC5 @aO5 @dir
                    }
                    else {
                        break
                    }
                }
                dist=newdist
                first = false
            }
    
            #set_dihedral_atoms(aC4, aC5, aO5, aP, 150.3)
            aOP2.xyz = get_tet_idx(aO3p.atomIndex, aP.atomIndex, aO5.atomIndex, 1.73)
            aOP1.xyz = get_tet_idx(aO5.atomIndex, aP.atomIndex, aO3p.atomIndex, 1.73)
            if (force) {
                var savemt = useMinimizationThread
                set useMinimizationThread false
                var ms = minimizationSilent
                set minimizationSilent true
                minimize select {(connected(aP) or aP) and not aO3p}
                set useMinimizationThread savemt
                set minimizationSilent ms
            }
        }   # endfor i
        select selsave
    }
}

function fix_p_res_range(res5, res3, iChain, force) {
    for (var i = res5; i <= res3; i++) {
        fix_p_res(i, iChain, force)
    }
}

function fix_all_nt_collisions( iChain) {
    var selsave = {selected}
    var savemt = useMinimizationThread
    set useMinimizationThread false
    var ms = minimizationSilent
    set minimizationSilent true
    chset = count_collisions(true)
    for (var i = 1; i <= chset.size; i++) {
        c = chset[i]
        cset = (within(kCtolerance, c) and  not c
            and not connected(chset[i]))
        rset = [{resno=@{c.resno}}]
        for (var j = 1; j <= cset.size; j++) {
            rset += {resno=@{cset[j].resno}}
        }
        
        if ({c and cset and not base}.size > 0) {
            select {@{rset} and base}
            minimize {selected}
        }
        else if (c.atomname[1][2] == "OP") {
            fix_p_res(chset[i].resno, iChain, true)
        }
        else {
            select {@{rset}}
            minimize {selected}
        }
    }
    measure off
    set useMinimizationThread savemt
    set minimizationSilent ms
    select selsave
}

# The following functions position one nt relative to another:
# Common positioning functions:
function get_rotors_res(res) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    var rotors = array()
    var sRes = res
    var mRes = sRes-1
    var iChain = {(resno=res) and (atomName="P")
        and (file=f) and (model=m)}.chain
    var mC4 = get_atom_rcn( mRes, iChain, "C4\'")
    var mC3 = get_atom_rcn( mRes, iChain, "C3\'")
    var mO3 = get_atom_rcn( mRes, iChain, "O3\'")
    var sP =  get_atom_rcn( sRes, iChain, "P"   )
    var sO5 = get_atom_rcn( sRes, iChain, "O5\'")
    var sC5 = get_atom_rcn( sRes, iChain, "C5\'")
    var sC4 = get_atom_rcn( sRes, iChain, "C4\'")
    var sC3 = get_atom_rcn( sRes, iChain, "C3\'")

    rotors += [mC4.atomIndex, mC3.atomIndex, mO3.atomIndex, sP.atomIndex]
    rotors += [mC3.atomIndex, mO3.atomIndex, sP.atomIndex, sO5.atomIndex]
    rotors += [mO3.atomIndex, sP.atomIndex, sO5.atomIndex, sC5.atomIndex]
    rotors += [sP.atomIndex, sO5.atomIndex, sC5.atomIndex, sC4.atomIndex]
    rotors += [sO5.atomIndex, sC5.atomIndex, sC4.atomIndex, sC3.atomIndex]
    return rotors
}

function get_nt_chi_rotor_res(res, iChain) {
    var rotors = array()
    var aO4 = get_atom_rcn( res, iChain, "O4\'")
    var aC1 = get_atom_rcn( res, iChain, "C1\'")
    var isR  = ((aC1 and {purine}).size > 0)
    var N1or9 = (isR ? "N9" : "N1")
    var C6or8 = (isR ? "C8" : "C6")

    var aN = get_atom_rcn(res, iChain, N1or9)
    var aC = get_atom_rcn(res, iChain, C6or8)

    rotors = [aO4.atomIndex, aC1.atomIndex, aN.atomIndex, aC.atomIndex]
    return rotors
}

function get_nt_ab_rotor_res(res, iChain) {
    var rotors = array()
    var aC5 = get_atom_rcn(res, iChain, "C5\'")
    var aC4 = get_atom_rcn(res, iChain, "C4\'")
    var aC3 = get_atom_rcn(res, iChain, "C3\'")
    var aO3 = get_atom_rcn(res, iChain, "O3\'")

    rotors = [aO3.atomIndex, aC3.atomIndex, aC4.atomIndex, aC5.atomIndex]
    return rotors
}

function gen_nt_rotors(res5, res3, iChain) {
   var rotors = array()
    for (var i = res5+1; i <= res3; i++) {
        rotors += get_rotors_res(i, iChain)
    }
    return rotors
}

# ri=moved rj=fixed
function position_nt_by_vs(ri, rj, ares, vs, iChain, jChain) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    if (ri > rj) {
        var as = gen_as(ri, rj, iChain, jChain)
        select {(resno < ares) and (resno >= ri)
            and (chain=iChain) and (file=f) and (model=m)}
    }
    else {
        var as = gen_as(rj, ri, jChain, iChain)
        select {(resno > ares) and (resno <= ri)
            and (chain=iChain) and (file=f) and (model=m)}
    }
    move_it(as, vs)
}
                
# Moved object must be selected, fixed object not
# as[6] = fixed[1-3] moved[4-6] chis [7-8]
# vs[6] = [distance(as[3-4]), angle(as[2-4]),
#  dihedral(as[1-4]), angle(as[5-3], dihedral(as[6-3],
#  dihedral(as[2-5]
function move_it(as, vs) {

    # Distance, angle, dihedral positions atom[4] to a point
    set_distance_atoms(as[3], as[4], vs[1])
    set_angle_atoms(as[2], as[3], as[4], vs[2])
    set_dihedral_atoms(as[1], as[2], as[3], as[4], vs[3])

    # Angle and dihedral orients atom[4]'s object
    set_angle_atoms(as[3], as[4], as[5], vs[4])
    set_dihedral_atoms(as[3], as[4], as[5], as[6], vs[5])

    # Dihedral sets TBD
    set_dihedral_atoms(as[2], as[3], as[4], as[5], vs[6])
    
    # If chis
    if (vs.size > 6) {
        var sel = {selected}
        select {(resno=@{as[4].resno}) and base}
        set_dihedral_atoms(as[6], as[5], as[4], as[8], vs[8])
    }
}

# ri=moved rj=fixed
function gen_as(ri, rj, iChain, jChain) {
    var as = array()
    as[1] = get_atom_rcn(rj, jChain, "C4\'")
    as[2] = get_atom_rcn(rj, jChain, "C1\'")
    as[3] = connected(as[2]) and {element="N"}
    as[5] = get_atom_rcn(ri, iChain, "C1\'")
    as[6] = get_atom_rcn(ri, iChain, "C4\'")
    as[4] = connected(as[5]) and {element="N"}
    
    as[7] = get_atom_rcn(rj, jChain,
        (((as[1] and {purine}).size > 0) ? "C8" : "C6"))
    as[8] = get_atom_rcn(ri, iChain,
        (((as[6] and {purine}).size > 0) ? "C8" : "C6"))
    return as
}

# Specific positioning functions:
# Pair res5 on res3 moving res5 <= res3
function pair_it_res(res5, res3, ares, iChain, jChain) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    var as = gen_as(res5, res3, iChain, jChain)
    var isA = is_form_a(res5, iChain)
    var vs = array()
    vs[1] = 8.83                    # distance res5 N9or1 and res3 N9or1      
    vs[2] = 126.12                  # angle res5 N9or1 and res3 N9or1 C1      
    vs[3] = (isA ? 160.0 : -134.97) # dihedral res5 N9or1 and res3 N9or1 C1 C4
    vs[4] = 125.32                  # angle res5 C1 N9or1 and res3 N9or1      
    vs[5] = (isA ? 160.0 : -141.46) # dihedral res5 C4 N9or1 C1 and res3 N9or1
    vs[6] = (isA ? -5.0 : -17.87)   # dihedral res5 N9or1 C1 and res3 N9or1 C1
    vs[7] = (isA ? -20.0 : 38)      # dihedral chi res3
    vs[8] = (isA ? -20.0 : 38)      # dihedral chi res5
    if (ares < 0) {
        select ((resno=res5) and (chain=iChain) and (file=f) and (model=m))
    }
    else if (ares > 0) {
        select ((resno <= ares) and (chain=iChain) and (file=f) and (model=m))
    }
    move_it(as, vs)
    fix_p_res(res5, iChain, true)
    fix_p_res(res5+1, iChain, true)
}

# Flatstack res5 on res3 moving just res5
function single_flatstack_res5_on_res3(res5, res3, iChain, jChain) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    var as = gen_as(res5, res3, iChain, jChain)

    var vs = array()
    vs[1] = 7.00    # distance res5 N9or1 and res3 N9or1      
    vs[2] = 89.1    # angle res5 N9or1 and res3 N9or1 C1      
    vs[3] = -49.9   # dihedral res5 N9or1 and res3 N9or1 C1 C4
    vs[4] = 83.4    # angle res5 C1 N9or1 and res3 N9or1      
    vs[5] = 125.7   # dihedral res5 C4 N9or1 C1 and res3 N9or1
    vs[6] = 5.8     # dihedral res5 N9or1 C1 and res3 N9or1 C1

    select {(resno=res5) and (chain=iChain) and (file=f) and (model=m)}
    move_it(as, vs)
    #force_p_res(res3, jChain)
    #move_it(as, vs)
    #fix_p_res(res3, jChain, true)
    #force_p_res(res3, jChain)
}

# Outstack res5 on res3 moving just res5
function single_outstack_res5_on_res3(res5, res3, iChain, jChain) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    var as = gen_as(res5, res3, iChain, jChain)

    var vs = array()
    vs[1] = 8.23   # distance res5 N9or1 and res3 N9or1      
    vs[2] = 32.4   # angle res5 N9or1 and res3 N9or1 C1      
    vs[3] = -26.8  # dihedral res5 N9or1 and res3 N9or1 C1 C4
    vs[4] = 99.6   # angle res5 C1 N9or1 and res3 N9or1      
    vs[5] = 57.4   # dihedral res5 C4 N9or1 C1 and res3 N9or1
    vs[6] = 179.1  # dihedral res5 N9or1 C1 and res3 N9or1 C1

    select {(resno=res5) and (chain=iChain) and (file=f) and (model=m)}
    move_it(as, vs)
    force_p_res(res3, jChain)
    move_it(as, vs)
    ##fix_p_res(res3, jChain, true)
}

# Flatstack res5 on res3 moving just res5
function single_flatstack_res5_on_res3(res3, res5, iChain, jChain) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    var as = gen_as(res5, res3, iChain, jChain)

    vs = array()
    vs[1] = 6.00      # distance res5 N9or1 and res3 N9or1      
    vs[2] = 90#75.1   # angle res5 N9or1 and res3 N9or1 C1      
    vs[3] = 90#135.3  # dihedral res5 N9or1 and res3 N9or1 C1 C4
    vs[4] = 90#89.9   # angle res5 C1 N9or1 and res3 N9or1      
    vs[5] = -90#-47.3 # dihedral res5 C4 N9or1 C1 and res3 N9or1
    vs[6] = 0#1.7     # dihedral res5 N9or1 C1 and res3 N9or1 C1

    select {(resno=res5) and (chain=iChain) and (file=f) and (model=m)}
    move_it(as, vs)
    force_p_res(res5, jChain)
}

# Outstack res3 on res5 moving just res5
function single_outstack_res3_on_res5(res5, res3, iChain, jChain) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    var as = gen_as(res5, res3, iChain, jChain)

    var vs = array()
    vs[1] = 8.9    # distance res5 N9or1 and res3 N9or1      
    vs[2] = 65.3   # angle res5 N9or1 and res3 N9or1 C1      
    vs[3] = 55.7   # dihedral res5 N9or1 and res3 N9or1 C1 C4
    vs[4] = 61.2   # angle res5 C1 N9or1 and res3 N9or1      
    vs[5] = -41.2  # dihedral res5 C4 N9or1 C1 and res3 N9or1
    vs[6] = -138.4 # dihedral res5 N9or1 C1 and res3 N9or1 C1

    select {(resno=res5) and (chain=iChain) and (file=f) and (model=m)}
    move_it(as, vs)
    force_p_res(res5, jChain)
    move_it(as, vs)
    ##fix_p_res(res5, jChain, true)
}

function make_major_groove_triplex(res5, res3, iChain, jChain) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    var as = gen_as(res5, res3, iChain, jChain)
    var vs = array()

    vs[1] = 8.11   # distance res5 N9or1 and res3 N9or1
    vs[2] = 166.2  # angle res5 N9or1 and res3 N9or1 C1
    vs[3] = 0.3    # dihedral res5 N9or1 and res3 N9or1 C1 C4
    vs[4] = 162.8  # angle res5 C1 N9or1 and res3 N9or1
    vs[5] = 114.6  # dihedral res5 C4 N9or1 C1 and res3 N9or1
    vs[6] = 138.1  # dihedral res5 N9or1 C1 and res3 N9or1 C1

    # Move the nt into final position
    select {(resno <= res5) and (chain=iChain) and (file=f) and (model=m)}
    move_it(as, vs)
    
    # Rotate ribose to hbond O2' to res5+1 N7
    select {(resno = res5) and not base
        and (chain=iChain) and (file=f) and (model=m)}
    var aC1 = get_atom_rcn( res5, iChain, "C1\'")
    var aN9 = get_atom_rcn( res5, iChain, "N9")
    rotate selected @aC1 @aN9 -40.0

    # Fix up     
    select {((resno=res5) or (resno=@{res5+1}))
        and (chain=iChain) and (file=f) and (model=m)}
    minimize {selected}
    fix_p_res(res5+1, iChain, true)
}


# Pair U res5 on A res3 Hoogsteen N3-N7, N6-O2, O4-O1p moving res5 => res3
function make_hoogsteen_pair_yr(res5, res3, iChain, jChain) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    var as = gen_as(res5, res3, iChain, jChain)
    var vs = array()
    var cp = as[6].xyz

    vs[1] = 7.05   # distance res5 N9or1 and res3 N9or1
    vs[2] = 150.7  # angle res5 N9or1 and res3 N9or1 C1
    vs[3] = -33.1  # dihedral res5 N9or1 and res3 N9or1 C1 C4
    vs[4] = 143.0  # angle res5 C1 N9or1 and res3 N9or1
    vs[5] = -173.9 # dihedral res5 C4 N9or1 C1 and res3 N9or1
    vs[6] = -179.8 # dihedral res5 N9or1 C1 and res3 N9or1 C1

    # Move the nt into final position
    select {(resno <= res5) and (chain=iChain) and (file=f) and (model=m)}
    move_it(as, vs)

    # Rotate 5 end out of the way
    select {(resno < res5) and (chain=iChain) and (file=f) and (model=m)}
    var aC4 = get_atom_rcn( res5, iChain, "C4\'")
    var aC5 = get_atom_rcn( res5, iChain, "C5\'")
    rotate selected @aC4 @aC5 160.0

    # Fix up     
    select {((resno=res5) or (resno=@{res5+1}))
     and (chain=iChain) and (file=f) and (model=m)}
    minimize {selected}
    fix_p_res(res5+1, iChain, true)
    fix_p_res(res5, iChain, true)
}

function level_base(rMove, rFixed, iChain, jChain)  {
    var selsave = {selected}
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    var mC1 = get_atom_rcn(rMove, iChain, "C1\'")
    var mIsR = ({mC1 and purine}.size > 0)
    var m9or1 = (mIsR ? "N9" : "N1")
    var m6or8 = (mIsR ? "C8" : "C6")
    var m4or2 = (mIsR ? "C4" : "C2")
    var mN  = get_atom_rcn(rMove, iChain, m9or1)
    var mC6or8  = get_atom_rcn(rMove, iChain, m6or8)
    var mC4or2  = get_atom_rcn(rMove, iChain, m4or2)
    
    var fC1 = get_atom_rcn(rFixed, jChain, "C1\'")
    var fIsR = ({fC1 and purine}.size > 0)
    var f9or1 = (fIsR ? "N9" : "N1")
    var f6or8 = (fIsR ? "C8" : "C6")
    var f4or2 = (fIsR ? "C4" : "C2")
    var fN  = get_atom_rcn(rFixed, jChain, f9or1)
    var fC6or8  = get_atom_rcn(rFixed, jChain, f6or8)
    var fC4or2  = get_atom_rcn(rFixed, jChain, f4or2)

    var dist = abs(distance(fc4or2, mc4or2) - distance(fc6or8, mc6or8))
    var newdist = dist
    var dir = 0.1
    select {(resno=rMove) and (chain=iChain) and base and (file=f) and (model=m)}
    while(newdist > 0.01) {
        if (newdist > dist) {
            if (dir == 0.1) {
                dir = -0.1
            }
            else {
                rotateSelected @mC1 @mN @{-dir}
                break
            }
        }
        dist = newdist
        rotateSelected @mC1 @mN @{dir}
        newdist = abs(distance(fc4or2, mc4or2) - distance(fc6or8, mc6or8))
    }
    select selsave    
}

# Stack res rMove on res rFixed
function base_stack_res( rMove, rFixed, iChain, jChain, sep , ang, single) {
    var isA = is_form_a(rMove, iChain)
    var is3on5 = (rMove > rFixed)
    var j = rFixed
    var i = rMove
    var as = array()
    var vs = array()
    as = gen_as(rMove, rFixed, iChain, jChain)
    var f = as[1].file
    var m = as[1].model
    if (single) {
        select {(resno = i) and (chain=iChain) and (file=f) and (model=m)}
    }
    else {
        if (is3on5) {
            select {(resno >= i) and (chain=iChain) and (file=f) and (model=m)}
        }
        else {
            select {(resno <= i) and (chain=iChain) and (file=f) and (model=m)}
        }
    }
    
    # Set distance of fres N1or9 from mres N1or9 (1tna=4.2)
    vs[1] = sep

    # Set angle fres C1' N1or9 and mres N1or9 (A=6tna B=1ana)
    vs[2] =  (isA ? (is3on5 ? 92.8 : 113.9) : (is3on5 ? 83.3 : 115.23))#78.3 : 110.23

    # Set dihedral fres C4' C1' N1or9 and mres N1or9 (A=6tna B=1ana)
    vs[3] = (isA ? (is3on5 ? 110.0 : -71.2) : (is3on5 ? 165.92 : -28.31))

    # Set angle fres N1or9 and mres N1or9 C1' (A=6tna B=1ana)
    vs[4] = (isA ? (is3on5 ? 113.9 : 92.8) : (is3on5 ? 115.23 : 83.3))

    # Set dihedral fres N1or9 and mres N1or9 C1' C4' (A=6tna B=1ana)
    vs[5] =  (isA ? (is3on5 ? -71.2 : 110.0) : (is3on5 ? -28.31 : 165.92))

    # Set dihedral of fres C5 N1or9 and mres N1or9 C5 (1tna=20)
    vs[6] = ang
    move_it(as, vs)
    #select {(resno=rMove) or (resno=rFixed)}
    #minimize {selected} 
    #force_p_res(i, iChain)
    ##fix_p_res(i+1, iChain, true)
}


# Rotate rotor set to move target atom to its proper place
# ares is the 5ward res limit exclusive of the mobile 
function move_atom_nt(targetIdx, targetPt, ares, rotors, force) {
    var set3
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    var pt = targetPt
    var targetNo = {atomIndex=targetIdx}.atomno
    var targetRes = {atomIndex=targetIdx}.resno
    var iChain = {atomIndex=targetIdx}.chain
    gOK = false
    var dist = distance(pt, {atomIndex=targetIdx}.xyz)

    # If target is a C1' atom, collect its base
    var tBase = ({})
    var i1 = 0
    var i2 = 0
    var i3 = 0
    var i4 = 0
    if ({atomIndex=targetIdx}.atomName == "C1\'") {
        tBase = {(resno = targetRes) and base}
    }

    # For idx number of passes
    for (var pass1 = 0; pass1 < 20; pass1++) {
        var blocked = ({})
        for (var pass2 = 0; pass2 < (rotors.size/4); pass2++) {

            var v1 = {atomIndex=targetIdx}.xyz - pt

            # Find the most orthgonal unused rotor
            var imax = 0
            var smax = 0.5
            for (var ri = 1; ri < rotors.size; ri += 4) {
                i2 = rotors[ri+1]
                i3 = rotors[ri+2]
                i4 = rotors[ri+3]
                if ((i2 != targetIdx) and (i3 != targetIdx) and (i4 != targetIdx)) {
                    if ({blocked and {atomIndex=i2}}.count == 0) {
                        v2 = {atomIndex=i3}.xyz - {atomIndex=i2}.xyz

                        var s = sin(abs(angle(v1, {0 0 0}, v2)))
                        if (s > smax) {
                            smax = s
                            imax = ri
                        }
                    }
                }
            }

            # If no more rotors, break to next full try
            if (imax == 0) {
               break
            }
            i1 = rotors[imax+0]
            i2 = rotors[imax+1]
            i3 = rotors[imax+2]
            i4 = rotors[imax+3]

            # Get dihedral of rotor with target point
            var dt = (angle({atomIndex=targetIdx}, {atomIndex=i2},
                {atomIndex=i3}, pt)/(rotors.size/20))

            # Select and rotate
            if (ares > targetRes) {
                select_3ward_atom({atomIndex=i3}, ares, iChain)
                res3 = {atomIndex=i4}.resno
            }
            else {
                select_5ward_atom({atomIndex=i3}, ares, iChain)
                res3 = {atomIndex=i1}.resno
            }
            select remove tbase
            #***************************************************
            rotateSelected {atomIndex=i3} {atomIndex=i2} @{-dt}

            # If collisions
            set3 = (within(kCtolerance, {selected}) and not {selected}
             and not connected({selected}))
            if ((force == false) and (set3.size > 0)) {
                # Binary undo until fixed
                while ((abs(dt) > kDtolerance)
                    and ((set5 and within(kCtolerance, set3)).size > 0)) {
                    dt /= 2.0
                    rotateSelected {atomIndex=i3} {atomIndex=i2} @{dt}
                }
                while ((abs(dt) > kDtolerance)
                    and ((set5 and within(kCtolerance, set3)).size > 0)) {
                    dt /= 2.0
                    rotateSelected {atomIndex=i3} {atomIndex=i2} @{-dt}
                }
                rotateSelected {atomIndex=i3} {atomIndex=i2} @{dt}
            }

            # If close enough, stop
            dist = distance(pt, {atomIndex=targetIdx})
            if (dist < kDtolerance) {
                gOK = true
                gTargetPt = pt
                break
            }

            # Block rotor
            blocked |= {atomIndex=i2}

        }   # endfor num rotors passes

        if (gOK) {
            break
        }
    }   # endfor 20 passes
    return set3
}

# Counter rotate rotor set to move target atom to its proper place
function move_atom_by_cr_nt(targetIdx, targetPt, ares, iRotors) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    var pt = targetPt
    var rotors = iRotors
    var targetNo = {atomIndex=targetIdx}.atomno
    var targetRes = {atomIndex=targetIdx}.resno
    var iChain = {atomIndex=targetIdx}.chain
    gOK = false
    var dist = distance(pt, {atomIndex=targetIdx}.xyz)

    # If target is a C1' atom, collect its base
    var tBase = ({})
    var i1 = 0
    var i2 = 0
    var i3 = 0
    var i4 = 0
    if ({atomIndex=targetIdx}.atomName == "C1\'") {
        tBase = {(resno = targetRes) and base}
    }

    # For all C4'-C5' axes
    for (var ri = 1; ri < rotors.size; ri += 4) {
        if ({atomIndex=@{rotors[ri]}}.atomName == "C4\'") {
        
            # While distance lessens
            var dist = distance(pt, {atomIndex=targetIdx})
            var first = true
            var dt = 5.0
            while (dist > kDtolerance) {
            
                # Counter rotate C4'-C5' and O5'-P axes
                var i1 = rotors[ri+8]
                var i2 = rotors[ri+9]
                var i3 = rotors[ri+10]
                var i4 = rotors[ri+11]
                var x2 = rotors[ri+17]
                var x3 = rotors[ri+18]
                var x4 = rotors[ri+19]
                var res3 = 0
                
                # Select and rotate
                if (ares > targetRes) {
                    select_3ward_atom({atomIndex=i3}, ares, iChain)
                    res3 = {atomIndex=i4}.resno
                }
                else {
                    select_5ward_atom({atomIndex=i3}, ares, iChain)
                    res3 = {atomIndex=i1}.resno
                }
                select remove tbase
                rotateSelected {atomIndex=i3} {atomIndex=i2} @{dt}
                
                # Select and counter rotate
                if (ares > targetRes) {
                    select_3ward_atom({atomIndex=x3}, ares, iChain)
                }
                else {
                    select_5ward_atom({atomIndex=x3}, ares, iChain)
                }
                select remove tbase
                rotateSelected {atomIndex=x3} {atomIndex=x2} @{-dt}
                
                # If first and worse, reverse
                var newdist = distance(pt, {atomIndex=targetIdx})
                if (newdist > dist) {
                    if (first) {
                        dt = -dt
                    }
                    else {
                        break
                    }
                }
                first = false
                dist = newdist

                /*# If collisions
                var res5 = res3-1
                var set3 = {(resno=res3) and (atomName!="P") and (atomName!="OP1")
                    and (file=f) and (model=m)}
                var set5 = {(resno=res5) and (atomName!="P") and (atomName!="OP1")
                    and (file=f) and (model=m)}
                if ((set5 and within(kCtolerance, set3)).size > 0) {
                    # Binary undo until fixed
                    while ((abs(dt) > kDtolerance)
                        and ((set5 and within(kCtolerance, set3)).size > 0)) {
                        dt /= 2.0
                        rotateSelected {atomIndex=i3} {atomIndex=i2} @{dt}
                    }
                    while ((abs(dt) > kDtolerance)
                        and ((set5 and within(kCtolerance, set3)).size > 0)) {
                        dt /= 2.0
                        rotateSelected {atomIndex=i3} {atomIndex=i2} @{-dt}
                    }
                    rotateSelected {atomIndex=i3} {atomIndex=i2} @{dt}
                }*/
    
            }   # endwhile
    
        }
    }   # endfor rotors
}

# If ares < 0 then adjust iRes only
function to_ab_nt_res(res, ares, iChain, toA) {
    var selsave = {selected}
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    var aO3 =  get_atom_rcn( res, iChain, "O3\'")
    var aC3 =  get_atom_rcn( res, iChain, "C3\'")
    var aC4 =  get_atom_rcn( res, iChain, "C4\'")
    var aC5 =  get_atom_rcn( res, iChain, "C5\'")
    var aC1 =  get_atom_rcn( res, iChain, "C1\'")
    var aC2 =  get_atom_rcn( res, iChain, "C2\'")
    var aO2 =  get_atom_rcn( res, iChain, "O2\'")
    var aO4 =  get_atom_rcn( res, iChain, "O4\'")

    if (ares < 0) {
        select ((resno=res) and (chain=iChain) and (file=f) and (model=m)
            and not aO3 and not aC3 and not aC4)
    }
    else {
        select ((resno >= ares) and (resno <= res) and (chain=iChain)
            and (file=f) and (model=m) and not aO3 and not aC3 and not aC4)
    }
    set_dihedral_atoms(aO3, aC3, aC4, aC5, (toA ? kO3C3C4C5A : kO3C3C4C5B))

    # Set chi
    var aNx = -1
    var aCx = -1
    var ang = 0.0
    select {(resno=res) and (chain=iChain) and (file=f) and (model=m) and base}
    if ((aC1 and {purine}).size > 0) {
        aNx =  get_atom_rcn( res, iChain, "N9")
        aCx =  get_atom_rcn( res, iChain, "C8")
        ang = (toA ? kPuA : kPuB)
    }
    else {
        aNx =  get_atom_rcn(res, iChain, "N1")
        aCx =  get_atom_rcn(res, iChain, "C6")
        ang = (toA ? kPyA : kPyB)
    }
    set_dihedral_atoms(aO4, aC1, aNx, aCx, ang)

    # Set pucker 3' endo or 2' endo
    var pSet = {aC1 or aC2 or aO2}
    select pSet or {(resno=res) and (chain=iChain)
        and (file=f) and (model=m) and base}
    set_dihedral_atoms(aC5, aC4, aO4, aC1, (toA ? kC5C4O4C1A : kC5C4O4C1B))
    set_dihedral_atoms(aC4, aO4, aC1, aC2, (toA ? kC4O4C1C2A : kC4O4C1C2B))
    set_dihedral_atoms(aC2, aO4, aC1, aNx, (toA ? kC2O4C1NxA : kC2O4C1NxB))
    if (aO2.size > 0) {
        select aO2 or aC2
        ang = (toA ? kC3C1C2O2A : kC3C1C2O2B)
        set_dihedral_atoms(aC3, aC1, aC2, aO2, (toA ? kC3C1C2O2A : kC3C1C2O2B))
    }
    set_distance_atoms(aC3, aC2, 1.52)
    set_distance_atoms(aC1, aC2, 1.52)
    select selsave
}

function adjust_nts(res5, res3, iChain, toab, a, s) {
    var savemt = useMinimizationThread
    set useMinimizationThread false

    # Collect any pairing
    var w = array()
    for (var i = res5; i <= res3; i++) {
        w = w + [who_pairs(i, iChain)]
    }

    # Twist and turn
    for (var i = res3; i >= res5; i--) {
        var j = i-res5+1
        if (toab.size > 0) {
            to_ab_nt_res(i, -1, iChain, (toab == "A"))
            if ((w[j])[1] >= 0) {
                to_ab_nt_res((w[j])[1], -1, (w[j])[2], (toab == "A"))
            }
        }
    }
    for (var i = res5; i < res3; i++) {
        base_stack_res(i, i+1, iChain, iChain, s, a, false)
    }

    # Restore pairings
    for (var i = res3; i >= res5; i--) {
        var j = i-res5+1
        if ((w[j])[1] >= 0) {
            pair_it_res((w[j])[1], i, -1, (w[j])[2], iChain)
        }
    }

    # Clean up
    for (var i = res3; i >= res5; i--) {
        var j = i-res5+1
        fix_p_res(i, iChain, true)
        if ((w[j])[1] >= 0) {
            fix_p_res((w[j])[1], (w[j])[2], true)
        }
    }
    set useMinimizationThread savemt
}

#########################################################
### STAND ALONE GENERAL PURPOSE FUNCTIONS             ###
#########################################################
function is_form_a( iResno, iChain) {
    var aO4 = get_atom_rcn( iResno, iChain, "O4\'")
    var aC1 = get_atom_rcn( iResno, iChain, "C1\'")
    var aC2 = get_atom_rcn( iResno, iChain, "C2\'")
    var aC3 = get_atom_rcn( iResno, iChain, "C3\'")
    return (angle(aO4, aC1, aC2, aC3) < 0.0)
}

function is_r_res( iResno, iChain) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    return ({(resno=iResno) and (chain=iChain) and (file=f)
        and (model=m) and purine}.size > 0)
}

function repair_p_res(res, iChain) {
    var aP = get_atom_rcn( res, iChain, "P")
    var ms = minimizationSilent
    set minimizationSilent true
    minimize select {connected(aP) or aP}
    set minimizationSilent ms
}

function who_pairs(iRes, iChain) {
    var aC4or6 =  get_atom_rcn( iRes, iChain, "C4")
    var aN1or3 =  get_atom_rcn( iRes, iChain, "N1")
    if ({aN1or3 and purine}.size = 0) {
        aC4or6 =  get_atom_rcn( iRes, iChain, "C6")
        aN1or3 =  get_atom_rcn( iRes, iChain, "N3")
    }
    if (aN1or3.size > 0) {
    var near = within(3.2, aN1or3) and {resno!=iRes} and {element="N"}
        for (var i = 1; i <= near.size; i++) {
            var dist = distance(near[i], aN1or3)
            var ang = abs(angle(near[i], aN1or3, aC4or6))
            if (ang > 150) {
                return [near[i].resno, near[i].chain, dist, ang]
            }
        }
    }
    return [-1, aC4or6.chain, -1, -1]
}

function who_almost_pairs(iRes, iChain) {
    var aC2 =  get_atom_rcn( iRes, iChain, "C2")
    var aC4or6 =  get_atom_rcn( iRes, iChain, "C4")
    var aN1or3 =  get_atom_rcn( iRes, iChain, "N1")
    var pname = "C6"
    if ({aN1or3 and purine}.size = 0) {
        aC4or6 =  get_atom_rcn( iRes, iChain, "C6")
        aN1or3 =  get_atom_rcn( iRes, iChain, "N3")
        pname = "C4"
    }
    if (aN1or3.size > 0) {
        var near = within(3.4, aN1or3) and {resno!=iRes} and {element="N"}
        for (var i = 1; i <= near.size; i++) {
            var aC6or4 = get_atom_rcn(near[i].resno, near[i].chain, pname)
            var aC2p = get_atom_rcn(near[i].resno, near[i].chain, "C2")
            var dist = distance(near[i], aN1or3)
            var puang = abs(angle(near[i], aN1or3, aC4or6))
            var pyang = abs(angle(aC6or4, near[i], aN1or3))
            var dihedral = abs(angle(aC2p, near[i], aN1or3, aC2))
if (x1) print format("%d puang=%f pyang=%f dihedral=%f", near[i].resno, puang, pyang, dihedral)            
            if ((puang > 110) and (pyang > 110) and (dihedral < 40)) {
                return [near[i].resno, near[i].chain, dist, puang]
            }
        }
    }
    return [-1, aC4or6.chain, -1, -1]
}

function who_stacks(iRes, iChain) {
    var ret = array()
    var aNear = ((within(4.0, {(resno=iRes) and base}) )
        and {base} and {not resno=iRes})
    var done = array()
    for (var i = 1; i <= aNear.size; i++) {
        var jRes = aNear[i].resno
        if (not done.find(jRes)) {
            var jChain = aNear[i].chain
            var as = gen_as(iRes, jRes, iChain, jChain)
            var d = distance({(resno=iRes) and base}, {(resno=jRes) and base})
            var a1 = angle(as[2], as[3], as[4])
            var a2 = angle(as[5], as[4], as[3])
            var dh = angle(as[5], as[4], as[3], as[2])
            var bset = ((connected(as[3]) and not as[2])
                or (connected(as[4]) and not as[5]))
            var a3 = angle(bset[1], bset[2], bset[3])
            var a4 = angle(bset[2], bset[3], bset[4])

            var isStacked = true

            # Bases are parallel as sin(a1) = sin(a2) and sin(a3) = sin(a4)
            if (abs(sin(a1)-sin(a2)) > 20) {
                isStacked = false
            }
            if (abs(sin(a3)-sin(a4)) > 20) {
                isStacked = false
            }

            # Bases are stacked as d*sin(a1) < 6.0 and d3 = 0.0
            if (d*sin(a1) > 6.2) {
                isStacked = false
            }
            if (abs(dh) > 30) {
                #isStacked = false
            }

            if (isStacked) {
                ret += aNear[i].resno
            }
            done += jRes
        }
    }

    return ret
}

function match_nt(mask, nt) {
    var ret = false
    switch (mask) {
    case "A":
    case "U":
    case "C":
    case "G":
        ret = (mask = nt)
        break
    case "N":
        ret = true
        break
    case "M":
        ret = ((nt=="A") or (nt=="C"))
        break
    case "Y":
        ret = ((nt=="U") or (nt=="C"))
        break
    case "R":
        ret = ((nt=="A") or (nt=="G"))
        break
    }
    return ret
}

# Calls function match_nt above
function select_seqs(seq, r5, r3, iChain, f, m) {
    select none
    for (var i = r5; i < r3; i++) {
        var j = 0
        for (; j < seq.size; j++) {
            if ((gNTres[i+j])[2] >= 0) {
                break
            }
            if ((i+j) >= r3) {
                break
            }
            if (not match_nt(seq[j+1], gSeq[i+j])) { # CALL
                break
            }
        }
        if (j == seq.size) {
            print format("%s at %d (%s-%s-%s)%s", seq, i,
                gSeq[i-1],
                gSeq[i][i+j-1],
                gSeq[i+j], aster)
            var rset = {(resno=i) and (chain=iChain) and (file=f) and (model=m)}
            rset.selected = true
        }
    }
}

function find_tetras(seq, r5, r3, based) {
    select none
    for (var i = r5; i < r3; i++) {
        var j = 0
        for (; j < seq.size; j++) {
            if ((i+j) >= r3) {
                break
            }
            if (not match_nt(seq[j+1], gSeq[i+j])) { # CALL
                break
            }
        }
        if (j == seq.size) {
            if (based) {
                var ends = gSeq[i-1] + gSeq[i+j]
                var bads = ["AA","GG","AG","GA"]
                if (bads.count(ends) > 0) {
                    continue
                }
            }
            print format("%s at %d (%s-%s-%s)%s", seq, i,
                gSeq[i-1],
                gSeq[i][i+j-1],
                gSeq[i+j], aster)
        }
    }
}

# Calls is_form_a
function select_b_form_nts(iChain) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    select none
    for (var i = {(chain=iChain) and (file=f) and (model=m)}.resno.min;
        i <= {(chain=iChain) and (file=f) and (model=m)}.resno.max; i++) {
        if (not is_form_a(i, iChain)) { # <== external call
            print format("Res %d is form B", i)
            var rset = {(resno=i) and (chain=iChain) and (file=f) and (model=m)}
            rset.selected = true
        }
    }
}

function select_3ward_atom(ar3, ares, iChain) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    var i = ar3.resno
    var aP = get_atom_rcn( i, iChain, "P")
    switch(ar3.atomName) {
    case "O3\'" :
        select {(resno>i) and (resno<ares) and (chain=iChain)
         and (file=f) and (model=m)}
        break
    case "P" :
        select {(resno>=i) and (resno<ares) and (chain=iChain)
            and (file=f) and (model=m)}
        break
    case "O5\'" :
    case "C5\'" :
    case "C4\'" :
        select {(resno>=i) and (resno<ares) and (chain=iChain)
            and (file=f) and (model=m) and not (connected(aP) or aP)}
        break
    case "C3\'" :
        var aO3 = get_atom_rcn( i, iChain, "O3\'")
        select {((resno>i) and (resno<ares) and (chain=iChain)
            and (file=f) and (model=m)) or aO3}
        break
    }
}

function select_5ward_atom(ar5, ares, iChain) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    var i = ar5.resno
    var aP = get_atom_rcn( i, iChain, "P")
    switch(ar5.atomName) {
    case "O3\'" :
        select {(resno<=i) and (resno>ares) and (chain=iChain)
            and (file=f) and (model=m)}
        break
    case "P" :
    case "O5\'" :
    case "C5\'" :
        select {((resno<i) and (resno>ares) and (chain=iChain)
            and (file=f) and (model=m)) or (connected(aP) or aP)}
        break
    case "C4\'" :
        var aC5 = get_atom_rcn( i, iChain, "C5\'")
        select {((resno<i) and (resno>ares) and (chain=iChain)
            and (file=f) and (model=m)) or (connected(aP) or aP or aC5)}
        break
    }
}

function plot_ab_chi( iChain) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    select none
    for (var i = {(chain=iChain) and (file=f) and (model=m)}.resno.min;
        i <= {(chain=iChain) and (file=f) and (model=m)}.resno.max; i++) {
        var aO4 = get_atom_rcn(i, iChain, "O4\'")
        var aC1 = get_atom_rcn(i, iChain, "C1\'")
        var isR = ({aC1 and purine}.size > 0)
        var a1or9 = (isR ? "N9" : "N1")
        var a6or8 = (isR ? "C8" : "C6")
        var aN  = get_atom_rcn(i, iChain, a1or9)
        var aC  = get_atom_rcn(i, iChain, a6or8)
        var aO3 = get_atom_rcn(i, iChain, "O3\'")
        var aC3 = get_atom_rcn(i, iChain, "C3\'")
        var aC4 = get_atom_rcn(i, iChain, "C4\'")
        var aC5 = get_atom_rcn(i, iChain, "C5\'")
        
        var chi = angle(aO4, aC1, aN, aC)
        aN.vx = chi
        var aorb = angle(aO3, aC3, aC4, aC5)
        aN.vy = aorb
        select ADD aN
    }
    plot properties vx vy resno
    set echo top left
    echo "vx = base chi angle        vy = a ==> b form"
}

function move_p_to_close_o3( aP, aO3, ares, force) {
    var cp = aP.xyz
    var aC3 = {connected(aO3) and (atomname="C3\'")}
    select aP
    set_distance_atoms(aO3, aP, 1.74)
    set_angle_atoms(aC3, aO3, aP, 109.0)
    var pt = aP.xyz
    aP.xyz = cp 
    var rotors = gen_nt_rotors(aP.resno, ares, aP.chain)
    move_atom_nt(aP.atomIndex, pt, aP.resno-1, rotors, force)
    ##fix_p_res(aP.resno, aP.chain, true)
}

function move_o3_to_close_p( aO3, aP, ares, force) {
    var cp = aO3.xyz
    var aO5 = {connected(aP) and (atomname="O5\'")}
    select aO3
    set_distance_atoms(aP, aO3, 1.74)
    set_angle_atoms(aO5, aP, aO3, 109.0)
    var pt = aO3.xyz
    aO3.xyz = cp 
    var rotors = gen_nt_rotors(ares, aO3.resno, aO3.chain)
    move_atom_nt(aO3.atomIndex, pt, aO3.resno+1, rotors, force)
    ##fix_p_res(aP.resno, aP.chain, true)
}

# Select mobile before calling
function pivot_to_close_atoms( aMov, aStat, aPivot, dist) {
    var axis = cross(aStat.xyz, aMov.xyz) - aPivot.xyz
    var dir = 1
    var d = distance(aMov, aStat)
    if (d > dist) {
        while (d > dist) {
            rotateSelected @aPivot @axis @dir
            var nd = distance(aMov, aStat)
            if (nd > d) {
                rotateSelected @aPivot @axis @{-dir}
                if (dir == 1) {
                    rotateSelected @aPivot @axis @{-dir}
                    dir = -1
                    continue
                }
                else {
                    break
                }
            }
            d = nd
        }
    }
    else {
        while (d < dist) {
            rotateSelected @aPivot @axis @dir
            var nd = distance(aMov, aStat)
            if (nd < d) {
                rotateSelected @aPivot @axis @{-dir}
                if (dir == 1) {
                    rotateSelected @aPivot @axis @{-dir}
                    dir = -1
                    continue
                }
                else {
                    break
                }
            }
            d = nd
        }
    }
}

function print_adjacent_vs( iChain) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    var tNN = 0
    var taA = 0
    var tbA = 0
    var taD = 0
    var tbD = 0
    var tabD = 0
    var tc = 0.0
    var rmin = {(chain=iChain) and (file=f) and (model=m)}.resno.min
    var rmax = {(chain=iChain) and (file=f) and (model=m)}.resno.max
    for (var i = rmin; i < rmax; i++) {
        var aC4 = get_atom_rcn(i, iChain, "C4\'")
        var aC1 = get_atom_rcn(i, iChain, "C1\'")
        var isR = ({aC1 and purine}.size > 0)
        var a1or9 = (isR ? "N9" : "N1")
        var aN  = get_atom_rcn(i, iChain, a1or9)
        
        var aC4p = get_atom_rcn(i+1, iChain, "C4\'")
        var aC1p = get_atom_rcn(i+1, iChain, "C1\'")
        isR = ({aC1p and purine}.size > 0)
        a1or9 = (isR ? "N9" : "N1")
        var aNp  = get_atom_rcn(i+1, iChain, a1or9)
        
        if ((aC4.size > 0) and (aC4p.size > 0)) {
            
            var NN = distance(aN, aNp)
            tNN += NN
            var aA = angle(aC1, aN, aNp)
            taA += aA
            var bA = angle(aC1p, aNp, aN)
            tbA += bA
            
            var aD = angle(aC4, aC1, aN, aNp)
            if ((aD < 0) and (taD > 0)) {
                aD += 360
            }
            taD += aD
            var bD = angle(aC4p, aC1p, aNp, aN)
            if ((bD < 0) and (tbD > 0)) {
                bD += 360
            }
            tbD += bD
            var abD = angle(aC1, aN, aNp, aC1p)
            tabD += abD
            tc++
            print format("%6.2f %6.2f %6.2f %6.2f %6.2f %6.2f %d%s %s",
                NN, aA, aD, bA, bD, abD, tc, aC1.group, aC1p.group)
        }
    }
    
    print format("v1=%6.2f v2=%6.2f v3=%6.2f v4=%6.2f v5=%6.2f v6=%6.2f",
        tNN/tc, taA/tc, taD/tc, tbA/tc, tbD/tc, tabD/tc)
}

function measure_adjacent_vs(r5, iChain) {
    var aC4 = get_atom_rcn(r5, iChain, "C4\'")
    var aC1 = get_atom_rcn(r5, iChain, "C1\'")
    var isR = ({aC1 and purine}.size > 0)
    var aN1or9  = get_atom_rcn(r5, iChain, (isR ? "N9" : "N1"))
    var aC8or6 =  get_atom_rcn(r5, iChain, (isR ? "C8" : "C6"))
    
    var aC4p = get_atom_rcn(r5+1, iChain, "C4\'")
    var aC1p = get_atom_rcn(r5+1, iChain, "C1\'")
    isR = ({aC1p and purine}.size > 0)
    var aN1or9p  = get_atom_rcn(r5+1, iChain, (isR ? "N9" : "N1"))
    var aC8or6p =  get_atom_rcn(r5+1, iChain, (isR ? "C8" : "C6"))

    measure @aN1or9 @aN1or9p
    measure @aC1 @aN1or9 @aN1or9p        
    measure @aC4 @aC1 @aN1or9 @aN1or9p        
    measure @aC1p @aN1or9p @aN1or9        
    measure @aC4p @aC1p @aN1or9p @aN1or9        
    measure @aC1p @aN1or9p @aN1or9 @aC1       
    
    measure @aC4 @aC1 @aN1or9 @aC8or6        
    measure @aC4p @aC1p @aN1or9p @aC8or6p        
}

function print_pair_vs( iChain) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    var tNN = 0.0
    var taA = 0.0
    var tbA = 0.0
    var taD = 0.0
    var tbD = 0.0
    var tabD = 0.0
    var tc = 0.0
    var taChi = 0.0
    var tbChi = 0.0
    var rmin = {(chain=iChain) and (file=f) and (model=m)}.resno.min
    var rmax = {(chain=iChain) and (file=f) and (model=m)}.resno.max
    for (var i = rmin; i < rmax; i++) {
        var aC4 = get_atom_rcn(i, iChain, "C4\'")
        if (aC4.size > 0) {
            var w = who_pairs(i, iChain) # CALL
            var aC1 = get_atom_rcn(i, iChain, "C1\'")
            var isR = ({aC1 and purine}.size > 0)
            var a1or9 = (isR ? "N9" : "N1")
            var aN  = get_atom_rcn(i, iChain, a1or9)
            var a6or8 = (isR ? "C8" : "C6")
            var aC  = get_atom_rcn(i, iChain, a6or8)
            var aC4p = get_atom_rcn(w[1], w[2], "C4\'")
            var aC1p = get_atom_rcn(w[1], w[2], "C1\'")
            
            a1or9 = (isR ? "N1" : "N9") # rev
            var aNp  = get_atom_rcn(w[1], w[2], a1or9)
            a6or8 = (isR ? "C6" : "C8") # rev
            var aCp  = get_atom_rcn(w[1], w[2], a6or8)
            
            var NN = distance(aN, aNp)
            tNN += NN
            var aA = angle(aC1, aN, aNp)
            taA += aA
            var bA = angle(aC1p, aNp, aN)
            tbA += bA
            
            var aD = angle(aC4, aC1, aN, aNp)
            if ((aD < 0) and (taD > 0)) {
                aD += 360
            }
            taD += aD
            var bD = angle(aC4p, aC1p, aNp, aN)
            if ((bD < 0) and (tbD > 0)) {
                bD += 360
            }
            tbD += bD
            var abD = angle(aC1, aN, aNp, aC1p)
            tabD += abD
            
            var aChi = angle(aC4, aC1, aN, aC)
            taChi += aChi
            var bChi = angle(aC4p, aC1p, aNp, aCp)
            tbChi += bChi
            
            tc++
            print format(
                "%6.2f %6.2f %6.2f %6.2f %6.2f %6.2f %6.2f %6.2f %d%s %d%s",
                NN, aA, aD, bA, bD, abD, aChi, bChi, tc, aC1.group, w[1],
                aC1p.group)
        }
    }
    
    print format(
        "v1=%6.2f v2=%6.2f v3=%6.2f v4=%6.2f v5=%6.2f v6=%6.2f v7=%6.2f v8=%6.2f",
        tNN/tc, taA/tc, taD/tc, tbA/tc, tbD/tc, tabD/tc, taChi/tc, tbChi/tc)
}

function measure_pair_vs(i, j, iChain, jChain) {
    var aC4 = get_atom_rcn(i, iChain, "C4\'")
    var aC4p = get_atom_rcn(j, jChain, "C4\'")
    if ((aC4.size > 0) and (aC4p.size > 0)) {
        var aC1 = get_atom_rcn(i, iChain, "C1\'")
        var isR = ({aC1 and purine}.size > 0)
        var a1or9 = (isR ? "N9" : "N1")
        var aN  = get_atom_rcn(i, iChain, a1or9)
        var a6or8 = (isR ? "C8" : "C6")
        var aC  = get_atom_rcn(i, iChain, a6or8)
        var aC1p = get_atom_rcn(j, jChain, "C1\'")
        isR = ({aC1p and purine}.size > 0)
        a1or9 = (isR ? "N9" : "N1")
        var aNp  = get_atom_rcn(j, jChain, a1or9)
        a6or8 = (isR ? "C8" : "C6")
        var aCp  = get_atom_rcn(j, jChain, a6or8)
    
        measure @aN @aNp
        measure @aC1p @aNp @aN        
        measure @aC4p @aC1p @aNp @aN        
        measure @aC1 @aN @aNp        
        measure @aC4 @aC1 @aN @aNp        
        measure @aC1p @aNp @aN @aC1
        measure @aC4p @aC1p @aNp @aCp
        measure @aC4 @aC1 @aN @aC
    }
    else {
        print "No pair found"
    }       
}

function minimize_for_collision( r, iChain) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    fix_p_res( r, iChain, true)

    # External
    var cset = (within(kCtolerance, {resno=r}) and not {resno=r} and not
        connected({resno=r}) and {(chain=iChain) and (file=f) and (model=m)})
    if (cset.size > 0) {
        var savemt = useMinimizationThread
        set useMinimizationThread false
        var ms = minimizationSilent
        set minimizationSilent true
        for (var i = 0; i < cset.size; i++) {
            minimize {(resno=r) or (resno=@{cset[i].resno})}
        }
        set useMinimizationThread savemt
        set minimizationSilent ms
    }

    # Internal
    cset = (within(kCtolerance, {(resno=r) and (atomName="OP?")}) and not
        {(atomName="OP?") or (atomName="P")}
        and {(chain=iChain) and (file=f) and (model=m)})
    if (cset.size > 0) {
        var savemt = useMinimizationThread
        set useMinimizationThread false
        var ms = minimizationSilent
        set minimizationSilent true
        for (var i = 0; i < cset.size; i++) {
            minimize {(resno=r) or (resno=@{cset[i].resno})}
        }
        set useMinimizationThread savemt
        set minimizationSilent ms
    }
}

function eval_pairing( seq, r5, r3, len) {
    var val = 0
    for (var i = 0; i < len; i++) {
        var c5 = seq[r5+i]
        var c3 = seq[r3-i]
        if ((c5 == "A") and (c3 == "U")) {
            val += 2
        }
        else if ((c5 == "U") and (c3 == "A")) {
            val += 2
        }
        else if ((c5 == "G") and (c3 == "C")) {
            val += 3
        }
        else if ((c5 == "C") and (c3 == "G")) {
            val += 3
        }
        else if ((c5 == "G") and (c3 == "U")) {
            val += 2
        }
        else if ((c5 == "U") and (c3 == "G")) {
            val += 1
        }
        else if ((c5 == "A") and (c3 == "A")) {
            val -= 3
        }
        else if ((c5 == "G") and (c3 == "G")) {
            val -= 3
        }
    }
    return val
}
 
function update_atomnos(iChain) {
    print "Update atomnos..."
    var f = {chain=iChain}.file
    var m = {chain=iChain}.model
    var minres = {chain=iChain}.resno.min
    var maxres = {chain=iChain}.resno.max
    var b = {(chain=iChain) and (file=f) and (model=m)}.atomno.min
    for (var r = {chain=iChain}.resno.min; r <= {chain=iChain}.resno.max; r++) {
        var rset = {(resno=r) and (chain=iChain) and (file=f) and (model=m)}
        for (var n = rset.atomno.min; n <= rset.atomno.max; n++) {
            var a = {(resno=r) and (chain=iChain) and (file=f)
                and (model=m) and (atomno=n)}
            a.atomno = -b
            b++
        }
    }
    for (var i = -b; i < 0; i++) {
        var a = {(chain=iChain) and (file=f) and (model=m)
            and (atomno=i)}
        a.atomno *= -1
    }
    print "Updated"    
}

function replane_bases(iChain) {
    var savemt = useMinimizationThread
    set useMinimizationThread false
    for (var i = {chain=iChain}.resno.min; i <= {chain=iChain}.resno.max; i++) {
        minimize {resno=i and base}
    }
    set useMinimizationThread savemt
}

function measure_p_dihedrals(i, iChain) {
        var j = i-1
        var as = array()
        as += get_atom_rcn( j, iChain, "C4\'")
        as += get_atom_rcn( j, iChain, "C3\'")
        as += get_atom_rcn( j, iChain, "O3\'")
        as += get_atom_rcn( i, iChain, "P")
        as += get_atom_rcn( i, iChain, "O5\'")
        as += get_atom_rcn( i, iChain, "C5\'")
        as += get_atom_rcn( i, iChain, "C4\'")
        as += get_atom_rcn( i, iChain, "C3\'")
        for (var k = 1; k <= (as.size-3); k++) {
            measure @{as[k+0]} @{as[k+1]} @{as[k+2]} @{as[k+3]}
        }
}

function pair_stem( r5, r3, ar5, iChain) {

    # Pair entire stem
    var c = r3 - r5 + 1
    for (var k = (c\2)-1 ; k >= 0; k--) {
        pair_it_res(r5+k, r3-k, ar5, iChain, iChain) # CALL
    }
}

# From 2LU0
function make_uncg_loop(res5, ares5, iChain) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    var va = array()
    va[1] = [4.46, 100.5, -83.4, 114.4, 99.8, 39.2, -22.2, -11.8]
    va[2] = [7.89, 93.6, 50.7, 29.7, 75.3, 163.6, 14.2 -22.2]
    va[3] = [7.57, 90.9, -11.9, 59.5, 75.6, 74.1, 33.5, 14.2]
    va[4] = [6.09, 124.9, -5.8, 46.4, -72.6, -27.1, -138.3, 33.5]
    va[5] = [5.1, 64.0, -102.5, 98.2, 87.0, 58.6, -9.2, -138.3]
    for (var i = 1; i <= 5; i++) {
        var as = gen_as(res5+i-2, res5+i-1, iChain, iChain)
    
        var vs = array()
        vs[1] = (va[i])[1]   # distance res5 N9or1 and res3 N9or1      
        vs[2] = (va[i])[2]   # angle res5 N9or1 and res3 N9or1 C1      
        vs[3] = (va[i])[3]   # dihedral res5 N9or1 and res3 N9or1 C1 C4
        vs[4] = (va[i])[4]   # angle res5 C1 N9or1 and res3 N9or1      
        vs[5] = (va[i])[5]   # dihedral res5 C4 N9or1 C1 and res3 N9or1
        vs[6] = (va[i])[6]   # dihedral res5 N9or1 C1 and res3 N9or1 C1
        vs[7] = (va[i])[7]   # dihedral chi res3
        vs[8] = (va[i])[8]   # dihedral chi res5
    
        select {(resno < @{res5+i-1}) and (resno > ares5)
            and (chain=iChain) and (file=f) and (model=m)}
        move_it(as, vs)
        fix_p_res(res5+i-1, iChain, true)
    }
}

# From 2LU0
function make_gnra_loop(res5, ares5, iChain) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    var va = array()
    va[1] = [4.37, 93.9, -84.9, 117.9, 99.1, 42.0, -19.4, 3.2]
    va[2] = [7.94, 77.5, 47.5, 58.9, 87.1, 179.5, 4.5 -19.4]
    va[3] = [4.9, 102.9, -98.6, 79.2, 112.4, 61.2, -29.6, 4.5]
    va[4] = [4.97, 124.5, -70.0, 99.8, 93.2, 34.0, 2.5, -29.6]
    va[5] = [4.31, 76.0, -98.4, 106.6, 97.2, 45.6, -15.5, 2.5]
    for (var i = 1; i <= 5; i++) {
        var as = gen_as(res5+i-2, res5+i-1, iChain, iChain)
    
        var vs = array()
        vs[1] = (va[i])[1]   # distance res5 N9or1 and res3 N9or1      
        vs[2] = (va[i])[2]   # angle res5 N9or1 and res3 N9or1 C1      
        vs[3] = (va[i])[3]   # dihedral res5 N9or1 and res3 N9or1 C1 C4
        vs[4] = (va[i])[4]   # angle res5 C1 N9or1 and res3 N9or1      
        vs[5] = (va[i])[5]   # dihedral res5 C4 N9or1 C1 and res3 N9or1
        vs[6] = (va[i])[6]   # dihedral res5 N9or1 C1 and res3 N9or1 C1
        vs[7] = (va[i])[7]   # dihedral chi res3
        vs[8] = (va[i])[8]   # dihedral chi res5
    
        select {(resno < @{res5+i-1}) and (resno > ares5)
            and (chain=iChain) and (file=f) and (model=m)}
        move_it(as, vs)
        fix_p_res(res5+i-1, iChain, true)        
    }
}


# end of plicoNTcommon.spt

Contributors

Remig

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