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

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(Jmol script to convert a polynucleotide chain from A-form to B-form or vice versa)
 
(Avoid "axis," a newly reserved word)
 
(12 intermediate revisions by the same user not shown)
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'''ToABnt''' allows the user to convert a polynucleotide chain from A-form to B-form and ''vice versa''.
+
'''ToABnt''' allows the user to convert a nucleotide or a polynucleotide chain or chain pair from A-form to B-form and ''vice versa''.
 +
 
 
When you ALT-CLICK on any atom, you are prompted to convert its chain from its current form to either the A-form or the B-form.  The two forms differ primarily in the pucker conformation of their sugar moieties. The A-form has its sugars in the C3'-endo conformation whereas the B-form has it in the C2'-endo conformation.  The A-form is characteristic of RNA while the B-form is characteristic of DNA.
 
When you ALT-CLICK on any atom, you are prompted to convert its chain from its current form to either the A-form or the B-form.  The two forms differ primarily in the pucker conformation of their sugar moieties. The A-form has its sugars in the C3'-endo conformation whereas the B-form has it in the C2'-endo conformation.  The A-form is characteristic of RNA while the B-form is characteristic of DNA.
 +
 +
When you SHIFT-CLICK on any atom, you are prompted to convert just the selected nucleotide.
  
 
This routine is called automatically by the Plico routine [[Recycling_Corner/DNA_Generator|Polymeraze]] when a polynucleotide is generated.
 
This routine is called automatically by the Plico routine [[Recycling_Corner/DNA_Generator|Polymeraze]] when a polynucleotide is generated.
Line 6: Line 9:
 
ToABnt is a member of the Plico suite of protein folding tools described  [[User:Remig/plico|here]]. It may be installed and accessed as a macro with the file:
 
ToABnt is a member of the Plico suite of protein folding tools described  [[User:Remig/plico|here]]. It may be installed and accessed as a macro with the file:
 
<pre>Title=PLICO toAB NT
 
<pre>Title=PLICO toAB NT
Script=script <path to your script folder>/toABnt.spt;plicotoABnt
+
Script=script <path to your script directory>/toABnt.spt;plico_to_ab_nt
</pre> saved as toABnt.macro in your .jmol/macros folder as described in [[Macro]].
+
</pre> saved as toABnt.macro in your .jmol/macros directory as described in [[Macro]].
  
 
Copy and paste the following into a text editor and save in your scripts directory as toABnt.spt.
 
Copy and paste the following into a text editor and save in your scripts directory as toABnt.spt.
 
<pre>#  toABnt - Jmol script by Ron Mignery
 
<pre>#  toABnt - Jmol script by Ron Mignery
#  v1.0 beta    3/28/2014 for Jmol 14
+
#  v1.13 beta    4/12/2016 -require latest common includes
 
#
 
#
#  Convert a polynucleotide chain from A-form to B-form or vice versa
+
#  Convert a nucleotide or polynucleotide chain
 +
from A-form to B-form or vice versa
 
#
 
#
var kC5O5PO3B = -71.0
+
gToab = false
var kO5PO3C3B = -106.50
+
gToabAlt = false
var kPO3C3C4B = -160.67
+
gToA = false
var kO3C3C4C5B = 125.44
+
gBusy = false
var kC3C4C5O5B = 55.65
 
var kC4C5O5PB = 169.10
 
  
var kO4C4C3C2B = 15.92
+
function to_ab_nt_auto(iChain, toA) {
var kC4O4C1C2B = -41.7
 
var kC4O4C1NxB = -159.03
 
var kC5C4O4C1B = 146.31
 
var kC3C1C2O2B = -167.9
 
  
var kPuB = 59.0
+
    # Load common functions if not already
var kPyB = 61.0
+
    load_common()
  
var kC5O5PO3A = -59.3
+
     gChain1 = iChain
var kO5PO3C3A = -56.9
+
     gToA = toA
var kPO3C3C4A = -157.4
+
     to_ab_nt(true)
var kO3C3C4C5A = 75.5
 
var kC3C4C5O5A = 49.55
 
var kC4C5O5PA = 170.8
 
 
 
var kO4C4C3C2A = -35.55
 
var kC4O4C1C2A = 3.8
 
var kC4O4C1NxA = -117.4
 
var kC5C4O4C1A = 144.85
 
var kC3C1C2O2A = 116.3
 
 
 
var kPuA = 15
 
var kPyA = 15
 
 
 
var gToab = FALSE
 
var gToabAlt = FALSE
 
var gToA = FALSE
 
 
 
kO3C3C2O2A = 42.2 # 1ana + O # 1tna=47.3
 
kO3C3C2O2B = -32.0 # 1bna + O
 
 
 
function getInterbaseRotors(stator, mover) {
 
     var rotors = array()
 
    var sRes = stator.resno
 
    var mRes = mover.resno
 
    var iChain = mover.chain
 
     var mC4 = {(resno=mRes) and (chain=iChain) and (atomName="C4\'")}
 
     var mC3 = {(resno=mRes) and (chain=iChain) and (atomName="C3\'")}
 
    var mO3 = {(resno=mRes) and (chain=iChain) and (atomName="O3\'")}
 
    var sP = {(resno=sRes) and (chain=iChain) and (atomName="P")}
 
    var sO5 = {(resno=sRes) and (chain=iChain) and (atomName="O5\'")}
 
    var sC5 = {(resno=sRes) and (chain=iChain) and (atomName="C5\'")}
 
    var sC4 = {(resno=sRes) and (chain=iChain) and (atomName="C4\'")}
 
    var sC3 = {(resno=sRes) and (chain=iChain) and (atomName="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 setResidueDistance(stator, mover, dist) {
+
function to_ab_single_nt(res, iChain) {
     var selsave = {selected}
+
     var f = {atomIndex=_atomPicked}.file
     var cp = mover.xyz
+
     var m = {atomIndex=_atomPicked}.model
     select mover
+
     var isForm = (is_form_a( res, iChain) ? "A" : "B")
     setDistanceAtoms(stator, mover, dist)
+
     var p = prompt(format("Convert residue %d from %s-form to:",
     var pt = mover.xyz
+
        res, isForm), "A-form|B-form|Cancel", true)
     mover.xyz = cp
+
     var toab = false
     select selsave
+
     if (p == "A-form") {
     var rotors = getInterbaseRotors(stator, mover)
+
        toab = true
     toabTrackIdx(mover.atomIndex, pt, rotors)
+
     }
     toabTrackIdx(mover.atomIndex, pt, rotors)
+
     else if (p != "B-form") {
     toabTrackIdx(mover.atomIndex, pt, rotors)
+
        color {all} @gScheme
 +
        return # early exit
 +
    }
 +
      
 +
     # Call worker function
 +
     to_ab_nt_res(res, res+1, iChain, toab)
 
}
 
}
  
# Rotate rotor set to move target atom to its proper place
+
function to_ab_nt(auto) {
function toabTrackIdx(targetIdx, targetPt, iRotors) {
+
     if (not gBusy) {
     gOK = FALSE
+
        gBusy = true
    var pt = targetPt
+
        var toab = (gToA ? "A" : "B")
    var dist = distance(pt, {atomIndex=targetIdx}.xyz)
+
       
    var baseSet = {selected}
+
         var a = (gToA ? 24.0 : 33.3)
    var rotors = iRotors
+
         var s = (gToA ? 4.6 : 4.46)
 
 
    # For a 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 minres = get_resno_min(gChain1)
            var imax = 0
+
        var maxres = get_resno_max(gChain1)
            var smax = 0.5
+
        var a0 = within(kDtolerance, {0 0 0})
            for (var ri = 1; ri < rotors.size; ri += 4) {
+
        if (auto == false) {
                var i2 = rotors[ri+1]
+
            var f = {atomIndex=_atomPicked}.file
                var i3 = rotors[ri+2]
+
            var m = {atomIndex=_atomPicked}.model
                var i4 = rotors[ri+3]
+
            var isForm = (is_form_a( maxres, gChain1) ? "A" : "B")
                if ((i2 != targetIdx) and (i3 != targetIdx) and (i4 != targetIdx)) {
+
            var p = prompt(format("Convert chain %s from %s-form to:",
                    if ({blocked and {atomIndex=i2}}.count == 0) {
+
                gChain1, isForm), "A-form|B-form|Cancel", true)
                        var v2 = {atomIndex=i3}.xyz - {atomIndex=i2}.xyz
+
            if (p == "A-form") {
 
+
                toab = "A"
                        var s = sin(abs(angle(v1, {0 0 0}, v2)))
+
                a = 24.0
                        if (s > smax) {
+
                 s = 4.6
                            smax = s
 
                            imax = ri
 
                        }
 
                    }
 
                 }
 
 
             }
 
             }
 
+
             else if (p == "B-form") {
            # If no more rotors, break to next full try
+
                toab = "B"
             if (imax == 0) {
+
                a = 33.3
              break
+
                s = 4.46
 
             }
 
             }
             var i1 = rotors[imax+0]
+
             else {
            var i2 = rotors[imax+1]
+
                 color {all} @gScheme
            var i3 = rotors[imax+2]
+
                 return # early exit
            var i4 = rotors[imax+3]
 
 
 
            # Get dihedral of rotor with target point
 
            var dt = angle({atomIndex=targetIdx}, {atomIndex=i2}, {atomIndex=i3}, pt)
 
 
 
            # Add rotor stators to select
 
            select baseSet
 
            for (var ri = 1; ri <= imax; ri += 4) {
 
                 {atomIndex=@{rotors[ri]}}.selected = TRUE
 
                 {atomIndex=@{rotors[ri+1]}}.selected = TRUE
 
 
             }
 
             }
 +
        }
 +
        else {
 +
            gEcho = ""
 +
        }
 +
        set echo TOP LEFT
 +
        background ECHO pink
 +
        var ps = "Converting to " + toab + " form..."
 +
        echo @ps
 +
        refresh
 +
       
 +
        # Call worker function
 +
        adjust_nts(minres, maxres, gChain1, toab, a, s)
  
            # Rotate to minimize vector ====================
+
        select {thisModel}
             rotateSelected {atomIndex=i2} {atomIndex=i3} @dt
+
        if (a0) {       
 +
             translateSelected @{-a0.xyz}
 +
        }
 +
       
 +
        background ECHO yellow
 +
        echo @gEcho
 +
        gBusy = false
 +
    }
 +
   
 +
}
  
            # If close enough, stop
+
# Bound to ALT-LEFT-CLICK by plicoto_ab_nt
            if (distance(pt, {atomIndex=targetIdx}) < (kDtolerance/4)) {
+
function to_ab_chain_mb() {
                gOK = TRUE
+
    color {thisModel} @gScheme
                gTargetPt = pt
+
    gChain1 = {atomIndex=_atomPicked}.chain
                break
+
    color {(chain=gChain1) and thisModel} @gAltScheme
            }
+
    refresh
 +
    to_ab_nt(false)
 +
}
  
            # Block rotor
+
# Bound to SHIFT-LEFT-CLICK by plicoto_ab_nt
            blocked |= {atomIndex=i2}
+
function to_ab_res_mb() {
 
+
    color {thisModel} @gScheme
        }   # endfor num rotors passes
+
    iChain = {atomIndex=_atomPicked}.chain
 
+
    res = {atomIndex=_atomPicked}.resno
        if (gOK) {
+
    color {(chain=iChain) and thisModel and (resno=res)} @gAltScheme
            break
+
    refresh
        }
+
     to_ab_single_nt(res, iChain)
     }  # endfor 20 passes
 
 
}
 
}
  
function toabNtAuto(iChain, toA) {
+
# Load common functions if not already
 
+
function load_common() {
    # Load common functions if not already
+
     if (kCommon < 7) {
     if (kCommon < 1) {
 
 
         script $SCRIPT_PATH$plicoCommon.spt
 
         script $SCRIPT_PATH$plicoCommon.spt
         if (kCommon < 1) {
+
         if (kCommon < 7) {
 
             prompt ("A newer version of plicoCommon.SPT is required")
 
             prompt ("A newer version of plicoCommon.SPT is required")
 
             quit
 
             quit
 
         }
 
         }
 
     }
 
     }
 
+
     if (kNTcommon < 6) {
     gChain1 = iChain
+
        script $SCRIPT_PATH$plicoNTcommon.spt
    gToA = toA
+
         if (kNTcommon < 6) {
    toabNt(TRUE)
+
            prompt ("A newer version of plicoNTcommon.SPT is required")
}
+
            quit
 
+
         }
function toabNt(auto) {
 
    select all
 
    g5cargoIdx = {(atomno=@{{chain=gChain1}.atomno.min})
 
         and (chain=gChain1)}.atomIndex
 
    g3cargoIdx = {(atomno=@{{chain=gChain1}.atomno.max})
 
        and (chain=gChain1)}.atomIndex
 
 
 
    # If new drag
 
    if (gNewDrag) {
 
        gNewDrag = FALSE
 
         save state gState
 
 
     }
 
     }
 
    # Move the cargo
 
    select {gCargoSet}
 
    gChain1 = {atomIndex=g3cargoIdx}.chain
 
    gChain2 = ""
 
 
    # Move between A-form and B-form
 
    var res5 = {atomIndex=g5cargoIdx}.resno
 
    var res3 = {atomIndex=g3cargoIdx}.resno
 
    var pSet = ({})
 
    var bSet = ({})
 
    var k = -1
 
    var ang = 0
 
    var pang = 0
 
    var isP = FALSE
 
    for (var i = res5; i <= res3; i++) {
 
        var j = i-1
 
        var aO3 = {(resno=i) and (chain=gChain1) and (atomName="O3\'")}
 
        var aC3 = {(resno=i) and (chain=gChain1) and (atomName="C3\'")}
 
        var aC4 = {(resno=i) and (chain=gChain1) and (atomName="C4\'")}
 
        var aC5 = {(resno=i) and (chain=gChain1) and (atomName="C5\'")}
 
        var aO5 = {(resno=i) and (chain=gChain1) and (atomName="O5\'")}
 
        var aP =  {(resno=i) and (chain=gChain1) and (atomName="P")}
 
        if (i == res5) {
 
            if (auto == FALSE) {
 
                isForm = "A"
 
                if (angle(aO3, aC3, aC4, aC5) > ((kO3C3C4C5A + kO3C3C4C5B)/2)) {
 
                    isForm = "B"
 
                }
 
                p = prompt(format("Convert chain %s from %s-form to:", gChain1, isForm),
 
                    "A-form|B-form", TRUE)
 
                if (p == "A-form") {
 
                    gToA = TRUE
 
                }
 
                else if (p == "B-form") {
 
                    gToA = FALSE
 
                }
 
                else {
 
                    color {all} @gScheme
 
                    break
 
                }
 
                print format("Converting to %s", p)
 
            }
 
 
            # If paired
 
            lcAtoms = (within(3.0, FALSE,
 
                {(resno=i) and (chain=gChain1) and base})
 
                and not {chain=gChain1})
 
            isP = (lcAtoms.size > 0)
 
            gChain2 = (isP ? lcAtoms[1].chain : "")
 
            k = (isP ? lcAtoms[1].resno : -1)
 
        }
 
        pSet = {(resno=k) and (chain=gChain2)}
 
        var bO3 = {(resno=k) and (chain=gChain2) and (atomName="O3\'")}
 
        var bC3 = {(resno=k) and (chain=gChain2) and (atomName="C3\'")}
 
        var bC4 = {(resno=k) and (chain=gChain2) and (atomName="C4\'")}
 
        var bC5 = {(resno=k) and (chain=gChain2) and (atomName="C5\'")}
 
        var bO5 = {(resno=k) and (chain=gChain2) and (atomName="O5\'")}
 
        var bP =  {(resno=k) and (chain=gChain2) and (atomName="P")}
 
 
        # If not 5' terminus
 
        var aC4p = ({})
 
        var aC3p = ({})
 
        var aO3p = ({})
 
        var bO5p = ({})
 
        var bC4p = ({})
 
        var bC3p = ({})
 
        var bO3p = ({})
 
        var bPp = ({})
 
        if (i > res5) {
 
            aC4p = {(resno=j) and (chain=gChain1) and (atomName="C4\'")}
 
            aC3p = {(resno=j) and (chain=gChain1) and (atomName="C3\'")}
 
            aO3p = {(resno=j) and (chain=gChain1) and (atomName="O3\'")}
 
 
            bO5p = {(resno=@{k+1}) and (chain=gChain2) and (atomName="O5\'")}
 
            bC4p = {(resno=@{k+1}) and (chain=gChain2) and (atomName="C4\'")}
 
            bC3p = {(resno=@{k+1}) and (chain=gChain2) and (atomName="C3\'")}
 
            bO3p = {(resno=@{k+1}) and (chain=gChain2) and (atomName="O3\'")}
 
            bPp = {(resno=@{k+1}) and (chain=gChain2) and (atomName="P")}
 
 
            select bSet or {(atomno < @{aP.atomno}) and
 
                (atomno >= @{{atomIndex=g5cargoIdx}.atomno}) and (chain=gChain1)}
 
            setDihedralAtoms(aP, aO3p, aC3p, aC4p, (gToA ? kPO3C3C4A : kPO3C3C4B))
 
 
            setDihedralAtoms(aO5, aP, aO3p, aC3p, (gToA ? kO5PO3C3A : kO5PO3C3B))
 
 
            select bSet or {(atomno < @{aO5.atomno}) and
 
                (atomno >= @{{atomIndex=g5cargoIdx}.atomno}) and (chain=gChain1)}
 
            setDihedralAtoms(aC5, aO5, aP, aO3p, (gToA ? kC5O5PO3A : kC5O5PO3B))
 
        }
 
        select bSet or {(atomno < @{aO5.atomno}) and
 
            (atomno >= @{{atomIndex=g5cargoIdx}.atomno}) and (chain=gChain1)}
 
        setDihedralAtoms(aC4, aC5, aO5, aP, (gToA ? kC4C5O5PA : kC4C5O5PB))
 
        select (bP or (connected(bP) and {resno=k}))
 
        setDihedralAtoms(bC4, bC5, bO5, bP, (gToA ? kC4C5O5PA : kC4C5O5PB))
 
 
        select bSet or {(atomno < @{aC5.atomno}) and
 
            (atomno >= @{{atomIndex=g5cargoIdx}.atomno}) and (chain=gChain1)}
 
        setDihedralAtoms(aC3, aC4, aC5, aO5, (gToA ? kC3C4C5O5A : kC3C4C5O5B))
 
        select (bP or (connected(bP) and {resno=k}))
 
        setDihedralAtoms(bC3, bC4, bC5, bO5, (gToA ? kC3C4C5O5A : kC3C4C5O5B))
 
 
        select (({(resno >= k) and (chain=gChain2)}
 
            or {(resno <= i) and (chain=gChain1)}) and not aO3)
 
        setDihedralAtoms(aO3, aC3, aC4, aC5, (gToA ? kO3C3C4C5A : kO3C3C4C5B))
 
        select bO3
 
        setDihedralAtoms(bC5, bC4, bC3, bO3, (gToA ? kO3C3C4C5A : kO3C3C4C5B))
 
 
 
        var aC1 =  {(resno=i) and (chain=gChain1) and (atomName="C1\'")}
 
        var aC2 =  {(resno=i) and (chain=gChain1) and (atomName="C2\'")}
 
        var aO2 =  {(resno=i) and (chain=gChain1) and (atomName="O2\'")}
 
        var aO4 =  {(resno=i) and (chain=gChain1) and (atomName="O4\'")}
 
 
        var bC1 =  {(resno=k) and (chain=gChain2) and (atomName="C1\'")}
 
        var bC2 =  {(resno=k) and (chain=gChain2) and (atomName="C2\'")}
 
        var bO2 =  {(resno=k) and (chain=gChain2) and (atomName="O2\'")}
 
        var bO4 =  {(resno=k) and (chain=gChain2) and (atomName="O4\'")}
 
 
        # Set chi
 
        var aNx = -1
 
        var aCx = -1
 
        var bNx = -1
 
        var bCx = -1
 
        if ((aC1 and {purine}).size > 0) {
 
            aNx =  {(resno=i) and (chain=gChain1) and (atomName="N9")}
 
            aCx =  {(resno=i) and (chain=gChain1) and (atomName="C8")}
 
            bNx =  {(resno=k) and (chain=gChain2) and (atomName="N1")}
 
            bCx =  {(resno=k) and (chain=gChain2) and (atomName="C6")}
 
            ang = (gToA ? kPuA : kPuB)
 
            pang = (gToA ? kPyA : kPyB)
 
        }
 
        else {
 
            aNx =  {(resno=i) and (chain=gChain1) and (atomName="N1")}
 
            aCx =  {(resno=i) and (chain=gChain1) and (atomName="C6")}
 
            bNx =  {(resno=k) and (chain=gChain2) and (atomName="N9")}
 
            bCx =  {(resno=k) and (chain=gChain2) and (atomName="C8")}
 
            ang = (gToA ? kPyA : kPyB)
 
            pang = (gToA ? kPuA : kPuB)
 
        }
 
        select pSet or {(resno=i) and (chain=gChain1) and base}
 
        setDihedralAtoms(aO4, aC1, aNx, aCx, ang)
 
        select {pSet and not base}
 
        setDihedralAtoms(bCx, bNx, bC1, bO4, pang)
 
 
        # Set pucker 3' endo or 2' endo
 
        select pSet or {(resno=i) and (chain=gChain1) and base}
 
        setDihedralAtoms(aC4, aO4, aC1, aNx, (gToA ? kC4O4C1NxA : kC4O4C1NxB))
 
        select {pSet and not base}
 
        setDihedralAtoms(bNx, bC1, bO4, bC4, (gToA ? kC4O4C1NxA : kC4O4C1NxB))
 
 
        select (pSet or
 
            {((resno=i) and (chain=gChain1) and base) or aC1})
 
        setDihedralAtoms(aC5, aC4, aO4, aC1, (gToA ? kC5C4O4C1A : kC5C4O4C1B))
 
        select {pSet and not base and not bC1}
 
        setDihedralAtoms(bC1, bO4, bC4, bC5, (gToA ? kC5C4O4C1A : kC5C4O4C1B))
 
 
        select aC2 or aO2
 
        setDihedralAtoms(aC4, aO4, aC1, aC2, (gToA ? kC4O4C1C2A : kC4O4C1C2B))
 
        if (aO2.size > 0) {
 
            ang = (gToA ? kC3C1C2O2A : kC3C1C2O2B)
 
            setDihedralAtoms(aC3, aC1, aC2, aO2, (gToA ? kC3C1C2O2A : kC3C1C2O2B))
 
        }
 
        setDistanceAtoms(aC3, aC2, 1.52)
 
        setDistanceAtoms(aC1, aC2, 1.52)
 
        select bC2 or bO2
 
        setDihedralAtoms(bC4, bO4, bC1, bC2, (gToA ? kC4O4C1C2A : kC4O4C1C2B))
 
        if (bO2.size > 0) {
 
            ang = (gToA ? kC3C1C2O2A : kC3C1C2O2B)
 
            setDihedralAtoms(bC3, bC1, bC2, bO2, (gToA ? kC3C1C2O2A : kC3C1C2O2B))
 
        }
 
        setDistanceAtoms(bC3, bC2, 1.52)
 
        setDistanceAtoms(bC1, bC2, 1.52)
 
 
        # compress
 
        if (i > res5) {
 
            select ({resno<i} or {resno>k}) and not aP
 
            #setResidueDistance(aC4, aC4p, 4.0)
 
        }
 
 
        # If paired, make minor adjustments
 
        if (isP and (i > res5)) {
 
 
            var cp = bPp.xyz
 
            select bPp
 
            setDistanceAtoms(bO3, bPp, 1.59)
 
            setAngleAtoms(bC3, bO3, bPp, 118.2)
 
            setDihedralAtoms(bC4, bC3, bO3, bPp, (gToA ? kPO3C3C4A : kPO3C3C4B))
 
            var pt = bPp.xyz
 
            bPp.xyz = cp
 
            rotors = [aC4p.atomIndex, aC3p.atomIndex, aO3p.atomIndex, aP.atomIndex]
 
            rotors += [aC3p.atomIndex, aO3p.atomIndex, aP.atomIndex, aO5.atomIndex]
 
            rotors += [aO3p.atomIndex, aP.atomIndex, aO5.atomIndex, aC5.atomIndex]
 
            rotors += [aP.atomIndex, aO5.atomIndex, aC5.atomIndex, aC4.atomIndex]
 
            rotors += [aO5.atomIndex, aC5.atomIndex, aC4.atomIndex, aC3.atomIndex]
 
            select ({((resno < i) and (chain=gChain1))} or
 
                {(resno > k) and (chain=gChain2)})
 
            toabTrackIdx(bPp.atomIndex, pt, rotors)
 
            var bOP1 =  {(resno=@{bPp.resno}) and (chain=gChain2) and (atomName="OP1")}
 
            var bOP2 =  {(resno=@{bPp.resno}) and (chain=gChain2) and (atomName="OP2")}
 
            bOP1.xyz = getTetIdx(bO3.atomIndex, bPp.atomIndex, bO5p.atomIndex, 1.5)
 
            bOP2.xyz = getTetIdx(bO5p.atomIndex, bPp.atomIndex, bO3.atomIndex, 1.5)
 
            var aOP1 =  {(resno=@{aP.resno}) and (chain=gChain1) and (atomName="OP1")}
 
            var aOP2 =  {(resno=@{aP.resno}) and (chain=gChain1) and (atomName="OP2")}
 
            aOP1.xyz = getTetIdx(aO3p.atomIndex, aP.atomIndex, aO5.atomIndex, 1.5)
 
            aOP2.xyz = getTetIdx(aO5.atomIndex, aP.atomIndex, aO3p.atomIndex, 1.5)
 
        }
 
 
        bSet = bset or pSet
 
        if (k > 0) {
 
            k--
 
        }
 
 
    } # endfor
 
 
}
 
 
# Bound to ALT-LEFT-CLICK by plicoToabNt
 
function toabChainMB() {
 
    color {all} @gScheme
 
    gChain1 = {atomIndex=_atomPicked}.chain
 
    color {chain=gChain1} @gAltScheme
 
    refresh
 
    toabNt(FALSE)
 
 
}
 
}
  
# Top level of ToABnt
+
# Top level of to_ab_nt
function plicoToabNT() {
+
function plico_to_ab_nt() {
  
 
     # Load common functions if not already
 
     # Load common functions if not already
     if (kCommon < 1) {
+
     if (kCommon < 7) {
 
         script $SCRIPT_PATH$plicoCommon.spt
 
         script $SCRIPT_PATH$plicoCommon.spt
         if (kCommon < 1) {
+
         if (kCommon < 7) {
 
             prompt ("A newer version of plicoCommon.SPT is required")
 
             prompt ("A newer version of plicoCommon.SPT is required")
 +
            quit
 +
        }
 +
    }
 +
    if (kNTCommon < 6) {
 +
        script $SCRIPT_PATH$plicoCommon.spt
 +
        if (kCommon < 6) {
 +
            prompt ("A newer version of plicoNTcommon.SPT is required")
 
             quit
 
             quit
 
         }
 
         }
Line 432: Line 166:
  
 
     gPlico = "TO A-FORM/B-FORM"
 
     gPlico = "TO A-FORM/B-FORM"
     plicoPrelim()
+
     plico_prelim(false, true)
  
     gEcho = ("________A <==> B_______|ALT-CLICK=mark chain|DOUBLE-CLICK=exit")
+
     gEcho = ("________A <==> B_______|ALT-CLICK=convert chain" +
 +
        "|SHIFT-CLICK=convert NT|SHIFT-DOUBLE-CLICK=exit")
 
     echo @gEcho
 
     echo @gEcho
    gChain = ""
 
    unbind
 
  
 
     bind "ALT-LEFT-CLICK" "_pickAtom";
 
     bind "ALT-LEFT-CLICK" "_pickAtom";
     bind "ALT-LEFT-CLICK" "+:toabChainMB";
+
     bind "ALT-LEFT-CLICK" "+:to_ab_chain_mb";
     bind "DOUBLE" "plicoExit";
+
     bind "SHIFT-LEFT-CLICK" "_pickAtom";
 +
    bind "SHIFT-LEFT-CLICK" "+:to_ab_res_mb";
 +
    bind "SHIFT-DOUBLE" "plico_exit(true)";
 +
    bind "LEFT-CLICK" "+:plico_menu_toggle";
 
}
 
}
 
+
# End of to_ab_nt.SPT
# End of TURN.SPT</pre>
+
</pre>

Latest revision as of 17:05, 12 April 2016

ToABnt allows the user to convert a nucleotide or a polynucleotide chain or chain pair from A-form to B-form and vice versa.

When you ALT-CLICK on any atom, you are prompted to convert its chain from its current form to either the A-form or the B-form. The two forms differ primarily in the pucker conformation of their sugar moieties. The A-form has its sugars in the C3'-endo conformation whereas the B-form has it in the C2'-endo conformation. The A-form is characteristic of RNA while the B-form is characteristic of DNA.

When you SHIFT-CLICK on any atom, you are prompted to convert just the selected nucleotide.

This routine is called automatically by the Plico routine Polymeraze when a polynucleotide is generated.

ToABnt is a member of the Plico suite of protein folding tools described here. It may be installed and accessed as a macro with the file:

Title=PLICO toAB NT
Script=script <path to your script directory>/toABnt.spt;plico_to_ab_nt

saved as toABnt.macro in your .jmol/macros directory as described in Macro.

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

#   toABnt - Jmol script by Ron Mignery
#   v1.13 beta    4/12/2016 -require latest common includes
#
#   Convert a nucleotide or polynucleotide chain
#   from A-form to B-form or vice versa
#
gToab = false
gToabAlt = false
gToA = false
gBusy = false

function to_ab_nt_auto(iChain, toA) {

    # Load common functions if not already
    load_common()

    gChain1 = iChain
    gToA = toA
    to_ab_nt(true)
}

function to_ab_single_nt(res, iChain) {
    var f = {atomIndex=_atomPicked}.file
    var m = {atomIndex=_atomPicked}.model
    var isForm = (is_form_a( res, iChain) ? "A" : "B")
    var p = prompt(format("Convert residue %d from %s-form to:",
        res, isForm), "A-form|B-form|Cancel", true)
    var toab = false
    if (p == "A-form") {
        toab = true
    }
    else if (p != "B-form") {
        color {all} @gScheme
        return # early exit
    }
    
    # Call worker function
    to_ab_nt_res(res, res+1, iChain, toab)
}

function to_ab_nt(auto) {
    if (not gBusy) {
        gBusy = true
        var toab = (gToA ? "A" : "B")
        
        var a = (gToA ? 24.0 : 33.3)
        var s = (gToA ? 4.6 : 4.46)

        var minres = get_resno_min(gChain1)
        var maxres = get_resno_max(gChain1)
        var a0 = within(kDtolerance, {0 0 0})
        if (auto == false) {
            var f = {atomIndex=_atomPicked}.file
            var m = {atomIndex=_atomPicked}.model
            var isForm = (is_form_a( maxres, gChain1) ? "A" : "B")
            var p = prompt(format("Convert chain %s from %s-form to:",
                gChain1, isForm), "A-form|B-form|Cancel", true)
            if (p == "A-form") {
                toab = "A"
                a = 24.0
                s = 4.6
            }
            else if (p == "B-form") {
                toab = "B"
                a = 33.3
                s = 4.46
            }
            else {
                color {all} @gScheme
                return # early exit
            }
        }
        else {
            gEcho = ""
        }
        set echo TOP LEFT
        background ECHO pink
        var ps = "Converting to " + toab + " form..."
        echo @ps
        refresh
        
        # Call worker function
        adjust_nts(minres, maxres, gChain1, toab, a, s)

        select {thisModel}
        if (a0) {        
            translateSelected @{-a0.xyz}
        }
        
        background ECHO yellow
        echo @gEcho
        gBusy = false
    }
    
}

# Bound to ALT-LEFT-CLICK by plicoto_ab_nt
function to_ab_chain_mb() {
    color {thisModel} @gScheme
    gChain1 = {atomIndex=_atomPicked}.chain
    color {(chain=gChain1) and thisModel} @gAltScheme
    refresh
    to_ab_nt(false)
}

# Bound to SHIFT-LEFT-CLICK by plicoto_ab_nt
function to_ab_res_mb() {
    color {thisModel} @gScheme
    iChain = {atomIndex=_atomPicked}.chain
    res = {atomIndex=_atomPicked}.resno
    color {(chain=iChain) and thisModel and (resno=res)} @gAltScheme
    refresh
    to_ab_single_nt(res, iChain)
}

# Load common functions if not already
function load_common() {
    if (kCommon < 7) {
        script $SCRIPT_PATH$plicoCommon.spt
        if (kCommon < 7) {
            prompt ("A newer version of plicoCommon.SPT is required")
            quit
        }
    }
    if (kNTcommon < 6) {
        script $SCRIPT_PATH$plicoNTcommon.spt
        if (kNTcommon < 6) {
            prompt ("A newer version of plicoNTcommon.SPT is required")
            quit
        }
    }
}

# Top level of to_ab_nt
function plico_to_ab_nt() {

    # Load common functions if not already
    if (kCommon < 7) {
        script $SCRIPT_PATH$plicoCommon.spt
        if (kCommon < 7) {
            prompt ("A newer version of plicoCommon.SPT is required")
            quit
        }
    }
    if (kNTCommon < 6) {
        script $SCRIPT_PATH$plicoCommon.spt
        if (kCommon < 6) {
            prompt ("A newer version of plicoNTcommon.SPT is required")
            quit
        }
    }

    gPlico = "TO A-FORM/B-FORM"
    plico_prelim(false, true)

    gEcho = ("________A <==> B_______|ALT-CLICK=convert chain" +
        "|SHIFT-CLICK=convert NT|SHIFT-DOUBLE-CLICK=exit")
    echo @gEcho

    bind "ALT-LEFT-CLICK" "_pickAtom";
    bind "ALT-LEFT-CLICK" "+:to_ab_chain_mb";
    bind "SHIFT-LEFT-CLICK" "_pickAtom";
    bind "SHIFT-LEFT-CLICK" "+:to_ab_res_mb";
    bind "SHIFT-DOUBLE" "plico_exit(true)";
    bind "LEFT-CLICK" "+:plico_menu_toggle";
}
# End of to_ab_nt.SPT

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Remig