Recycling Corner/DNA Generator

POLYMERAZE takes a string message encoding a nucleotide (nt) sequence and generates a corresponding double helix one nt at a time from the 5' terminus to the 3' terminus rotating the emerging helix as it goes.

The resulting polynucleotide defaults to an open B-form. If the script "to_ab_nt" described here is available, it prompts to converts to a regular B-form if DNA or to a regular A-form if RNA or mixed.

The message is a string entered by the user at a prompt. It may be typed in or pasted in and be of any length. If the first character is '+' then the polynucleotide is created in a new frame. If prepended with '3' then the string is considered as 3' to 5'. If prepended with 'R' then RNA is generated instead of DNA. If prepended with 'S' then a single strand helix is produced. If prepended with 'M' then a mixed helix is produced where the first strand is DNA and the second RNA. Multiple prepends are allowed (though 'M' would be inconsistent with 'R' or 'S').

If the 3d character is ':' (4th if the first is '+') then the two chains are labeled by the two preceding characters instead of the default 'A' and 'B'. Likewise if the 2d character is ':' then the presumably single chain is labeled by the preceding single character.

With this script you can generate a polynucleotide helix chain from a sequence string in 1-char NT coding. You can optionally give it chain labels other than the default :A :B. You can also add to an existing chain(s), add new chains to an existing model or now create the chain(s) in a new frame by prepending a '+' to the sequence string.

Chains start from the origin and extend along the -X+Y+Z axis as they are built. If a chain with the same chain label as the new chain is at the origin, the new sequence is added to the old. If a chain with a different chain label is at the origin, all existing chains are shifted 20 angstroms to the left along the YZ axis until the origin is clear.

Note that a single chain helix could then be added to a double chain or RNA to DNA or whatever. Have fun...

The IUPAC/IUBMB 1 letter code is used: A=Adenine C=Cytosine G=Guanine T=Thymine U=Uracil

The top level function plicoGenNt prompts the user for input.

The top level function plicoGenHelix accepts a string as a parameter.

Polymeraze 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 Generate Polynucleotide
Script=script <path to your script directory>/polymeraze.spt;plico_gen_nt

saved as plicoGenNT.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 polymeraze.spt.

#   POLYMERAZE - Jmol script by Ron Mignery
#   v1.13 beta    8/26/2014 -fix naming conflict
#
#   POLYMERAZE takes a string message encoding a nucleotide (nt) sequence
#   and generates a corresponding double helix one nt at a time from the
#   5' terminus to the 3' terminus rotating the emerging helix as it goes.
#
#   The resulting polynucleotide defaults to an open B-form.  If double-stranded
#   and the script "to_ab_nt" is available, it prompts to converts to a regular
#   B-form if DNA or to a regular A-form if RNA or mixed.
#
#   The message is a string entered by the user at a prompt.
#   It may be typed in or pasted in and be of any length
#   If the 1st character is '+' then the chain is created in a new frame.
#   If prepended with '3' then the string is considered as 3' to 5'
#   If prepended with 'R' then RNA is generated instead of DNA (Ts convert to Us)
#   If prepended with 'S' then a single strand helix is produced
#   If prepended with 'M' then a mixed helix is produced where the first
#   strand is DNA and the second RNA - multiple prepends are allowed
#   though 'M' is inconsistent with 'R' or 'S'
#
#   If the 3d (4th if 1st is '+') character is ':' then the two chains are labeled
#   by the two preceding characters instead of the default 'A' and 'B'
#   Likewise if the 2d character is ':' then the presumably single chain is
#   labeled by the single preceding character
#
#   The IUPAC/IUBMB 1 letter code is used:
#   A=Adenine C=Cytosine G=Guanine T=Thymine U=Uracil

# The following constant values determine the pitch of the helices
kC5O5PO3 = -27.0
kO5PO3C3 = -117.8
kPO3C3C4 = -171.9
kO3C3C4C5 = 121
kC3C4C5O5 = 54
kC4C5O5P = 164
kPu = 65
kPy = 52
gChain1 = 'A'    # The default chain id
gChain2 = 'B'    # The default complementary chain id
gA = ""
gSeq = ""
gAppendNew = false
gNewFrame = false

# Lookup 3 letter code from 1 letter code
kNt3from1 = {"A":" DA", "C":" DC", "G":" DG", "T":" DT", "U":" DU", "D":" DD", "X":" DX"}
kNtComp = {"A":"T", "C":"G", "G":"C", "T":"A", "U":"A", "D":"G", "X":"C"}

# Generate PDB atom record
# Writes gNa or gNb
function gen_atom_nt(atomname, group, resno, xyz, comp) {
    # Fixed column format:
    #ATOM    500  O4'  DA B  29      -3.745   7.211  45.474
    while (atomname.size < 3) {
        atomname += " ";
    }
    var a =  format("ATOM  %5d %4s %3s ", (comp ? gNb : gNa), atomname, group )
    a +=  format("%s%4d    %8.3f", (comp ? gChain2 : gChain1), resno, xyz[1] )
    a +=  format("%8.3f%8.3f\n", xyz[2], xyz[3] )
    if (comp) gNb++; else gNa++

    return a
};

# Generate a PDB nucleotide record set
# Calls gen_atom_nt that writes gNa or gNb
function gen_nt(i, nt, rna, comp) {

    # From constructed nucleotides
    var P0 =  [0.000, 0.000, 0.000]
    var OP1=  [-0.973,0.363,-1.067]
    var OP2=  [0.297,-1.428, 0.272]
    var O5p=  [1.351, 0.795,-0.286]
    var C5p=  [1.345, 2.211,-0.125]
    var C4p=  [2.732, 2.786,-0.255]
    var O4p=  [3.413, 2.900, 1.019]
    var C3p=  [3.670, 2.020,-1.178]
    var O3p=  [4.269, 2.960,-2.051]
    var C2p=  [4.717, 1.445,-0.238]
    var O2p=  [6.046, 1.365,-0.884]
    var C1p=  [4.758, 2.505, 0.846]

    var N1ct= [5.277, 2.056, 2.143]
    var C2ct= [6.236, 2.836, 2.740]
    var O2ct= [6.670, 3.853, 2.230]
    var N3ct= [6.674, 2.381, 3.958]
    var C4ct= [6.256, 1.245, 4.622]
    var NO4ct=[6.726, 0.972, 5.728]
    var C5ct= [5.255, 0.455, 3.924]
    var C6ct= [4.820, 0.900, 2.737]
    var nC7ct=[4.762,-0.811, 4.551]

    var N9ag= [5.256, 2.091, 2.152]
    var C8ag= [4.867, 1.016, 2.913]
    var N7ag= [5.532, 0.894, 4.035]
    var C5ag= [6.425, 1.959, 4.013]
    var C6ag= [7.401, 2.391, 4.922]
    var NO6ag=[7.656, 1.780, 6.081]
    var N1ag= [8.118, 3.493, 4.599]
    var C2ag= [7.865, 4.104, 3.438]
    var nN2ag=[8.616, 5.197, 3.181]
    var N3ag= [6.968, 3.796, 2.503]
    var C4ag= [6.271, 2.701, 2.856]

    # Build PDB atom records common to all NTs
    var n3 = kNt3from1[nt]
    if (n3 = "") {
        n3 = " D?"
    }
    if (rna) {
        if (n3 == " DD") {
            n3 = "  D"
        }
        else {
            n3 = n3.replace('D', ' ')
        }
    }
    var a = gen_atom_nt(" P  ", n3, i, P0, comp)
    a += gen_atom_nt(" OP1", n3, i, OP1, comp)
    a += gen_atom_nt(" OP2", n3, i, OP2, comp)
    a += gen_atom_nt(" O5'", n3, i, O5p, comp)
    a += gen_atom_nt(" C5'", n3, i, C5p, comp)
    a += gen_atom_nt(" C4'", n3, i, C4p, comp)
    a += gen_atom_nt(" O4'", n3, i, O4p, comp)
    a += gen_atom_nt(" C3'", n3, i, C3p, comp)
    a += gen_atom_nt(" O3'", n3, i, O3p, comp)
    a += gen_atom_nt(" C2'", n3, i, C2p, comp)
    a += gen_atom_nt(" C1'", n3, i, C1p, comp)
    if (rna) {
        a += gen_atom_nt(" O2'", n3, i, O2p, comp)
    }

    # Now add NT specific atom records
    switch (nt) {
    case 'A' :
        a += gen_atom_nt(" N9 ", n3, i, N9ag, comp)
        a += gen_atom_nt(" C8 ", n3, i, C8ag, comp)
        a += gen_atom_nt(" N7 ", n3, i, N7ag, comp)
        a += gen_atom_nt(" C5 ", n3, i, C5ag, comp)
        a += gen_atom_nt(" C6 ", n3, i, C6ag, comp)
        a += gen_atom_nt(" N6 ", n3, i, NO6ag, comp)
        a += gen_atom_nt(" N1 ", n3, i, N1ag, comp)
        a += gen_atom_nt(" C2 ", n3, i, C2ag, comp)
        a += gen_atom_nt(" N3 ", n3, i, N3ag, comp)
        a += gen_atom_nt(" C4 ", n3, i, C4ag, comp)
        break;
    case 'C' :
        a += gen_atom_nt(" N1 ", n3, i, N1ct, comp)
        a += gen_atom_nt(" C2 ", n3, i, C2ct, comp)
        a += gen_atom_nt(" O2 ", n3, i, O2ct, comp)
        a += gen_atom_nt(" N3 ", n3, i, N3ct, comp)
        a += gen_atom_nt(" C4 ", n3, i, C4ct, comp)
        a += gen_atom_nt(" N4 ", n3, i, NO4ct, comp)
        a += gen_atom_nt(" C5 ", n3, i, C5ct, comp)
        a += gen_atom_nt(" C6 ", n3, i, C6ct, comp)
        break;
    case 'X' :
    case 'G' :
        a += gen_atom_nt(" N9 ", n3, i, N9ag, comp)
        a += gen_atom_nt(" C8 ", n3, i, C8ag, comp)
        a += gen_atom_nt(" N7 ", n3, i, N7ag, comp)
        a += gen_atom_nt(" C5 ", n3, i, C5ag, comp)
        a += gen_atom_nt(" C6 ", n3, i, C6ag, comp)
        a += gen_atom_nt(" O6 ", n3, i, NO6ag, comp)
        a += gen_atom_nt(" N1 ", n3, i, N1ag, comp)
        a += gen_atom_nt(" C2 ", n3, i, C2ag, comp)
        a += gen_atom_nt(" N2 ", n3, i, nN2ag, comp)
        a += gen_atom_nt(" N3 ", n3, i, N3ag, comp)
        a += gen_atom_nt(" C4 ", n3, i, C4ag, comp)
        break;
    case 'T' :
        a += gen_atom_nt(" N1 ", n3, i, N1ct, comp)
        a += gen_atom_nt(" C2 ", n3, i, C2ct, comp)
        a += gen_atom_nt(" O2 ", n3, i, O2ct, comp)
        a += gen_atom_nt(" N3 ", n3, i, N3ct, comp)
        a += gen_atom_nt(" C4 ", n3, i, C4ct, comp)
        a += gen_atom_nt(" O4 ", n3, i, NO4ct, comp)
        a += gen_atom_nt(" C5 ", n3, i, C5ct, comp)
        a += gen_atom_nt(" C6 ", n3, i, C6ct, comp)
        a += gen_atom_nt(" C7 ", n3, i, nC7ct, comp)
        break;
    case 'D' :
    case 'U' :
        a += gen_atom_nt(" N1 ", n3, i, N1ct, comp)
        a += gen_atom_nt(" C2 ", n3, i, C2ct, comp)
        a += gen_atom_nt(" O2 ", n3, i, O2ct, comp)
        a += gen_atom_nt(" N3 ", n3, i, N3ct, comp)
        a += gen_atom_nt(" C4 ", n3, i, C4ct, comp)
        a += gen_atom_nt(" O4 ", n3, i, NO4ct, comp)
        a += gen_atom_nt(" C5 ", n3, i, C5ct, comp)
        a += gen_atom_nt(" C6 ", n3, i, C6ct, comp)
        break;
    default :
        break;
    }

    return a
};

# Rotate a1 on a2 in the plane of a1, a2 and a3 to the given angle
# a1 and all connected except by a2 must be selected
function set_angle_no (a1no, a2no, a3no, toangle) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    var c = gChain1
    var a1 =  {(atomno=a1no) and (chain=c) and (file=f) and (model=m)}
    var a2 =  {(atomno=a2no) and (chain=c) and (file=f) and (model=m)}
    var a3 =  {(atomno=a3no) and (chain=c) and (file=f) and (model=m)}
    var v1 = (a1.xyz - a2.xyz)
    var v2 = (a3.xyz - a2.xyz)
    var axis = cross(v1, v2) + a2.xyz
    var curangle =  angle(a1, a2, a3)
    rotateselected @axis @a2 @{curangle-toangle}
}

# Set the dihedral to the given angle
# a1 (or a4) and all connected except by a2 (or a3) must be selected
# If selected < unselected ==> a2 < a3 and vice versa
function set_dihedral_no (a1no, a2no, a3no, a4no, toangle) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    var c = gChain1
    var a1 =  {(atomno=a1no) and (chain=c) and (file=f) and (model=m)}
    var a2 =  {(atomno=a2no) and (chain=c) and (file=f) and (model=m)}
    var a3 =  {(atomno=a3no) and (chain=c) and (file=f) and (model=m)}
    var a4 =  {(atomno=a4no) and (chain=c) and (file=f) and (model=m)}
    var curangle =  angle(a1, a2, a3, a4)
    rotateselected @a2 @a3 @{toangle-curangle}
}

function count_atoms(seq, rna, start, finish) {
    var ntc = {"A":21, "C":20, "G":22, "T":20, "U":19}
    var cnt = 0
    for (var i = start; i <= finish; i++) {
        cnt += (ntc[seq[i]] + (rna ? 1 : 0))
    }
    return cnt
}

# Generate a helix
function gen_helix_strand(reverse, drm, double) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    var cha = ":" + gChain1
    var chb = ":" + gChain2
    var seq = ""
    if (reverse) {
        for (var i = gSeq.count; i > 0; i--) {
            seq += gSeq[i]%9999%0
        }
    }
    else {
        seq = gSeq%9999%0
    }

    var cSeq = ""
    if (double) {
        for (var i = seq.count; i > 0; i--) {
            cSeq += ((seq[i] == 'A') and (drm > 0)) ? "U" : kNtComp[seq[i]]
        }
    }
    var aAtomCount = count_atoms(seq, (drm == 1), 1, seq.count)
    var bAtomCount = count_atoms(cSeq, (drm > 0), 1, cSeq.count)

    # global new P atom index for chain A
    gNa = ((m > 0) ? {(file=f) and (model=m)}.atomno.max + 1 : 1)
    gNb = 0
    if (double) {
        gNb = (aAtomCount + bAtomCount
         - count_atoms(cSeq, (drm>0), cSeq.count, cSeq.count)) # last P in cSeq
    }

    var aResno = 1
    var pNa = 1    # previous gNa

    gAppendNew = appendNew
    if (gNewFrame) {
        appendNew = true
        gNa = 1
    }
    else {
        appendNew = false

        # While there is an atom at the origin
        while (m > 0) {

            var ai = {within(0.1, {0 0 0}) and (file=f) and (model=m)}
            if (ai.size > 0) {

                # If on the same chain
                if (ai[1].chain = gChain1) {

                    # Add to existing strand
                    echo "Adding to existing strand..."
                    pNa = ai.atomno
                    aResno = {(chain=gChain1) and (file=f)
                        and (model=m)}.resno.max + 1
                    gNa = {(chain=gChain1) and (file=f)
                        and (model=m)}.atomno.max + 1
                    gNb += gNa

                    # Bump up all B chain atomno and resno
                    savNb = gNb
                    gNb = aAtomCount + bAtomCount + gNa
                    gA = "data \"append nt\"\n"    # global PDB atom record
                    for (j = 1; j <= all.atomno.max; j++) {
                        var aj = {(atomno=j) and (file=f) and (model=m)
                            and (chain == gChain2)}
                        if (aj.size > 0) {
                            gA += gen_atom_nt(aj.atomName, aj.group,
                                (aj.resno+seq.count+cSeq.count),
                                array(aj.x, aj.y, aj.z), true)
                        }
                    }
                    gA += "end \"append nt\""
                    delete @chb
                    script inline @{gA} # <== new atoms added here
                    gNb = savNb
                    break;
                }
                # Else move all from the new chain rightward on X axis
                else {
                    select {(file=f) and (model=m) and (chain!=gChain1)
                        and (chain!=gChain2)}
                    translateselected {0, -20, -20 }
                }
            }
            else {
                break
            }
        } # endwhile
    }
    var bResno = aResno + seq.count + cSeq.count - 1

    var nNa = gNa    # new P
    var nNb = 0#bBase  # new comp P

    # For each NT
    for (var i = 1; i <= seq.count; i++) {

        if (seq[i] == "") {
            continue
        }

        # Move polynucleotide O3p to bond distance 1.59 from new nt P
        var pO3 = {  -0.759, 0.925, 1.048}
        if (double) {
            select ((@cha or @chb) and (file=f) and (model=m))
        }
        else {
            select (@cha and (file=f) and (model=m))
        }
        if ((i + aResno) > 2) {
            var nO3 =  {@cha and (atomno=@{pNa+8})
                and (file=f) and (model=m)}.xyz
            var xyz = @{pO3 - nO3}
            translateselected @xyz
        }

        # Gen NT ==================================================
        gA = "data \"append nt\"\n"    # global PDB atom record
        gA += gen_nt(aResno, seq[i], (drm == 1), false); # gNa updated
        if (double) {
            nNb = gNb
            var nti = cSeq.count-i+1
            gA += gen_nt(bResno, cSeq[nti], (drm > 0), true); # gNb++
            if (i > 0) {
                gNb -= count_atoms(cSeq, (drm>0), nti-1, nti)
            }
        }
        gA += "end \"append nt\""
        script inline @{gA} # <== new atoms added here

        f = (_frameID/1000000)
        m = (_frameID%1000000)
        appendNew = false

        # Flip comp to comp strand
        if (double) {
            select @{("" + bResno + chb + "/" + f + "." + m)}
            var v1={8.238, 2.809, 6.004}
            var v2={8.461, 4.646, 4.125}
            rotateSelected @v2 @v1 180.0
        }

        # If any older NTs
        if ((i + aResno) > 2) {

            # Set the angles between the new NT and the old NTs
            select (((@cha and (atomno < nNa)) or (@chb and (resno != bResno)))
                and (file=f) and (model=m))
            set_angle_no(nNa, pNa+8, pNa+7, 120.0)
            select (((@cha and (atomno < @{nNa+3}))
                or (@chb and (resno != bResno))) and (file=f) and (model=m))
            set_dihedral_no(nNa+4, nNa+3, nNa, pNa+8, kC5O5PO3)

            select (((@cha and (atomno < nNa)) or (@chb and (resno != bResno)))
                and (file=f) and (model=m))
            set_dihedral_no(nNa+3, nNa, pNa+8, pNa+7, kO5PO3C3)

            set_dihedral_no(nNa, pNa+8, pNa+7, pNa+5, kPO3C3C4)
        }

        # Step new and previous N
        aResno++; bResno--
        pNa = nNa
        nNa = gNa; nNb = gNb
    }

    # Make the nucleotide bonds
    connect

    # Clean up
    appendNew = gAppendNew
    echo
    select ((file=f) and (model=m))
    refresh

    # Convert to A-form if RNA or mixed else B-form
    try {
        script $SCRIPT_PATH$toabNT.spt
        var s = format("Convert to %s-form?", ((drm > 0) ? "A" : "tight B"))
        var p = prompt(s, "Yes|No", true)
        if (p = "Yes") {
            to_ab_nt_auto(gChain1, (drm > 0))
        }
    }
    catch {
    }
}

# Generate a helix or two
function plico_gen_helix(seq) {

    if (gPlicoRecord != "") {
        var g = format("show file \"%s\"", gPlicoRecord)
        var ls = script(g)
        if (ls.find("FileNotFoundException")) {
            ls = ""
        }
        ls += format("plico_gen_helix(\"%s\");", gSeq)
        write var ls @gPlicoRecord
    }

    var single = false
    var reverse = false
    var drm = 0
    var done = false
    gSeq = seq%9999%0
    print format ("Seq=%s", gSeq)

    gNewFrame = false
    if (gSeq[1] == '+') {
        gNewFrame = true
        gSeq = gSeq[2][9999]
    }
    if (gSeq[2] == ':') {
        gChain1 = gSeq[1]
        gSeq = gSeq[3][9999]
    }
    else if (gSeq[3] == ':') {
        gChain1 = gSeq[1]
        gChain2 = gSeq[2]
        gSeq = gSeq[4][9999]
    }
    while (done == false) {
        done = true;
        if (gSeq[1] == 'S') {
            single = true;
            done = false;
        }
        else if (gSeq[1] == '3') {
            reverse = true;
            done = false;
        }
        else if (gSeq[1] == 'R') {
            drm = 1;
            done = false;
        }
        else if (gSeq[1] == 'M') {
            drm = 2;
            done = false;
        }
        if (done == false) {
            gSeq = gSeq[2][9999]
        }
    }

    if (drm = 1) {
        gSeq = gSeq.replace('T', 'U')
    }
    else {
        gSeq = gSeq.replace('U', 'T')
    }

    # Generate
    gen_helix_strand(reverse, drm, single ? false : true)

}

function plico_gen_nt {
    echo Generating Nucleotide Helix

    # Get the sequence from the user
    var seq = prompt("Enter NT sequence (<+AB:3RSM>ACGTU...)", "")%9999%0
    if ((seq != "NULL") and (seq.count > 0)) {
        plico_gen_helix(seq)
    }
}
# end of polymeraze.spt

Contributors

Remig