User:Remig

My interest is in protein folding for which I have written software tools in Java over the years. I had always displayed in JMol and only now realize I could have written in JMol script directly and have folded and viewed in the same application. I am now doing so and will present scripts of possible interest to others in the discussion tab for the general amusement.

The script shown here before that generates polypeptide helices is now available in the Recycling Corner: Recycling_Corner/Alpha_Helix_Generator so I have removed it from here. In its place is a similar script I wrote that accepts a nucleotide sequence (1 letter encoding: "TACGAAC...GCT" for example) and generates a DNA or RNA single or double helix using the Model Kit:

#   POLYMERAZE - Jmol script by Ron Mignery
#   v1.0 beta    10/31/2013
#
#   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 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 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
#
#   Multiple runs append to the previous helix if any unless it is moved
#
#   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
gO4C4C5O5 = -82.3 - 10      # Values from 30-31:B of 3BSE
gC4C5O5P = 172.5 + 0        # with the indicated tweaks to make
gC5O5PO3 = -44.0 + 9        # it work (sort of - yes, I know
gO5PO3C3 = -109.8 + 0       # the B chain P is a bit screwy)
gPO3C3C4 = -172.9 - 1       #
gCHAIN1 = 'A'    # The chain id
gCHAIN2 = 'B'    # The complementary chain id

# Lookup 3 letter code from 1 letter code
g3from1 = {"A":" DA", "C":" DC","G":" DG", "T":" DT", "U":" DU"}
gComp = {"A":"T", "C":"G","G":"C", "T":"A", "U":"A"}

# Generate PDB atom record
# Writes gNa or gNb
function genAtom(e, aa, i, xyz, comp) {
    # Fixed column format:
    #ATOM    500  O4'  DA B  29      -3.745   7.211  45.474
    var a =  format("ATOM  %5d %4s %3s ", (comp ? gNb : gNa), e, aa )
    a +=  format("%s%4d    %8.3f", (comp ? gCHAIN2 : gCHAIN1), i, 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 genAtom that writes gNa or gNb
function genNT(i, nt, rna, comp) {

    # From constructed nucleotides
    var P0 = (comp ? [16.753, 4.551, 8.935] : [0.000, 0.000, 0.000])
    var OP1= (comp ? [17.916, 5.432, 9.209] : [-0.973, 0.363, -1.067])
    var OP2= (comp ? [16.030, 4.050, 10.108] : [0.297, -1.428, 0.272])
    var O5p= (comp ? [16.110, 5.278, 7.954] : [1.351, 0.795, -0.286])
    var C5p= (comp ? [16.536, 5.450, 6.610] : [1.345, 2.211, -0.125])
    var C4p= (comp ? [15.487, 6.211, 5.838] : [2.739, 2.779, -0.195])
    var O4p= (comp ? [14.427, 5.302, 5.454] : [3.469, 2.629, 1.048])
    var C3p= (comp ? [14.830, 7.309, 6.676] : [3.624, 2.197, -1.288])
    var O3p= (comp ? [14.657, 8.490, 5.878] : [4.212, 3.282, -1.983])
    var C2p= (comp ? [13.509, 6.688, 7.119] : [4.692, 1.432, -0.523])
    var O2p= (comp ? [12.530, 7.743, 7.153] : [5.994, 1.461, -1.226])
    var C1p= (comp ? [13.175, 5.739, 5.976] : [4.797, 2.255, 0.746])
    
    var N1ct=(comp ? [12.404, 4.556, 6.401] :  [5.353, 1.551, 1.907])
    var C2ct=(comp ? [11.423, 4.111, 5.551] : [6.351, 2.183, 2.606])
    var O2ct=(comp ? [11.137, 4.685, 4.516] : [6.789, 3.274, 2.289])
    var N3ct=(comp ? [10.784, 2.966, 5.956] :  [6.823, 1.489, 3.692])
    var C4ct=(comp ? [11.025, 2.241, 7.106] :  [6.404, 0.251, 4.135])
    var NO4ct=(comp ?[10.382, 1.213, 7.329] :  [6.908, -0.242, 5.146])
    var C5ct=(comp ? [12.061, 2.780, 7.971] :  [5.360, -0.370, 3.337])
    var C6ct=(comp ? [12.692, 3.894, 7.575] :  [4.892, 0.307, 2.279])
    var nC7ct=(comp ?[12.421, 2.090, 9.243] :  [4.862, -1.727, 3.721])
    
    var N9ag=(comp ? [12.426, 4.545, 6.367] :  [5.333, 1.584, 1.923])
    var C8ag=(comp ? [12.706, 3.662, 7.382] :  [4.870, 0.450, 2.545])
    var N7ag=(comp ? [11.856, 2.668, 7.467] :  [5.595, 0.076, 3.570])
    var C5ag=(comp ? [10.952, 2.911, 6.441] :  [6.608, 1.025, 3.629])
    var C6ag=(comp ? [9.818, 2.215, 5.997] :   [7.694, 1.194, 4.500])
    var NO6ag=(comp ?[9.379, 1.083, 6.552] :   [7.955, 0.379, 5.525])
    var N1ag=(comp ? [9.137, 2.727, 4.945] :   [8.517, 2.246, 4.283])
    var C2ag=(comp ? [9.573, 3.862, 4.390] :   [8.259, 3.061, 3.256])
    var nN2ag=(comp ?[8.847, 4.313, 3.345] :   [9.119, 4.090, 3.100])
    var N3ag=(comp ? [10.630, 4.605, 4.715] :  [7.265, 3.009, 2.370])
    var C4ag=(comp ? [11.285, 4.068, 5.759] :  [6.465, 1.956, 2.616])
    
    # Build PDB atom records common to all NTs
    n3 = g3from1[nt]
    if (n3 = "") {
        n3 = " D?"
    }
    print format("+ %s%d/%d", n3, i, gSeq.count + gResno)
    var a = genAtom(" P  ", n3, i, P0, comp)
    a += genAtom(" OP1", n3, i, OP1, comp)
    a += genAtom(" OP2", n3, i, OP2, comp)
    a += genAtom(" O5'", n3, i, O5p, comp)
    a += genAtom(" C5'", n3, i, C5p, comp)
    a += genAtom(" C4'", n3, i, C4p, comp)
    a += genAtom(" O4'", n3, i, O4p, comp)
    a += genAtom(" C3'", n3, i, C3p, comp)
    a += genAtom(" O3'", n3, i, O3p, comp)
    a += genAtom(" C2'", n3, i, C2p, comp)
    a += genAtom(" C1'", n3, i, C1p, comp)
    if (rna) {
        a += genAtom(" O2'", n3, i, O2p, comp)
    }

    # Now add NT specific atom records
    switch (nt) {
    case 'A' :
        a += genAtom(" N9 ", n3, i, N9ag, comp)
        a += genAtom(" C8 ", n3, i, C8ag, comp)
        a += genAtom(" N7 ", n3, i, N7ag, comp)
        a += genAtom(" C5 ", n3, i, C5ag, comp)
        a += genAtom(" C6 ", n3, i, C6ag, comp)
        a += genAtom(" N6 ", n3, i, NO6ag, comp)
        a += genAtom(" N1 ", n3, i, N1ag, comp)
        a += genAtom(" C2 ", n3, i, C2ag, comp)
        a += genAtom(" N3 ", n3, i, N3ag, comp)
        a += genAtom(" C4 ", n3, i, C4ag, comp)
        break;
    case 'C' :
        a += genAtom(" N1 ", n3, i, N1ct, comp)
        a += genAtom(" C2 ", n3, i, C2ct, comp)
        a += genAtom(" O2 ", n3, i, O2ct, comp)
        a += genAtom(" N3 ", n3, i, N3ct, comp)
        a += genAtom(" C4 ", n3, i, C4ct, comp)
        a += genAtom(" N4 ", n3, i, NO4ct, comp)
        a += genAtom(" C5 ", n3, i, C5ct, comp)
        a += genAtom(" C6 ", n3, i, C6ct, comp)
        break;
    case 'G' :
        a += genAtom(" N9 ", n3, i, N9ag, comp)
        a += genAtom(" C8 ", n3, i, C8ag, comp)
        a += genAtom(" N7 ", n3, i, N7ag, comp)
        a += genAtom(" C5 ", n3, i, C5ag, comp)
        a += genAtom(" C6 ", n3, i, C6ag, comp)
        a += genAtom(" O6 ", n3, i, NO6ag, comp)
        a += genAtom(" N1 ", n3, i, N1ag, comp)
        a += genAtom(" C2 ", n3, i, C2ag, comp)
        a += genAtom(" N2 ", n3, i, nN2ag, comp)
        a += genAtom(" N3 ", n3, i, N3ag, comp)
        a += genAtom(" C4 ", n3, i, C4ag, comp)
        break;
    case 'T' :
        a += genAtom(" N1 ", n3, i, N1ct, comp)
        a += genAtom(" C2 ", n3, i, C2ct, comp)
        a += genAtom(" O2 ", n3, i, O2ct, comp)
        a += genAtom(" N3 ", n3, i, N3ct, comp)
        a += genAtom(" C4 ", n3, i, C4ct, comp)
        a += genAtom(" O4 ", n3, i, NO4ct, comp)
        a += genAtom(" C5 ", n3, i, C5ct, comp)
        a += genAtom(" C6 ", n3, i, C6ct, comp)
        a += genAtom(" C7 ", n3, i, nC7ct, comp)
        break;
    case 'U' :
        a += genAtom(" N1 ", n3, i, N1ct, comp)
        a += genAtom(" C2 ", n3, i, C2ct, comp)
        a += genAtom(" O2 ", n3, i, O2ct, comp)
        a += genAtom(" N3 ", n3, i, N3ct, comp)
        a += genAtom(" C4 ", n3, i, C4ct, comp)
        a += genAtom(" O4 ", n3, i, NO4ct, comp)
        a += genAtom(" C5 ", n3, i, C5ct, comp)
        a += genAtom(" 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 setAngle (a1, a2, a3, toangle) {
    var v1={atomno = a1}.xyz - {atomno = a2}.xyz
    var v2={atomno = a3}.xyz - {atomno = a2}.xyz
    var axis = cross(v1, v2) + {atomno = a2}.xyz
    var curangle =  angle({atomno=a1}, {atomno=a2}, {atomno=a3})
    rotateselected @axis {atomno = 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 setDihedral (a1, a2, a3, a4, toangle) {
    var curangle =  angle({atomno=a1}, {atomno=a2}, {atomno=a3}, {atomno=a4})
    rotateselected {atomno=a2} {atomno=a3} @{toangle-curangle}
}

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

# Generate a helix
function genHelixStrand(gSeq, reverse, rna, double) {
    var cha = ":A"
    var chb = ":B"
    var seq = ""
    if (reverse) {
        for (var i = gSeq.count; i > 0; i--) {
            seq += gSeq[i]
        }
    }
    else {
        seq = gSeq
    }

    gNa = all.count + 1 # global new N atom index
    gNb = (double ? (gNa + countAtoms(seq) + ((gResno > 0) ? 0 : 1)) : 0)

    # Find last linkable P if any
    gResno = 0    # global pre-existing NT count
    var pna = 1    # previous gN
    for (var i = all.count-1; i  > 0; i--) {

        # If found
        if (distance({atomno=i}, {0,0,0})  < 0.1) {
            if ({atomno=i}.chain == cha[2]) {
                pna = i
            }
            gResno = {atomno=i}.resno
            break;
        }
    }

    # For each nt
    set appendnew false
    var nna = gNa    # new P
    var nnb = gNb    # new P
    for (var i = 1; i <= seq.count; i++) {
        if (seq[i] == "") {
            continue
        }
           
        gA = "data \"append nt\"\n"    # global PDB atom record
        
        # Move polynucleotide O3p to bond distance from new nt P
        var pO3 = {-0.521, 0.638, 1.234}
        select all
        if ((i + gResno) > 1) {
            var nO3 =  {atomno=@{pna+8}}.xyz
            var xyz = @{pO3 - nO3}
            translateselected @xyz
        }

        # Else 1st 5' nt so add OP3
        else {
            var O3n = {pO3n}.xyz
            gA += genAtom(" OP3", g3from1[seq[i]], i + gResno, O3n, FALSE)
            nna++
        }
                
        # Gen NT ==================================================
        gA += genNT(i + gResno, seq[i], rna, FALSE);    # gNa updated
        if (double) {
            gA += genNT(i + gResno + seq.count, gComp[seq[i]], rna, TRUE);    # gNb updated
        }
        gA += "end \"append nt\""
        script inline @{gA} # <== new atoms added here

        # First shape up the comp side
        if (double) {
            select (@chb and (atomno < @{nnb + 6}) && (atomno >= nnb))
            setDihedral(nnb+6, nnb+5, nnb+4, nnb+3, gO4C4C5O5)
            select selected and (atomno != @{nnb + 5})
            setDihedral(nnb+5, nnb+4, nnb+3, nnb, gC4C5O5P)
        }
        # Adjust link dihedrals of the new
        select (@cha and (atomno > @{nna+4}) or (@chb and (atomno >= nnb)))
        setDihedral(nna+3, nna+4, nna+5, nna+6, gO4C4C5O5)
        setDihedral(nna, nna+3, nna+4, nna+5, gC4C5O5P)
     
        # If any older
        if (i > 1) {
            # Now move the old
            select (@cha and (atomno < nna) or (@chb and (atomno < nnb)))
            setAngle(nna, pna+8, pna+7, 120.0)
            
            select (@cha and (atomno < @{nna+3}) or (@chb and (atomno < nnb)))
            setDihedral(nna+4, nna+3, nna, pna+8, gC5O5PO3)
            
            select (@cha and (atomno < nna) or (@chb and (atomno < nnb)))
            setDihedral(nna+3, nna, pna+8, pna+7, gO5PO3C3)
            
            setDihedral(nna, pna+8, pna+7, pna+5, gPO3C3C4)
        }
        
        # Step new and previous N
        pna = nna; pnb = nnb
        nna = gNa; nnb = gNb
    }
    
    # Make the nucleotide bonds
    connect
    
    # Clean up
    select all
    print format("%d atoms generated for chain %s", gNa+gNb,
        (comp ? gCHAIN2 : gCHAIN1))
}

# Generate a helix or two
function genHelix(gSeq) {
var single = FALSE
var reverse = FALSE
var rna = FALSE
var done = FALSE
    if (gSeq[2] == ':') {
        gCHAIN1 = gSeq[1]
        gSeq[1] = ' '; gSeq[2] = ' '
        gSeq = gSeq%0
    }
    else if (gSeq[3] == ':') {
        gCHAIN1 = gSeq[1]
        gCHAIN2 = gSeq[2]
        gSeq[1] = ' '; gSeq[2] = ' '; gSeq[3] = ' '
        gSeq = gSeq%0
    }
    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') {
            rna = TRUE;
            done = FALSE;
        }
        if (done == FALSE) {
            gSeq[1] = ' '
            gSeq = gSeq%0
        }
    }
    print format ("Sequence=%s single=%s reverse=%s", gSeq, single, reverse)
    print format ("rna=%s", rna)
    
    # Gen first strand
    genHelixStrand(gSeq, reverse, rna, single ? FALSE : TRUE)

}

# ==============================================
echo Generating Alpha Helix

# Get the sequence from the user
gSeq = prompt("Enter NT sequence (ACGTU)", "")%9999%0
if (gSeq.count > 0) {
    genHelix(gSeq)
}

I thought adapting the Ribozome script to polynucleotides would be easy since there are only four types rather than 20. I was not easy and this script has its problems. With five rotors in a row for each nucleotide, finding correct values for the bond angles was beyond me. If anyone can tweak them better, please do and let me know. Regardless I plan to develop some more utility scripts to make that process easier and hope to update this script in the hopefully not too distant future.

Contributors

Remig