User:Remig
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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.
