Remig: Replaced content with "What I had here before belongs on the user page - so I moved it..."

2013-10-31T21:32:49Z

Replaced content with "What I had here before belongs on the user page - so I moved it..."

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Remig at 20:16, 31 October 2013

2013-10-31T20:16:53Z

Remig: Polymeraze - a DNA generator script

2013-10-31T20:06:53Z

Polymeraze - a DNA generator script

Remig: Polymeraze - a DNA Generator Script

2013-10-31T19:25:45Z

Polymeraze - a DNA Generator Script

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Remig at 22:59, 24 October 2013

2013-10-24T22:59:47Z

Remig: Alpha Helix generator

2013-10-23T12:39:35Z

Alpha Helix generator

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Remig: Ribozome - an Alpha Helix Generator

2013-10-20T03:07:33Z

Ribozome - an Alpha Helix Generator

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Remig: Alpha helix generater

2013-10-18T16:39:38Z

Alpha helix generater

New page

I use Jmol to study protein folding. Here is a script I wrote that accepts an amino acid sequence (1 letter encoding: "AAC...FYW" for example) and generates an alpha helix using the Model Kit:
<pre>function get3from1(c) {
ret = ""
switch (c) {
case 'A':
ret = "ALA";
break;
case 'C':
ret = "CYS";
break;
case 'D':
ret = "ASP";
break;
case 'E':
ret = "GLU";
break;
case 'F':
ret = "PHE";
break;
case 'G':
ret = "GLY";
break;
case 'H':
ret = "HIS";
break;
case 'I':
ret = "ILE";
break;
case 'K':
ret = "LYS";
break;
case 'L':
ret = "LEU";
break;
case 'M':
ret = "MET";
break;
case 'N':
ret = "ASN";
break;
case 'P':
ret = "PRO";
break;
case 'Q':
ret = "GLN";
break;
case 'R':
ret = "ARG";
break;
case 'S':
ret = "SER";
break;
case 'T':
ret = "THR";
break;
case 'U':
ret = "SEC";
break;
case 'V':
ret = "VAL";
break;
case 'W':
ret = "TRP";
break;
case 'Y':
ret = "TYR";
break;
}
return ret
};

function genAtom(n, e, aa, i, xyz) {
a = format("ATOM %5d %3s %3s A", n, e, aa )
a += format("%4d %8.3f", i, xyz[1] )
a += format("%8.3f%8.3f\n", xyz[2], xyz[3] )
return a
};

function genAA(i, aa, x) {
n = x

N0 = [0.0, 0.0, 0.0]
CA = [ 0.200, 1.174, 0.911 ]
C = [ -1.129, 1.783, 1.241 ]
O = [ -1.241, 1.967, 2.726 ]
CB = [ 1.062, 2.1950, 0.230 ]
G1 = [ 2.396, 1.588, -0.091 ]
G2 = [ 0.680, 3.652, 0.423]
Gfy = [ 2.368, 1.471, -0.0152 ]
Ghw = [ 2.406, 1.626, -0.134 ]
D1 = [ 3.225, 2.340, -1.096]
D1hw = [3.498, 1.936, 0.675]
D1fy = [ 3.346, 1.524, 0.921 ]
D2 = [ 3.189, 1.093, 1.087]
D2hw = [ 2.713, 0.901, -1.211 ]
D2fy = [ 2.493, 0.516, -1.151 ]
E1fy = [ 4.513, 0.615, 0.8244 ]
E1hw = [ 4.160, 0.518, -1.178 ]
E2fy = [ 3.528, -0.336, -1.206 ]
E2hw = [ 4.622, 1.160, 0.0816 ]
E3hw = [ 3.789, 2.523, 1.944 ]
Z2hw = [ 5.973, 1.177, 0.689 ]
Z3hw = [ 5.014, 2.550, 2.503 ]
H2hw = [ 6.153, 1.846, 1.844 ]
Zfy = [ 4.588, -0.285, -0.168 ]
Hfy = [ 5.738, -1.245, -0.233 ]
N1 = [ -1.965, 2.307, 0.206 ]
Gp = [ 2.008, 1.24, -0.46 ]
Dp = [1.022, 0.213, -1.031 ]
E1 = [ 3.652, 3.503, -0.111 ]
E2 = [ 4.342, 1.591, -1.456 ]
Z = [ 4.115, 3.339, 1.403 ]
H1 = [4.087, 4.572, 2.139]
H2 = [5.469, 2.866, 1.296]

a3 = get3from1(seq[i])
a = genAtom(n++, "N ", a3, i, N0)
a += genAtom(n++, "CA ", a3, i, CA)
a += genAtom(n++, "C ", a3, i, C)
a += genAtom(n++, "O ", a3, i, O)
if (seq[i] != 'G') {
a += genAtom(n++, "CB ", a3, i, CB)
}

switch (aa) {
case 'A' :
break;
case 'C' :
a += genAtom(n++, "SG ", a3, i, G1)
break;
case 'D' :
a += genAtom(n++, "CG ", a3, i, G1)
a += genAtom(n++, "OD1", a3, i, D1)
a += genAtom(n++, "OD2", a3, i, D2)
break;
case 'E' :
a += genAtom(n++, "CG ", a3, i, G1)
a += genAtom(n++, "CD ", a3, i, D1)
a += genAtom(n++, "OE1", a3, i, E1)
a += genAtom(n++, "OE2", a3, i, E2)
break;
case 'F' :
a += genAtom(n++, "CG ", a3, i, Gfy)
a += genAtom(n++, "CD1", a3, i, D1fy)
a += genAtom(n++, "CD2", a3, i, D2fy)
a += genAtom(n++, "CE1", a3, i, E1fy)
a += genAtom(n++, "CE2", a3, i, E2fy)
a += genAtom(n++, "CZ ", a3, i, Zfy)
break;
case 'G' :
break;
case 'H' :
a += genAtom(n++, "CG ", a3, i, Ghw)
a += genAtom(n++, "ND1", a3, i, D1hw)
a += genAtom(n++, "CD2", a3, i, D2hw)
a += genAtom(n++, "CE1", a3, i, E2hw)
a += genAtom(n++, "NE2", a3, i, E1hw)
break;
case 'I' :
a += genAtom(n++, "CG1", a3, i, G1)
a += genAtom(n++, "CG2", a3, i, G2)
a += genAtom(n++, "CD1", a3, i, D1)
break;
case 'K' :
a += genAtom(n++, "CG ", a3, i, G1)
a += genAtom(n++, "CD ", a3, i, D1)
a += genAtom(n++, "CE ", a3, i, E1)
a += genAtom(n++, "NZ ", a3, i, Z)
break;
case 'L' :
a += genAtom(n++, "CG1", a3, i, G1)
a += genAtom(n++, "CD1", a3, i, D1)
a += genAtom(n++, "CD2", a3, i, D2)
break;
case 'M' :
a += genAtom(n++, "CG ", a3, i, G1)
a += genAtom(n++, "SD ", a3, i, D1)
a += genAtom(n++, "CE ", a3, i, E1)
break;
case 'N' :
a += genAtom(n++, "CG ", a3, i, G1)
a += genAtom(n++, "OD1", a3, i, D1)
a += genAtom(n++, "ND2", a3, i, D2)
break;
case 'P' :
a += genAtom(n++, "CG ", a3, i, GP)
a += genAtom(n++, "CD ", a3, i, DP)
break;
case 'Q' :
a += genAtom(n++, "CG ", a3, i, G1)
a += genAtom(n++, "CD ", a3, i, D1)
a += genAtom(n++, "OE1", a3, i, E1)
a += genAtom(n++, "NE2", a3, i, E2)
break;
case 'R' :
a += genAtom(n++, "CG ", a3, i, G1)
a += genAtom(n++, "CD ", a3, i, D1)
a += genAtom(n++, "NE ", a3, i, E1)
a += genAtom(n++, "CZ ", a3, i, Z)
a += genAtom(n++, "NH1", a3, i, H1)
a += genAtom(n++, "NH2", a3, i, H2)
break;
case 'S' :
a += genAtom(n++, "OG ", a3, i, G1)
break;
case 'T' :
a += genAtom(n++, "OG1", a3, i, G1)
a += genAtom(n++, "CG2", a3, i, G2)
break;
case 'U' :
a += genAtom(n++, "SeG", a3, i, G1)
break;
case 'V' :
a += genAtom(n++, "CG1", a3, i, G1)
a += genAtom(n++, "CG2", a3, i, G2)
break;
case 'W' :
a += genAtom(n++, "CG ", a3, i, Ghw)
a += genAtom(n++, "CD1", a3, i, D1hw)
a += genAtom(n++, "CD2", a3, i, D2hw)
a += genAtom(n++, "CE2", a3, i, E2hw)
a += genAtom(n++, "NE1", a3, i, E1hw)
a += genAtom(n++, "CE3", a3, i, E3hw)
a += genAtom(n++, "CZ2", a3, i, Z2hw)
a += genAtom(n++, "CZ3", a3, i, Z3hw)
a += genAtom(n++, "CH2", a3, i, H2hw)
break;
case 'Y' :
a += genAtom(n++, "CG ", a3, i, Gfy)
a += genAtom(n++, "CD1", a3, i, D1fy)
a += genAtom(n++, "CD2", a3, i, D2fy)
a += genAtom(n++, "CE1", a3, i, E1fy)
a += genAtom(n++, "CE2", a3, i, E2fy)
a += genAtom(n++, "CZ ", a3, i, Zfy)
a += genAtom(n++, "OH ", a3, i, Hfy)
break;
default :
break;
}

return a
}

# GenAlph
function genAlpha(seq, pa) {

# For each aa
set appendnew false
n = 1
pn = 0
pc= 0 # previous C
for (var i = 1; i <= seq.count; i++) {

pn = n
m = pn + 1

# Anticipate PRO
dpsi = 0
dphi = 0
if ((seq.count - i) >= 4) {
if (seq[i + 4] == 'P') {
dpsi = =9
}
}
if ((seq.count - i) >= 3) {
if (seq[i + 3] == 'P') {
dphi = 10
}
}
if ((seq.count - i) >= 2) {
if (seq[i + 2] == 'P') {
dpsi = -11
#dphi = -0
}
}
if ((seq.count - i) >= 1) {
if (seq[i + 1] == 'P') {
dpsi = 25
#dphi = -81
}
}

# Move polypeptide C to bond distance to next AA N
select all
fix none
translateselected { 1.955, -1.993, 0.000 }

# Gen AA
a = "data \"append aa\"\n"
a += genAA(i, seq[i], n);
a += "end \"append aa\""
script inline @{a}

# If not first AA
if (pc > 0) {
v1={atomno=pc}.xyz - {atomno=pn}.xyz
v2={atomno=m}.xyz - {atomno=pn}.xyz
# Gen normalized axis perpendicular to the plane contaoning atoms pc, pn and m
axis = cross(v1, v2) - {atomno=pn}.xyz

# Center on atom pn
axis += {atomno=pn}.xyz

# Rotate the polypeptide on the new AA
select atomno<pn
fix atomno>=pn

# pull peptide angle trigonal
rotateselected @axis {atomno=pn} @{pa-62}

# Make peptide bond dihedral 180
rotateselected {atomno=pc} {atomno=pn} 52

# Make the phi -60
rotateselected {atomno=pn} {atomno=m} @{dphi - 68}

# Make the psi -45
pca = pc - 1
fix atomno>pca
select atomno<pn and (atomno != @{pc+1})
rotateselected {atomno=pc} {atomno=pca} @{dpsi}

# If aromatic go trans on chi 1
select atomno>@{pn+4} and atomno<n
if ((seq[i] == 'H') || (seq[i] == 'W') || (seq[i] == 'F') || (seq[i] == 'Y')) {
rotateselected {atomno=@{pn+1}} {atomno=@{pn+4}} -120
}

}
pc =pn + 2

connect
}
select all
fix none
}

echo Generating Alpha Helix
zap

# Get the sequence from the user
seq = prompt("Enter AA sequence (1 char coded)", "")%9999
pa = prompt("Enter the peptide angle", "120")
print format ("seq=%s at %d deg", seq, pa)
genAlpha(seq , pa)

</pre>

@@ Line 12: / Line 12: @@
 #   If prepended with 'R' then RNA is generated instead of DNA
 #   If prepended with 'S' then a single strand helix is produced
+#
 #   The IUPAC/IUBMB 1 letter code is used:

@@ Line 211: / Line 211: @@
      gNa = all.count + 1 # global new N atom index
      gNb = (double ? (gNa + countAtoms(seq) + ((gResno > 0) ? 0 : 1)) : 0)
-print format("gNa=%d gNb = %d", gNa, gNb)
      # Find last linkable P if any
      gResno = 0    # global pre-existing NT count
@@ Line 219: / Line 219: @@
          # If found
          if (distance({atomno=i}, {0,0,0})  < 0.1) {
-             if ({atomno=i}.chain == chain[2]) {
+             if ({atomno=i}.chain == cha[2]) {
                  pna = i
+             }

@@ Line 48: / Line 48: @@
      gA +=  format("%s%4d    %8.3f", gCHAIN, i, xyz[1] )
      gA +=  format("%8.3f%8.3f\n", xyz[2], xyz[3] )
-     gn++
+     gN++
      return gA
 };

User talk:Remig - Revision history

Remig: Replaced content with "What I had here before belongs on the user page - so I moved it..."

Remig at 20:16, 31 October 2013

Remig: Polymeraze - a DNA generator script

Remig: Polymeraze - a DNA Generator Script

Remig at 22:59, 24 October 2013

Remig: Alpha Helix generator

Remig: Ribozome - an Alpha Helix Generator

Remig: Alpha helix generater