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| − | 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: | + | What I had here before belongs on the user page - so I moved it... |
| − | <pre>function get3from1(c) {
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| − | ret = ""
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| − | switch (c) {
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| − | case 'A':
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| − | ret = "ALA";
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| − | break;
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| − | case 'C':
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| − | ret = "CYS";
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| − | break;
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| − | case 'D':
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| − | ret = "ASP";
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| − | break;
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| − | case 'E':
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| − | ret = "GLU";
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| − | break;
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| − | case 'F':
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| − | ret = "PHE";
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| − | break;
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| − | case 'G':
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| − | ret = "GLY";
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| − | break;
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| − | case 'H':
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| − | ret = "HIS";
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| − | break;
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| − | case 'I':
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| − | ret = "ILE";
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| − | break;
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| − | case 'K':
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| − | ret = "LYS";
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| − | break;
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| − | case 'L':
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| − | ret = "LEU";
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| − | break;
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| − | case 'M':
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| − | ret = "MET";
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| − | break;
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| − | case 'N':
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| − | ret = "ASN";
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| − | break;
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| − | case 'P':
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| − | ret = "PRO";
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| − | break;
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| − | case 'Q':
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| − | ret = "GLN";
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| − | break;
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| − | case 'R':
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| − | ret = "ARG";
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| − | break;
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| − | case 'S':
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| − | ret = "SER";
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| − | break;
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| − | case 'T':
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| − | ret = "THR";
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| − | break;
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| − | case 'U':
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| − | ret = "SEC";
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| − | break;
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| − | case 'V':
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| − | ret = "VAL";
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| − | break;
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| − | case 'W':
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| − | ret = "TRP";
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| − | break;
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| − | case 'Y':
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| − | ret = "TYR";
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| − | break;
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| − | }
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| − | return ret
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| − | };
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| − | | |
| − | function genAtom(n, e, aa, i, xyz) {
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| − | a = format("ATOM %5d %3s %3s A", n, e, aa )
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| − | a += format("%4d %8.3f", i, xyz[1] )
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| − | a += format("%8.3f%8.3f\n", xyz[2], xyz[3] )
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| − | return a
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| − | };
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| − | | |
| − | function genAA(i, aa, x) {
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| − | n = x
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| − | | |
| − | N0 = [0.0, 0.0, 0.0]
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| − | CA = [ 0.200, 1.174, 0.911 ]
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| − | C = [ -1.129, 1.783, 1.241 ]
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| − | O = [ -1.241, 1.967, 2.726 ]
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| − | CB = [ 1.062, 2.1950, 0.230 ]
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| − | G1 = [ 2.396, 1.588, -0.091 ]
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| − | G2 = [ 0.680, 3.652, 0.423]
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| − | Gfy = [ 2.368, 1.471, -0.0152 ]
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| − | Ghw = [ 2.406, 1.626, -0.134 ]
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| − | D1 = [ 3.225, 2.340, -1.096]
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| − | D1hw = [3.498, 1.936, 0.675]
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| − | D1fy = [ 3.346, 1.524, 0.921 ]
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| − | D2 = [ 3.189, 1.093, 1.087]
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| − | D2hw = [ 2.713, 0.901, -1.211 ]
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| − | D2fy = [ 2.493, 0.516, -1.151 ]
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| − | E1fy = [ 4.513, 0.615, 0.8244 ]
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| − | E1hw = [ 4.160, 0.518, -1.178 ]
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| − | E2fy = [ 3.528, -0.336, -1.206 ]
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| − | E2hw = [ 4.622, 1.160, 0.0816 ]
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| − | E3hw = [ 3.789, 2.523, 1.944 ]
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| − | Z2hw = [ 5.973, 1.177, 0.689 ]
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| − | Z3hw = [ 5.014, 2.550, 2.503 ]
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| − | H2hw = [ 6.153, 1.846, 1.844 ]
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| − | Zfy = [ 4.588, -0.285, -0.168 ]
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| − | Hfy = [ 5.738, -1.245, -0.233 ]
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| − | N1 = [ -1.965, 2.307, 0.206 ]
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| − | Gp = [ 2.008, 1.24, -0.46 ]
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| − | Dp = [1.022, 0.213, -1.031 ]
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| − | E1 = [ 3.652, 3.503, -0.111 ]
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| − | E2 = [ 4.342, 1.591, -1.456 ]
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| − | Z = [ 4.115, 3.339, 1.403 ]
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| − | H1 = [4.087, 4.572, 2.139]
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| − | H2 = [5.469, 2.866, 1.296]
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| − |
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| − | a3 = get3from1(seq[i])
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| − | a = genAtom(n++, "N ", a3, i, N0)
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| − | a += genAtom(n++, "CA ", a3, i, CA)
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| − | a += genAtom(n++, "C ", a3, i, C)
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| − | a += genAtom(n++, "O ", a3, i, O)
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| − | if (seq[i] != 'G') {
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| − | a += genAtom(n++, "CB ", a3, i, CB)
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| − | }
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| − | | |
| − | switch (aa) {
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| − | case 'A' :
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| − | break;
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| − | case 'C' :
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| − | a += genAtom(n++, "SG ", a3, i, G1)
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| − | break;
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| − | case 'D' :
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| − | a += genAtom(n++, "CG ", a3, i, G1)
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| − | a += genAtom(n++, "OD1", a3, i, D1)
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| − | a += genAtom(n++, "OD2", a3, i, D2)
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| − | break;
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| − | case 'E' :
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| − | a += genAtom(n++, "CG ", a3, i, G1)
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| − | a += genAtom(n++, "CD ", a3, i, D1)
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| − | a += genAtom(n++, "OE1", a3, i, E1)
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| − | a += genAtom(n++, "OE2", a3, i, E2)
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| − | break;
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| − | case 'F' :
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| − | a += genAtom(n++, "CG ", a3, i, Gfy)
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| − | a += genAtom(n++, "CD1", a3, i, D1fy)
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| − | a += genAtom(n++, "CD2", a3, i, D2fy)
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| − | a += genAtom(n++, "CE1", a3, i, E1fy)
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| − | a += genAtom(n++, "CE2", a3, i, E2fy)
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| − | a += genAtom(n++, "CZ ", a3, i, Zfy)
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| − | break;
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| − | case 'G' :
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| − | break;
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| − | case 'H' :
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| − | a += genAtom(n++, "CG ", a3, i, Ghw)
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| − | a += genAtom(n++, "ND1", a3, i, D1hw)
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| − | a += genAtom(n++, "CD2", a3, i, D2hw)
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| − | a += genAtom(n++, "CE1", a3, i, E2hw)
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| − | a += genAtom(n++, "NE2", a3, i, E1hw)
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| − | break;
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| − | case 'I' :
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| − | a += genAtom(n++, "CG1", a3, i, G1)
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| − | a += genAtom(n++, "CG2", a3, i, G2)
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| − | a += genAtom(n++, "CD1", a3, i, D1)
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| − | break;
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| − | case 'K' :
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| − | a += genAtom(n++, "CG ", a3, i, G1)
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| − | a += genAtom(n++, "CD ", a3, i, D1)
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| − | a += genAtom(n++, "CE ", a3, i, E1)
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| − | a += genAtom(n++, "NZ ", a3, i, Z)
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| − | break;
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| − | case 'L' :
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| − | a += genAtom(n++, "CG1", a3, i, G1)
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| − | a += genAtom(n++, "CD1", a3, i, D1)
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| − | a += genAtom(n++, "CD2", a3, i, D2)
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| − | break;
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| − | case 'M' :
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| − | a += genAtom(n++, "CG ", a3, i, G1)
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| − | a += genAtom(n++, "SD ", a3, i, D1)
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| − | a += genAtom(n++, "CE ", a3, i, E1)
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| − | break;
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| − | case 'N' :
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| − | a += genAtom(n++, "CG ", a3, i, G1)
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| − | a += genAtom(n++, "OD1", a3, i, D1)
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| − | a += genAtom(n++, "ND2", a3, i, D2)
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| − | break;
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| − | case 'P' :
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| − | a += genAtom(n++, "CG ", a3, i, GP)
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| − | a += genAtom(n++, "CD ", a3, i, DP)
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| − | break;
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| − | case 'Q' :
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| − | a += genAtom(n++, "CG ", a3, i, G1)
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| − | a += genAtom(n++, "CD ", a3, i, D1)
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| − | a += genAtom(n++, "OE1", a3, i, E1)
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| − | a += genAtom(n++, "NE2", a3, i, E2)
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| − | break;
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| − | case 'R' :
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| − | a += genAtom(n++, "CG ", a3, i, G1)
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| − | a += genAtom(n++, "CD ", a3, i, D1)
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| − | a += genAtom(n++, "NE ", a3, i, E1)
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| − | a += genAtom(n++, "CZ ", a3, i, Z)
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| − | a += genAtom(n++, "NH1", a3, i, H1)
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| − | a += genAtom(n++, "NH2", a3, i, H2)
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| − | break;
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| − | case 'S' :
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| − | a += genAtom(n++, "OG ", a3, i, G1)
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| − | break;
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| − | case 'T' :
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| − | a += genAtom(n++, "OG1", a3, i, G1)
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| − | a += genAtom(n++, "CG2", a3, i, G2)
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| − | break;
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| − | case 'U' :
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| − | a += genAtom(n++, "SeG", a3, i, G1)
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| − | break;
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| − | case 'V' :
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| − | a += genAtom(n++, "CG1", a3, i, G1)
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| − | a += genAtom(n++, "CG2", a3, i, G2)
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| − | break;
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| − | case 'W' :
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| − | a += genAtom(n++, "CG ", a3, i, Ghw)
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| − | a += genAtom(n++, "CD1", a3, i, D1hw)
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| − | a += genAtom(n++, "CD2", a3, i, D2hw)
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| − | a += genAtom(n++, "CE2", a3, i, E2hw)
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| − | a += genAtom(n++, "NE1", a3, i, E1hw)
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| − | a += genAtom(n++, "CE3", a3, i, E3hw)
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| − | a += genAtom(n++, "CZ2", a3, i, Z2hw)
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| − | a += genAtom(n++, "CZ3", a3, i, Z3hw)
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| − | a += genAtom(n++, "CH2", a3, i, H2hw)
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| − | break;
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| − | case 'Y' :
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| − | a += genAtom(n++, "CG ", a3, i, Gfy)
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| − | a += genAtom(n++, "CD1", a3, i, D1fy)
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| − | a += genAtom(n++, "CD2", a3, i, D2fy)
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| − | a += genAtom(n++, "CE1", a3, i, E1fy)
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| − | a += genAtom(n++, "CE2", a3, i, E2fy)
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| − | a += genAtom(n++, "CZ ", a3, i, Zfy)
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| − | a += genAtom(n++, "OH ", a3, i, Hfy)
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| − | break;
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| − | default :
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| − | break;
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| − | }
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| − | | |
| − | return a
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| − | }
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| − | | |
| − | # GenAlph
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| − | function genAlpha(seq, pa) {
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| − | | |
| − | # For each aa
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| − | set appendnew false
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| − | n = 1
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| − | pn = 0
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| − | pc= 0 # previous C
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| − | for (var i = 1; i <= seq.count; i++) {
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| − | | |
| − | pn = n
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| − | m = pn + 1
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| − | | |
| − | # Anticipate PRO
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| − | dpsi = 0
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| − | dphi = 0
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| − | if ((seq.count - i) >= 4) {
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| − | if (seq[i + 4] == 'P') {
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| − | dpsi = =9
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| − | }
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| − | }
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| − | if ((seq.count - i) >= 3) {
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| − | if (seq[i + 3] == 'P') {
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| − | dphi = 10
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| − | }
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| − | }
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| − | if ((seq.count - i) >= 2) {
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| − | if (seq[i + 2] == 'P') {
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| − | dpsi = -11
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| − | #dphi = -0
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| − | }
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| − | }
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| − | if ((seq.count - i) >= 1) {
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| − | if (seq[i + 1] == 'P') {
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| − | dpsi = 25
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| − | #dphi = -81
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| − | }
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| − | }
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| − |
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| − | # Move polypeptide C to bond distance to next AA N
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| − | select all
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| − | fix none
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| − | translateselected { 1.955, -1.993, 0.000 }
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| − | | |
| − | # Gen AA
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| − | a = "data \"append aa\"\n"
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| − | a += genAA(i, seq[i], n);
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| − | a += "end \"append aa\""
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| − | script inline @{a}
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| − | | |
| − | # If not first AA
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| − | if (pc > 0) {
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| − | v1={atomno=pc}.xyz - {atomno=pn}.xyz
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| − | v2={atomno=m}.xyz - {atomno=pn}.xyz
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| − | # Gen normalized axis perpendicular to the plane contaoning atoms pc, pn and m
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| − | axis = cross(v1, v2) - {atomno=pn}.xyz
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| − | | |
| − | # Center on atom pn
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| − | axis += {atomno=pn}.xyz
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| − | | |
| − | # Rotate the polypeptide on the new AA
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| − | select atomno<pn
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| − | fix atomno>=pn
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| − | | |
| − | # pull peptide angle trigonal
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| − | rotateselected @axis {atomno=pn} @{pa-62}
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| − | | |
| − | # Make peptide bond dihedral 180
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| − | rotateselected {atomno=pc} {atomno=pn} 52
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| − | | |
| − | # Make the phi -60
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| − | rotateselected {atomno=pn} {atomno=m} @{dphi - 68}
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| − | | |
| − | # Make the psi -45
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| − | pca = pc - 1
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| − | fix atomno>pca
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| − | select atomno<pn and (atomno != @{pc+1})
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| − | rotateselected {atomno=pc} {atomno=pca} @{dpsi}
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| − | | |
| − | # If aromatic go trans on chi 1
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| − | select atomno>@{pn+4} and atomno<n
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| − | if ((seq[i] == 'H') || (seq[i] == 'W') || (seq[i] == 'F') || (seq[i] == 'Y')) {
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| − | rotateselected {atomno=@{pn+1}} {atomno=@{pn+4}} -120
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| − | }
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| − | | |
| − | }
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| − | pc =pn + 2
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| − | | |
| − | connect
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| − | }
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| − | select all
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| − | fix none
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| − | }
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| − | | |
| − | | |
| − | echo Generating Alpha Helix
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| − | zap
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| − | | |
| − | # Get the sequence from the user
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| − | seq = prompt("Enter AA sequence (1 char coded)", "")%9999
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| − | pa = prompt("Enter the peptide angle", "120")
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| − | print format ("seq=%s at %d deg", seq, pa)
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| − | genAlpha(seq , pa)
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| − | | |
| − | | |
| − | | |
| − | </pre>
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