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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 for the general amusement. | + | 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 for the general amusement. Some are now available here [[User:Remig/plico]]. |
| − | | |
| − | 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 (now revised) that 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:
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| − | | |
| − | <pre># POLYMERAZE - Jmol script by Ron Mignery
| |
| − | # v1.1 beta 11/02/2013 for Jmol 13.4
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| − | #
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| − | # POLYMERAZE takes a string message encoding a nucleotide (nt) sequence
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| − | # and generates a corresponding double helix one nt at a time from the
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| − | # 5' terminus to the 3' terminus rotating the emerging helix as it goes.
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| − | #
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| − | # The message is a string entered by the user at a prompt.
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| − | # It may be typed in or pasted in and be of any length
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| − | # If prepended with '3' then the string is considered as 3' to 5'
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| − | # If prepended with 'R' then RNA is generated instead of DNA
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| − | # If prepended with 'S' then a single strand helix is produced
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| − | # If prepended with 'M' then a mixed helix is produced where the first
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| − | # strand is DNA and the second RNA - multiple prepends are allowed
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| − | # though 'M' is inconsistent with 'R' or 'S'
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| − | #
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| − | # If the 3d character is ':' then the two chains are labeled by the
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| − | # two preceding characters instead of the default 'A' and 'B'
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| − | # Likewise if the 2d character is ':' then the presumably single chain is
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| − | # labeled by the preceding single character
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| − | #
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| − | # The IUPAC/IUBMB 1 letter code is used:
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| − | # A=Adenine C=Cytosine G=Guanine T=Thymine U=Uracil
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| − | | |
| − | # The following constant values determine the pitch of the helices
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| − | gC5O5PO3 = -27.0
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| − | gO5PO3C3 = -117.8
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| − | gPO3C3C4 = -171.9
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| − | gCHAIN1 = 'A' # The chain id
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| − | gCHAIN2 = 'B' # The complementary chain id
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| − | | |
| − | # Lookup 3 letter code from 1 letter code
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| − | gNt3from1 = {"A":" DA", "C":" DC", "G":" DG", "T":" DT", "U":" DU"}
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| − | gNtComp = {"A":"T", "C":"G", "G":"C", "T":"A", "U":"A"}
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| − | | |
| − | # Generate PDB atom record
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| − | # Writes gNa or gNb
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| − | function genAtom(atomname, group, resno, xyz, comp) {
| |
| − | # Fixed column format:
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| − | #ATOM 500 O4' DA B 29 -3.745 7.211 45.474
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| − | while (atomname.size < 3) {
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| − | atomname += " ";
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| − | }
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| − | var a = format("ATOM %5d %4s %3s ", (comp ? gNb : gNa), atomname, group )
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| − | a += format("%s%4d %8.3f", (comp ? gCHAIN2 : gCHAIN1), resno, xyz[1] )
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| − | a += format("%8.3f%8.3f\n", xyz[2], xyz[3] )
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| − | if (comp) gNb++; else gNa++
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| − |
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| − | return a
| |
| − | };
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| − | | |
| − | # Generate a PDB nucleotide record set
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| − | # Calls genAtom that writes gNa or gNb
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| − | function genNT(i, nt, rna, comp) {
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| − | | |
| − | # From constructed nucleotides
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| − | var P0 = [0.000, 0.000, 0.000]
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| − | var OP1= [-0.973,0.363,-1.067]
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| − | var OP2= [0.297,-1.428, 0.272]
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| − | var O5p= [1.351, 0.795,-0.286]
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| − | var C5p= [1.345, 2.211,-0.125]
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| − | var C4p= [2.732, 2.786,-0.255]
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| − | var O4p= [3.413, 2.900, 1.019]
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| − | var C3p= [3.670, 2.020,-1.178]
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| − | var O3p= [4.269, 2.960,-2.051]
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| − | var C2p= [4.717, 1.445,-0.238]
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| − | var O2p= [6.046, 1.365,-0.884]
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| − | var C1p= [4.758, 2.505, 0.846]
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| − |
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| − | var N1ct= [5.277, 2.056, 2.143]
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| − | var C2ct= [6.236, 2.836, 2.740]
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| − | var O2ct= [6.670, 3.853, 2.230]
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| − | var N3ct= [6.674, 2.381, 3.958]
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| − | var C4ct= [6.256, 1.245, 4.622]
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| − | var NO4ct [6.726, 0.972, 5.728]
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| − | var C5ct= [5.255, 0.455, 3.924]
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| − | var C6ct= [4.820, 0.900, 2.737]
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| − | var nC7ct [4.762,-0.811, 4.551]
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| − |
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| − | var N9ag= [5.256, 2.091, 2.152]
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| − | var C8ag= [4.867, 1.016, 2.913]
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| − | var N7ag= [5.532, 0.894, 4.035]
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| − | var C5ag= [6.425, 1.959, 4.013]
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| − | var C6ag= [7.401, 2.391, 4.922]
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| − | var NO6ag=[7.656, 1.780, 6.081]
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| − | var N1ag= [8.118, 3.493, 4.599]
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| − | var C2ag= [7.865, 4.104, 3.438]
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| − | var nN2ag [8.616, 5.197, 3.181]
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| − | var N3ag= [6.968, 3.796, 2.503]
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| − | var C4ag= [6.271, 2.701, 2.856]
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| − |
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| − | # Build PDB atom records common to all NTs
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| − | n3 = gNt3from1[nt]
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| − | if (n3 = "") {
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| − | n3 = " D?"
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| − | }
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| − | var a = genAtom(" P ", n3, i, P0, comp)
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| − | a += genAtom(" OP1", n3, i, OP1, comp)
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| − | a += genAtom(" OP2", n3, i, OP2, comp)
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| − | a += genAtom(" O5'", n3, i, O5p, comp)
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| − | a += genAtom(" C5'", n3, i, C5p, comp)
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| − | a += genAtom(" C4'", n3, i, C4p, comp)
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| − | a += genAtom(" O4'", n3, i, O4p, comp)
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| − | a += genAtom(" C3'", n3, i, C3p, comp)
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| − | a += genAtom(" O3'", n3, i, O3p, comp)
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| − | a += genAtom(" C2'", n3, i, C2p, comp)
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| − | a += genAtom(" C1'", n3, i, C1p, comp)
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| − | if (rna) {
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| − | a += genAtom(" O2'", n3, i, O2p, comp)
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| − | }
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| − | | |
| − | # Now add NT specific atom records
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| − | switch (nt) {
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| − | case 'A' :
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| − | a += genAtom(" N9 ", n3, i, N9ag, comp)
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| − | a += genAtom(" C8 ", n3, i, C8ag, comp)
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| − | a += genAtom(" N7 ", n3, i, N7ag, comp)
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| − | a += genAtom(" C5 ", n3, i, C5ag, comp)
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| − | a += genAtom(" C6 ", n3, i, C6ag, comp)
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| − | a += genAtom(" N6 ", n3, i, NO6ag, comp)
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| − | a += genAtom(" N1 ", n3, i, N1ag, comp)
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| − | a += genAtom(" C2 ", n3, i, C2ag, comp)
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| − | a += genAtom(" N3 ", n3, i, N3ag, comp)
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| − | a += genAtom(" C4 ", n3, i, C4ag, comp)
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| − | break;
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| − | case 'C' :
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| − | a += genAtom(" N1 ", n3, i, N1ct, comp)
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| − | a += genAtom(" C2 ", n3, i, C2ct, comp)
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| − | a += genAtom(" O2 ", n3, i, O2ct, comp)
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| − | a += genAtom(" N3 ", n3, i, N3ct, comp)
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| − | a += genAtom(" C4 ", n3, i, C4ct, comp)
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| − | a += genAtom(" N4 ", n3, i, NO4ct, comp)
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| − | a += genAtom(" C5 ", n3, i, C5ct, comp)
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| − | a += genAtom(" C6 ", n3, i, C6ct, comp)
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| − | break;
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| − | case 'G' :
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| − | a += genAtom(" N9 ", n3, i, N9ag, comp)
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| − | a += genAtom(" C8 ", n3, i, C8ag, comp)
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| − | a += genAtom(" N7 ", n3, i, N7ag, comp)
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| − | a += genAtom(" C5 ", n3, i, C5ag, comp)
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| − | a += genAtom(" C6 ", n3, i, C6ag, comp)
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| − | a += genAtom(" O6 ", n3, i, NO6ag, comp)
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| − | a += genAtom(" N1 ", n3, i, N1ag, comp)
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| − | a += genAtom(" C2 ", n3, i, C2ag, comp)
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| − | a += genAtom(" N2 ", n3, i, nN2ag, comp)
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| − | a += genAtom(" N3 ", n3, i, N3ag, comp)
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| − | a += genAtom(" C4 ", n3, i, C4ag, comp)
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| − | break;
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| − | case 'T' :
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| − | a += genAtom(" N1 ", n3, i, N1ct, comp)
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| − | a += genAtom(" C2 ", n3, i, C2ct, comp)
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| − | a += genAtom(" O2 ", n3, i, O2ct, comp)
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| − | a += genAtom(" N3 ", n3, i, N3ct, comp)
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| − | a += genAtom(" C4 ", n3, i, C4ct, comp)
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| − | a += genAtom(" O4 ", n3, i, NO4ct, comp)
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| − | a += genAtom(" C5 ", n3, i, C5ct, comp)
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| − | a += genAtom(" C6 ", n3, i, C6ct, comp)
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| − | a += genAtom(" C7 ", n3, i, nC7ct, comp)
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| − | break;
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| − | case 'U' :
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| − | a += genAtom(" N1 ", n3, i, N1ct, comp)
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| − | a += genAtom(" C2 ", n3, i, C2ct, comp)
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| − | a += genAtom(" O2 ", n3, i, O2ct, comp)
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| − | a += genAtom(" N3 ", n3, i, N3ct, comp)
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| − | a += genAtom(" C4 ", n3, i, C4ct, comp)
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| − | a += genAtom(" O4 ", n3, i, NO4ct, comp)
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| − | a += genAtom(" C5 ", n3, i, C5ct, comp)
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| − | a += genAtom(" C6 ", n3, i, C6ct, comp)
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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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| − | | |
| − | # Rotate a1 on a2 in the plane of a1, a2 and a3 to the given angle
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| − | # a1 and all connected except by a2 must be selected
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| − | function setAngle (a1, a2, a3, toangle) {
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| − | var v1={atomno = a1}.xyz - {atomno = a2}.xyz
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| − | var v2={atomno = a3}.xyz - {atomno = a2}.xyz
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| − | var axis = cross(v1, v2) + {atomno = a2}.xyz
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| − | var curangle = angle({atomno=a1}, {atomno=a2}, {atomno=a3})
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| − | rotateselected @axis {atomno = a2} @{curangle-toangle}
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| − | }
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| − | | |
| − | # Set the dihedral to the given angle
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| − | # a1 (or a4) and all connected except by a2 (or a3) must be selected
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| − | # If selected < unselected ==> a2 < a3 and vice versa
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| − | function setDihedral (a1, a2, a3, a4, toangle) {
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| − | var curangle = angle({atomno=a1}, {atomno=a2}, {atomno=a3}, {atomno=a4})
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| − | rotateselected {atomno=a2} {atomno=a3} @{toangle-curangle}
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| − | }
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| − | | |
| − | function countAtoms(seq, rna, start, finish) {
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| − | var ntc = {"A":21, "C":20, "G":22, "T":20, "U":19}
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| − | var cnt = 0
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| − | for (var i = start; i <= finish; i++) {
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| − | cnt += (ntc[seq[i]] + (rna ? 1 : 0))
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| − | }
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| − | return cnt
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| − | }
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| − | | |
| − | # Generate a helix
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| − | function genHelixStrand(gSeq, reverse, drm, double) {
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| − | var cha = ":" + gCHAIN1
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| − | var chb = ":" + gCHAIN2
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| − | var seq = ""
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| − | if (reverse) {
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| − | for (var i = gSeq.count; i > 0; i--) {
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| − | seq += gSeq[i]%9999%0
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| − | }
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| − | }
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| − | else {
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| − | seq = gSeq%9999%0
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| − | }
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| − | | |
| − | cSeq = ""
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| − | if (double) {
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| − | for (var i = seq.count; i > 0; i--) {
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| − | cSeq += ((seq[i] == 'A') and (dr > 0)) ? "U" : gNtComp[seq[i]]
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| − | }
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| − | }
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| − | var aAtomCount = countAtoms(seq, (drm == 1), 1, seq.count)
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| − | var bAtomCount = countAtoms(cSeq, (drm > 0), 1, cSeq.count)
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| − |
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| − | gNa = 1 # global new P atom index for chain A
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| − | gNb = 0
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| − | if (double) {
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| − | gNb = (aAtomCount + bAtomCount
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| − | - countAtoms(cSeq, (drm>0), cSeq.count, cSeq.count)) # last P in cSeq
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| − | }
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| − | #var bBase = (all.count + countAtoms(seq, (drm > 0), seq.count) + 1)
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| − | | |
| − | # Find last linkable P if any
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| − | var aResno = 1
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| − | var pNa = 1 # previous gNa
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| − | for (var i = all.count; i > 0; i--) {
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| − | | |
| − | # If A strand found at {0,0,0}
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| − | if (distance({atomno=i}, {0,0,0}) < 0.1) {
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| − | if ({atomno=i}.chain == gCHAIN1) {
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| − |
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| − | # Add to existing strand
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| − | echo "Adding to existing strand..."
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| − | pNa = i
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| − | aResno = {chain=gCHAIN1}.resno.max + 1
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| − | gNa = {chain=gCHAIN1}.atomno.max + 1
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| − | gNb += gNa
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| − |
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| − | # Bump up all B chain atomno and resno
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| − | # KLUDGE to work-around of Jmol's lack of resno rewrite
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| − | savNb = gNb
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| − | gNb = aAtomCount + bAtomCount + gNa
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| − | gA = "data \"append nt\"\n" # global PDB atom record
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| − | for (j = 1; j <= all.atomno.max; j++) {
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| − | if ({atomno=j}.chain == gCHAIN2) {
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| − | gA += genAtom({atomno=j}.atomName, {atomno=j}.group,
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| − | ({atomno=j}.resno+seq.count+cSeq.count),
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| − | array({atomno=j}.x, {atomno=j}.y, {atomno=j}.z), true)
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| − | }
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| − | }
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| − | gA += "end \"append nt\""
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| − | delete @chb
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| − | script inline @{gA} # <== new atoms added here
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| − | gNb = savNb
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| − | break;
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| − | }
| |
| − | }
| |
| − | }
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| − | | |
| − | var bResno = aResno + seq.count + cSeq.count - 1
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| − |
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| − | var nNa = gNa # new P
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| − | var nNb = 0#bBase # new comp P
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| − | | |
| − | # For each NT
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| − | set appendnew false
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| − | for (var i = 1; i <= seq.count; i++) {
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| − |
| |
| − | if (seq[i] == "") {
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| − | continue
| |
| − | }
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| − |
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| − | # Move polynucleotide O3p to bond distance from new nt P
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| − | var pO3 = {-0.521, 0.638, 1.234}
| |
| − | select all
| |
| − | if ((i + aResno) > 2) {
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| − | var nO3 = {atomno=@{pNa+8}}.xyz
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| − | var xyz = @{pO3 - nO3}
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| − | translateselected @xyz
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| − | }
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| − |
| |
| − | # Gen NT ==================================================
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| − | gA = "data \"append nt\"\n" # global PDB atom record
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| − | gA += genNT(aResno, seq[i], (drm == 1), FALSE); # gNa updated
| |
| − | if (double) {
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| − | nNb = gNb
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| − | var nti = cSeq.count-i+1
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| − | gA += genNT(bResno, cSeq[nti], (drm > 0), TRUE); # gNb++
| |
| − | if (i > 0) {
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| − | gNb -= countAtoms(cSeq, (drm>0), nti-1, nti)
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| − | }
| |
| − | }
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| − | gA += "end \"append nt\""
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| − | script inline @{gA} # <== new atoms added here
| |
| − |
| |
| − | # Flip comp to comp strand
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| − | if (double) {
| |
| − | select @{"" + bResno + chb}
| |
| − | 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)))
| |
| − | setAngle(nNa, pNa+8, pNa+7, 120.0)
| |
| − | | |
| − | select (@cha and (atomno < @{nNa+3}) or (@chb and (resno != bResno)))
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| − | setDihedral(nNa+4, nNa+3, nNa, pNa+8, gC5O5PO3)
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| − |
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| − | select (@cha and (atomno < nNa) or (@chb and (resno != bResno)))
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| − | setDihedral(nNa+3, nNa, pNa+8, pNa+7, gO5PO3C3)
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| − |
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| − | setDihedral(nNa, pNa+8, pNa+7, pNa+5, gPO3C3C4)
| |
| − | }
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| − |
| |
| − | # Step new and previous N
| |
| − | aResno++; bResno--
| |
| − | 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 drm = 0
| |
| − | var done = FALSE
| |
| − | gSeq = gSeq%9999%0
| |
| − | print format ("Seq=%s", gSeq)
| |
| − |
| |
| − | 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') {
| |
| − | drm = 1;
| |
| − | done = FALSE;
| |
| − | }
| |
| − | else if (gSeq[1] == 'M') {
| |
| − | drm = 2;
| |
| − | done = FALSE;
| |
| − | }
| |
| − | if (done == FALSE) {
| |
| − | gSeq[1] = ' '
| |
| − | gSeq = gSeq%0
| |
| − | }
| |
| − | }
| |
| − |
| |
| − | # Generate
| |
| − | genHelixStrand(gSeq, reverse, drm, single ? FALSE : TRUE)
| |
| − | | |
| − | }
| |
| − | | |
| − | # ==============================================
| |
| − | echo Generating Alpha Helix
| |
| − | | |
| − | # Get the sequence from the user
| |
| − | gSeq = prompt("Enter NT sequence (<3RSM>ACGTU)", "")%9999%0
| |
| − | if (gSeq.count > 0) {
| |
| − | genHelix(gSeq)
| |
| − | }
| |
| − | </pre>
| |
