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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. | + | 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 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
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| − | # v1.0 beta 10/31/2013
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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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| − | #
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| − | # Multiple runs append to the previous helix if any unless it is moved
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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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| − | gO4C4C5O5 = -82.3 - 10 # Values from 30-31:B of 3BSE
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| − | gC4C5O5P = 172.5 + 0 # with the indicated tweaks to make
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| − | gC5O5PO3 = -44.0 + 9 # it work (sort of - yes, I know
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| − | gO5PO3C3 = -109.8 + 0 # the B chain P is a bit screwy)
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| − | gPO3C3C4 = -172.9 - 1 #
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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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| − | g3from1 = {"A":" DA", "C":" DC","G":" DG", "T":" DT", "U":" DU"}
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| − | gComp = {"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(e, aa, i, xyz, comp) {
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| − | # Fixed column format:
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| − | #ATOM 500 O4' DA B 29 -3.745 7.211 45.474
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| − | var a = format("ATOM %5d %4s %3s ", (comp ? gNb : gNa), e, aa )
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| − | a += format("%s%4d %8.3f", (comp ? gCHAIN2 : gCHAIN1), i, 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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| − | };
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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 = (comp ? [16.753, 4.551, 8.935] : [0.000, 0.000, 0.000])
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| − | var OP1= (comp ? [17.916, 5.432, 9.209] : [-0.973, 0.363, -1.067])
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| − | var OP2= (comp ? [16.030, 4.050, 10.108] : [0.297, -1.428, 0.272])
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| − | var O5p= (comp ? [16.110, 5.278, 7.954] : [1.351, 0.795, -0.286])
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| − | var C5p= (comp ? [16.536, 5.450, 6.610] : [1.345, 2.211, -0.125])
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| − | var C4p= (comp ? [15.487, 6.211, 5.838] : [2.739, 2.779, -0.195])
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| − | var O4p= (comp ? [14.427, 5.302, 5.454] : [3.469, 2.629, 1.048])
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| − | var C3p= (comp ? [14.830, 7.309, 6.676] : [3.624, 2.197, -1.288])
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| − | var O3p= (comp ? [14.657, 8.490, 5.878] : [4.212, 3.282, -1.983])
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| − | var C2p= (comp ? [13.509, 6.688, 7.119] : [4.692, 1.432, -0.523])
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| − | var O2p= (comp ? [12.530, 7.743, 7.153] : [5.994, 1.461, -1.226])
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| − | var C1p= (comp ? [13.175, 5.739, 5.976] : [4.797, 2.255, 0.746])
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| − |
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| − | var N1ct=(comp ? [12.404, 4.556, 6.401] : [5.353, 1.551, 1.907])
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| − | var C2ct=(comp ? [11.423, 4.111, 5.551] : [6.351, 2.183, 2.606])
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| − | var O2ct=(comp ? [11.137, 4.685, 4.516] : [6.789, 3.274, 2.289])
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| − | var N3ct=(comp ? [10.784, 2.966, 5.956] : [6.823, 1.489, 3.692])
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| − | var C4ct=(comp ? [11.025, 2.241, 7.106] : [6.404, 0.251, 4.135])
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| − | var NO4ct=(comp ?[10.382, 1.213, 7.329] : [6.908, -0.242, 5.146])
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| − | var C5ct=(comp ? [12.061, 2.780, 7.971] : [5.360, -0.370, 3.337])
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| − | var C6ct=(comp ? [12.692, 3.894, 7.575] : [4.892, 0.307, 2.279])
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| − | var nC7ct=(comp ?[12.421, 2.090, 9.243] : [4.862, -1.727, 3.721])
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| − |
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| − | var N9ag=(comp ? [12.426, 4.545, 6.367] : [5.333, 1.584, 1.923])
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| − | var C8ag=(comp ? [12.706, 3.662, 7.382] : [4.870, 0.450, 2.545])
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| − | var N7ag=(comp ? [11.856, 2.668, 7.467] : [5.595, 0.076, 3.570])
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| − | var C5ag=(comp ? [10.952, 2.911, 6.441] : [6.608, 1.025, 3.629])
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| − | var C6ag=(comp ? [9.818, 2.215, 5.997] : [7.694, 1.194, 4.500])
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| − | var NO6ag=(comp ?[9.379, 1.083, 6.552] : [7.955, 0.379, 5.525])
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| − | var N1ag=(comp ? [9.137, 2.727, 4.945] : [8.517, 2.246, 4.283])
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| − | var C2ag=(comp ? [9.573, 3.862, 4.390] : [8.259, 3.061, 3.256])
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| − | var nN2ag=(comp ?[8.847, 4.313, 3.345] : [9.119, 4.090, 3.100])
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| − | var N3ag=(comp ? [10.630, 4.605, 4.715] : [7.265, 3.009, 2.370])
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| − | var C4ag=(comp ? [11.285, 4.068, 5.759] : [6.465, 1.956, 2.616])
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| − |
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| − | # Build PDB atom records common to all NTs
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| − | n3 = g3from1[nt]
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| − | if (n3 = "") {
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| − | n3 = " D?"
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| − | }
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| − | print format("+ %s%d/%d", n3, i, gSeq.count + gResno)
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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) {
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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 = 1; i <= seq.count; 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, rna, double) {
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| − | var cha = ":A"
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| − | var chb = ":B"
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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]
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| − | }
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| − | }
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| − | else {
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| − | seq = gSeq
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| − | }
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| − | | |
| − | gNa = all.count + 1 # global new N atom index
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| − | gNb = (double ? (gNa + countAtoms(seq) + ((gResno > 0) ? 0 : 1)) : 0)
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| − | | |
| − | # Find last linkable P if any
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| − | gResno = 0 # global pre-existing NT count
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| − | var pna = 1 # previous gN
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| − | for (var i = all.count-1; i > 0; i--) {
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| − | | |
| − | # If found
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| − | if (distance({atomno=i}, {0,0,0}) < 0.1) {
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| − | if ({atomno=i}.chain == cha[2]) {
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| − | pna = i
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| − | }
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| − | gResno = {atomno=i}.resno
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| − | break;
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| − | }
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| − | }
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| − | | |
| − | # For each nt
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| − | set appendnew false
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| − | var nna = gNa # new P
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| − | var nnb = gNb # new P
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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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| − |
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| − | gA = "data \"append nt\"\n" # global PDB atom record
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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}
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| − | select all
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| − | if ((i + gResno) > 1) {
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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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| − | | |
| − | # Else 1st 5' nt so add OP3
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| − | else {
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| − | var O3n = {pO3n}.xyz
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| − | gA += genAtom(" OP3", g3from1[seq[i]], i + gResno, O3n, FALSE)
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| − | nna++
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| − | }
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| − |
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| − | # Gen NT ==================================================
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| − | gA += genNT(i + gResno, seq[i], rna, FALSE); # gNa updated
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| − | if (double) {
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| − | gA += genNT(i + gResno + seq.count, gComp[seq[i]], rna, TRUE); # gNb updated
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| − | }
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| − | gA += "end \"append nt\""
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| − | script inline @{gA} # <== new atoms added here
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| − | | |
| − | # First shape up the comp side
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| − | if (double) {
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| − | select (@chb and (atomno < @{nnb + 6}) && (atomno >= nnb))
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| − | setDihedral(nnb+6, nnb+5, nnb+4, nnb+3, gO4C4C5O5)
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| − | select selected and (atomno != @{nnb + 5})
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| − | setDihedral(nnb+5, nnb+4, nnb+3, nnb, gC4C5O5P)
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| − | }
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| − | # Adjust link dihedrals of the new
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| − | select (@cha and (atomno > @{nna+4}) or (@chb and (atomno >= nnb)))
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| − | setDihedral(nna+3, nna+4, nna+5, nna+6, gO4C4C5O5)
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| − | setDihedral(nna, nna+3, nna+4, nna+5, gC4C5O5P)
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| − |
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| − | # If any older
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| − | if (i > 1) {
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| − | # Now move the old
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| − | select (@cha and (atomno < nna) or (@chb and (atomno < nnb)))
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| − | setAngle(nna, pna+8, pna+7, 120.0)
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| − |
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| − | select (@cha and (atomno < @{nna+3}) or (@chb and (atomno < nnb)))
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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 (atomno < nnb)))
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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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| − | }
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| − |
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| − | # Step new and previous N
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| − | pna = nna; pnb = nnb
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| − | nna = gNa; nnb = gNb
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| − | }
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| − |
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| − | # Make the nucleotide bonds
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| − | connect
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| − |
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| − | # Clean up
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| − | select all
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| − | print format("%d atoms generated for chain %s", gNa+gNb,
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| − | (comp ? gCHAIN2 : gCHAIN1))
| |
| − | }
| |
| − | | |
| − | # Generate a helix or two
| |
| − | function genHelix(gSeq) {
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| − | var single = FALSE
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| − | var reverse = FALSE
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| − | var rna = FALSE
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| − | var done = FALSE
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| − | if (gSeq[2] == ':') {
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| − | gCHAIN1 = gSeq[1]
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| − | gSeq[1] = ' '; gSeq[2] = ' '
| |
| − | gSeq = gSeq%0
| |
| − | }
| |
| − | else if (gSeq[3] == ':') {
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| − | gCHAIN1 = gSeq[1]
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| − | gCHAIN2 = gSeq[2]
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| − | 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
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| − | | |
| − | # Get the sequence from the user
| |
| − | gSeq = prompt("Enter NT sequence (ACGTU)", "")%9999%0
| |
| − | if (gSeq.count > 0) {
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| − | genHelix(gSeq)
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| − | }
| |
| − | </pre>
| |
| − | 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.
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