Recycling Corner/DNA Generator - Revision history

Remig: Avoid "axis," a newly reserved word

2016-04-12T17:02:08Z

Avoid "axis," a newly reserved word

Remig at 14:23, 11 September 2015

2015-09-11T14:23:31Z

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Remig: O2' now numbers before C1'

2015-07-13T18:54:48Z

O2' now numbers before C1'

Remig at 19:05, 26 August 2014

2014-08-26T19:05:12Z

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Remig: Fix atomno bug with +

2014-07-21T15:56:00Z

Fix atomno bug with +

Remig at 14:19, 12 July 2014

2014-07-12T14:19:03Z

Remig: Support multiple frames

2014-07-11T22:45:24Z

Support multiple frames

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Remig: lc all functions

2014-05-16T14:54:25Z

lc all functions

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Remig: autoconvert U-T

2014-04-29T17:08:58Z

autoconvert U-T

Remig: Do not var globals

2014-04-03T15:28:54Z

Do not var globals

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@@ Line 33: / Line 33: @@
 Copy and paste the following into a text editor and save in your scripts directory as polymeraze.spt.
 <pre>#   POLYMERAZE - Jmol script by Ron Mignery
-#   v1.15 beta    9/10/2015 -use thisModel
+#   v1.16 beta    4/12/2016 -axis is now a reserved word
+#
 #   POLYMERAZE takes a string message encoding a nucleotide (nt) sequence
@@ Line 242: / Line 242: @@
      var v1 = (a1.xyz - a2.xyz)
      var v2 = (a3.xyz - a2.xyz)
-     var axis = cross(v1, v2) + a2.xyz
+     var caxis = cross(v1, v2) + a2.xyz
      var curangle =  angle(a1, a2, a3)
-     rotateselected @axis @a2 @{curangle-toangle}
+     rotateselected @caxis @a2 @{curangle-toangle}
+}

@@ Line 33: / Line 33: @@
 Copy and paste the following into a text editor and save in your scripts directory as polymeraze.spt.
 <pre>#   POLYMERAZE - Jmol script by Ron Mignery
-#   v1.13 beta    8/26/2014 -fix naming conflict
+#   v1.14 beta    1/23/2015 -O2' now numbers before C1'
+#
 #   POLYMERAZE takes a string message encoding a nucleotide (nt) sequence
@@ Line 61: / Line 61: @@
 #   A=Adenine C=Cytosine G=Guanine T=Thymine U=Uracil
 # The following constant values determine the pitch of the helices
 kC5O5PO3 = -27.0
@@ Line 160: / Line 161: @@
      a += gen_atom_nt(" O3'", n3, i, O3p, comp)
      a += gen_atom_nt(" C2'", n3, i, C2p, comp)
      if (rna) {
          a += gen_atom_nt(" O2'", n3, i, O2p, comp)
+     }
      # Now add NT specific atom records
@@ Line 338: / Line 339: @@
                      gNb = aAtomCount + bAtomCount + gNa
                      gA = "data \"append nt\"\n"    # global PDB atom record
-                     for (j = 1; j <= all.atomno.max; j++) {
+                     for (var j = 1; j <= all.atomno.max; j++) {
                          var aj = {(atomno=j) and (file=f) and (model=m)
                              and (chain == gChain2)}

@@ Line 28: / Line 28: @@
 Polymeraze is a member of the Plico suite of protein folding tools described [[User:Remig/plico|here]]. It may be installed and accessed as a macro with the file:
 <pre>Title=PLICO Generate Polynucleotide
-Script=script <path to your script folder>/polymeraze.spt;plico_gen_nt</pre>
+Script=script <path to your script directory>/polymeraze.spt;plico_gen_nt</pre>
 saved as plicoGenNT.macro in your .jmol/macros directory as described in [[Macro]].
-<pre>#   POLYMERAZE - Jmol script by Ron Mignery
+Copy and paste the following into a text editor and save in your scripts directory as polymeraze.spt.
-#   v1.11 beta    7/11/2014 -add multi-frame support-fixed
+<pre>##   POLYMERAZE - Jmol script by Ron Mignery
+#
 #   POLYMERAZE takes a string message encoding a nucleotide (nt) sequence
@@ Line 235: / Line 236: @@
 function set_angle_no (a1no, a2no, a3no, toangle) {
      var f = (_frameID/1000000)
-     var m = (_frameID%100000)
+     var m = (_frameID%1000000)
      var c = gChain1
      var a1 =  {(atomno=a1no) and (chain=c) and (file=f) and (model=m)}
@@ Line 252: / Line 253: @@
 function set_dihedral_no (a1no, a2no, a3no, a4no, toangle) {
      var f = (_frameID/1000000)
-     var m = (_frameID%100000)
+     var m = (_frameID%1000000)
      var c = gChain1
      var a1 =  {(atomno=a1no) and (chain=c) and (file=f) and (model=m)}
@@ Line 274: / Line 275: @@
 function gen_helix_strand(reverse, drm, double) {
      var f = (_frameID/1000000)
-     var m = (_frameID%100000)
+     var m = (_frameID%1000000)
      var cha = ":" + gChain1
      var chb = ":" + gChain2
@@ Line 310: / Line 311: @@
      if (gNewFrame) {
          appendNew = TRUE
+     }
      else {
@@ Line 316: / Line 318: @@
          # While there is an atom at the origin
          while (m > 0) {
              var ai = {within(0.1, {0 0 0}) and (file=f) and (model=m)}
              if (ai.size > 0) {
@@ Line 404: / Line 407: @@
          f = (_frameID/1000000)
-         m = (_frameID%100000)
+         m = (_frameID%1000000)
          appendNew = FALSE
@@ Line 444: / Line 447: @@
      # Clean up
      appendNew = gAppendNew
-     select all
+    echo
      refresh
@@ Line 450: / Line 454: @@
      try {
          script $SCRIPT_PATH$toabNT.spt
-         var s = format("Convert to %s-form?", ((drm > 0) ? "A" : "B"))
+         var s = format("Convert to %s-form?", ((drm > 0) ? "A" : "tight B"))
          var p = prompt(s, "Yes|No", TRUE)
          if (p = "Yes") {

@@ Line 32: / Line 32: @@
 <pre>#   POLYMERAZE - Jmol script by Ron Mignery
-#   v1.10 beta    7/11/2014 -add multi-frame support
+#   v1.11 beta    7/11/2014 -add multi-frame support-fixed
+#
 #   POLYMERAZE takes a string message encoding a nucleotide (nt) sequence
@@ Line 296: / Line 296: @@
      var bAtomCount = count_atoms(cSeq, (drm > 0), 1, cSeq.count)
-     gNa = 1 # global new P atom index for chain A
+     # global new P atom index for chain A
      gNb = 0
      if (double) {
@@ Line 312: / Line 313: @@
      else {
          appendNew = FALSE
          # While there is an atom at the origin

@@ Line 22: / Line 22: @@
 <pre>Title=PLICO Generate Polynucleotide
 Script=script <path to your script folder>/polymeraze.spt;plicoGenNT</pre>
-saved as plicoGenNT.macro in your .jmol/macros folder as described in [[Macro]].
+saved as plicoGenNT.macro in your .jmol/macros directory as described in [[Macro]].
 <pre>#   POLYMERAZE - Jmol script by Ron Mignery
-#   v1.8 beta    4/3/2014 -do not var globals for Jmol 14.0.13+
+#   v1.9 beta    4/29/2014 -autoconvert U-T
+#
 #   POLYMERAZE takes a string message encoding a nucleotide (nt) sequence
@@ Line 32: / Line 32: @@
+#
 #   The resulting polynucleotide defaults to an open B-form.  If double-stranded
-#   and the script "toABnt" is available, it converts to a regular B-form if DNA
+#   and the script "toABnt" is available, it prompts to convert to a regular B-form if DNA
 #   or to a regular A-form if RNA or mixed.
+#
@@ Line 38: / Line 38: @@
 #   It may be typed in or pasted in and be of any length
 #   If prepended with '3' then the string is considered as 3' to 5'
-#   If prepended with 'R' then RNA is generated instead of DNA
+#   If prepended with 'R' then RNA is generated instead of DNA (Ts convert to Us)
 #   If prepended with 'S' then a single strand helix is produced
 #   If prepended with 'M' then a mixed helix is produced where the first
@@ Line 136: / Line 136: @@
+         }
          else {
-             n3 = n3.replace("D", " ")
+             n3 = n3.replace('D', ' ')
+         }
+     }
@@ Line 254: / Line 254: @@
 # Generate a helix
-function genHelixStrand(gSeq, reverse, drm, double) {
+function genHelixStrand(reverse, drm, double) {
      var cha = ":" + gChain1
      var chb = ":" + gChain2
@@ Line 396: / Line 396: @@
      select all
-     # If double, convert to A-form if RNA or mixed else B-form
+     # Convert to A-form if RNA or mixed else B-form
-     if (double) {
+     try {
-         try {
+         script $SCRIPT_PATH$toabNT.spt
-            script $SCRIPT_PATH$toabNT.spt
+        p = prompt(format("Convert to %s-form?", ((drm > 0) ? "A" : "B")),
-            p = prompt(format("Convert to %s-form?", ((drm > 0) ? "A" : "B")),
+            "Yes|No", TRUE)
-                "Yes|No", TRUE)
+        if (p = "Yes") {
-            if (p = "Yes") {
+            toabNtAuto(gChain1, (drm > 0))
+         }
+     }
+}
 # Generate a helix or two
-function plicoGenHelix(gSeq) {
+function plicoGenHelix(seq) {
      if (gPlicoRecord != "") {
@@ Line 428: / Line 426: @@
      var drm = 0
      var done = FALSE
-     gSeq = gSeq%9999%0
+     gSeq = seq%9999%0
      print format ("Seq=%s", gSeq)
@@ Line 462: / Line 460: @@
+         }
+     }
-−
      # Generate
-     genHelixStrand(gSeq, reverse, drm, single ? FALSE : TRUE)
+     genHelixStrand(reverse, drm, single ? FALSE : TRUE)
+}
@@ Line 472: / Line 477: @@
      # Get the sequence from the user
-     gSeq = prompt("Enter NT sequence (<3RSM>ACGTU)", "")%9999%0
+     var seq = prompt("Enter NT sequence (<3RSM>ACGTU)", "")%9999%0
-     if ((gSeq != "NULL") and (gSeq.count > 0)) {
+     if ((seq != "NULL") and (seq.count > 0)) {
-         plicoGenHelix(gSeq)
+         plicoGenHelix(seq)
+     }
+}
 # end of polymeraze.spt</pre>