Recycling Corner/Alpha Helix Generator - Revision history

AngelHerraez: /* RIBOZOME - a Polypeptide Alpha Helix Generator script */

2019-10-09T19:34:16Z

‎RIBOZOME - a Polypeptide Alpha Helix Generator script

Remig: Avoid "axis" as a newly reserved word

2016-04-12T16:57:15Z

Avoid "axis" as a newly reserved word

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Remig: Add start resno prepend and fix kphi/kpsi logic

2015-10-03T19:41:52Z

Add start resno prepend and fix kphi/kpsi logic

Remig at 18:35, 10 September 2015

2015-09-10T18:35:33Z

AngelHerraez: update of the webpage version

2015-07-15T17:23:03Z

update of the webpage version

Remig at 18:52, 13 July 2015

2015-07-13T18:52:08Z

Remig: /* Script for the Jmol application */

2014-07-11T22:31:30Z

‎Script for the Jmol application

Remig: Add multi-frame support

2014-07-10T22:08:59Z

Add multi-frame support

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Remig: lc all functions

2014-05-16T14:44:55Z

lc all functions

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Remig: Do not var globals

2014-04-03T15:27:07Z

Do not var globals

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@@ Line 2: / Line 2: @@
 Creates an alpha helix from a user input string.
-Jmol script by Ron Mignery with help from [[User:AngelHerraez|Angel HerrÃ¡ez]]
+Jmol script by Ron Mignery with help from [[User:AngelHerraez|Angel Herráez]]
 __TOC__

@@ Line 11: / Line 11: @@
 The top-level function plico_gen_alpha accepts a sequence string as a parameter.
-''With this script you can generate a polypeptide alpha helix chain from a sequence string in 1-char amino-acid coding.  You can optionally give it a chain label other than the default :A. You can also add to an existing chain, add new chains to an existing model or now create the chain in a new frame by prepending a '+' to the sequence string.''
+''With this script you can generate a polypeptide alpha helix chain from a sequence string in 1-char amino-acid coding.  You can optionally give it a chain label other than the default :A or start at a residue number other than the default 1. You can also add to an existing chain, add new chains to an existing model or now create the chain in a new frame by prepending a '+' to the sequence string.''
 ''Chains start from the origin and extend along the Z-axis as they are built.  If a chain with the same chain label as the new chain is at the origin, the new sequence is added to the old.  If a chain with a different chain label is at the origin, all existing chains are shifted 20 angstroms to the right along the X axis until the origin is clear.''
@@ Line 22: / Line 22: @@
 Copy and paste the following into a text editor and save in your scripts directory as ribozome.spt.
 <pre>#   RIBOZOME - Jmol script by Ron Mignery
-#   v1.17 beta    8/19/2015 -minor edits
+#   v1.18 beta    10/1/2015 -add start resno prepend and fix kphi/kpsi logic
+#
 #   RIBOZOME takes a string message encoding an amino acid (aa) sequence
@@ Line 28: / Line 28: @@
 #   N terminus to the C terminus rotating the emerging helix as it goes.
+#
-#   The message is a string entered by the user at a prompt. [+A:...]
+#   The message is a string entered by the user at a prompt. <+A:><n...>[A-Z]...
 #   It may be typed in or pasted in and be of any length
 #   If the message is prepended with "+" then the chain is created in a new
 #   frame. Otherwise it is added to the current frame
-#   If the message is prepended with <C>: (where C is any single letter)
+#   If the message is then prepended with <C>: (where C is any single letter)
 #   then the chain is so labeled and separated from existing chains
 #   if different from the first chain.
+#
 #   The IUPAC/IUBMB 1 letter code is used:
@@ Line 57: / Line 59: @@
 gAppendNew = true
 gNewFrame = false
 # Lookup 3 letter code from 1 letter code
@@ Line 271: / Line 274: @@
 # Generate an alpha helix
-function plico_gen_alpha(gSeq) {
+function plico_gen_alpha(seq) {
      gPdbAddHydrogens = pdbAddHydrogens
      set pdbAddHydrogens false
@@ Line 280: / Line 284: @@
              ls = ""
+         }
-         ls += format("plico_gen_alpha(\"%s\");", gSeq)
+         ls += format("plico_gen_alpha(\"%s\");", seq)
          write var ls @gPlicoRecord
+     }
-     gSeq = gSeq%9999%0
+     seq = seq%9999%0
      gNewFrame = false
-     if (gSeq[1] == '+') {
+     if (seq[1] == '+') {
          gNewFrame = true
-         gSeq = gSeq[2][9999]
+         seq = seq[2][9999]
+     }
-     if (gSeq[2] == ':') {
+     if (seq[2] == ':') {
-         gCHAIN = gSeq[1]
+         gCHAIN = seq[1]
-         gSeq = gSeq[3][9999]
+         seq = seq[3][9999]
+     }
      var c = gCHAIN
-     gResno = 0    # global pre-existing AA count
+     if (resStart.size > 0) {
      var pn = 1    # previous gN
      gAppendNew = appendNew
@@ Line 383: / Line 398: @@
              var v1=aPn2.xyz - aNn.xyz
              var v2=aNn1.xyz - aNn.xyz
              var axis = cross(v1, v2)
@@ Line 397: / Line 414: @@
              # Make the new phi dihedral = kPHI (nominally -57)
-             rotateselected @aNn @aNn1 @{kPHI - 2.5}
+             rotateselected @aNn @aNn1 @{-kPHI - 116.5}
              # Make the old psi dihedral = kPSI (nominally -47)
              select {(atomno < nn) and thisModel and (chain=c)
                  and not aPn2 and not aPn3}
-             rotateselected @aPn1 @aPn2 @{kPSI + 33.4 + pb}
+             rotateselected @aPn1 @aPn2 @{-kPSI - 60.6 + pb}
              # Make the peptide bond
@@ Line 434: / Line 451: @@
      appendNew = gAppendNew
      pdbAddHydrogens = gPdbAddHydrogens
+}
 function plico_gen_pp {
-     echo Generating Alpha Helix
+     print "Generating Alpha Helix..."
      # Get the sequence from the user
-     gSeq = prompt("Enter AA sequence (<+A:>[A-Z]...)", "")%9999%0
+     gSeq = prompt("Enter AA sequence (<+A:><n...>[A-Z]...)", "")%9999%0
      if ((gSeq != "NULL") and (gSeq.count > 0)) {
          print format ("Sequence=%s  phi=%d  psi=%d", gSeq, kPHI, kPSI)

@@ Line 22: / Line 22: @@
 Copy and paste the following into a text editor and save in your scripts directory as ribozome.spt.
 <pre>#   RIBOZOME - Jmol script by Ron Mignery
-#   v1.16 beta    7/13/2015 -minor edits
+#   v1.17 beta    8/19/2015 -minor edits
+#
 #   RIBOZOME takes a string message encoding an amino acid (aa) sequence
@@ Line 295: / Line 295: @@
+     }
      var c = gCHAIN
      gResno = 0    # global pre-existing AA count
@@ Line 312: / Line 310: @@
              # Get the largest atomno in frame
-             gN = {(file=f) and (model=m)}.atomno.max
+             gN = {thisModel}.atomno.max
              # While there is an atom at the origin
              while (true) {
-                 var ai = {within(0.1, {0 0 0}) and (file=f) and (model=m)}
+                 var ai = {within(0.1, {0 0 0}) and thisModel}
-                 if (ai.size > 0) {
+                 if (ai) {
                      # If on the same chain
@@ Line 323: / Line 321: @@
                          # Delete OXT
-                         delete {(atomName="OXT") and (file=f) and (model=m)
+                         delete {(atomName="OXT") and thisModel
                              and (chain=c)}
                          gResno = ai.resno
@@ Line 331: / Line 329: @@
                      # Else move all from the new chain rightward on X axis
                      else {
-                         select {(file=f) and (model=m) and (chain!=c)}
+                         select {thisModel and (chain!=c)}
                          translateselected {20, 0, 0 }
                          gN++
@@ Line 350: / Line 348: @@
              # Move polypeptide C to bond distance from new AA N
-             select {(file=f) and (model=m) and (chain=c)}
+             select {thisModel and (chain=c)}
              fix none
              translateselected {2.069, -2.122, -0.554 } #N1
@@ Line 378: / Line 376: @@
              # Gen axis on new N perpendicular to the plane
              # containing atoms nn, pn+2 and nn+1
-             var aNn = {(atomno=nn) and (file=f) and (model=m) and (chain=c)}
+             var aNn = {(atomno=nn) and thisModel and (chain=c)}
-             var aNn1 = {(atomno=@{nn+1}) and (file=f) and (model=m) and (chain=c)}
+             var aNn1 = {(atomno=@{nn+1}) and thisModel and (chain=c)}
-             var aPn1 = {(atomno=@{pn+1}) and (file=f) and (model=m) and (chain=c)}
+             var aPn1 = {(atomno=@{pn+1}) and thisModel and (chain=c)}
-             var aPn2 = {(atomno=@{pn+2}) and (file=f) and (model=m) and (chain=c)}
+             var aPn2 = {(atomno=@{pn+2}) and thisModel and (chain=c)}
-             var aPn3 = {(atomno=@{pn+3}) and (file=f) and (model=m) and (chain=c)}
+             var aPn3 = {(atomno=@{pn+3}) and thisModel and (chain=c)}
              var v1=aPn2.xyz - aNn.xyz
              var v2=aNn1.xyz - aNn.xyz
@@ Line 391: / Line 389: @@
              # Rotate the polypeptide N on the new AA C to tetrahedral (nominally 110)
-             select {(atomno < nn) and (file=f) and (model=m) and (chain=c)}
+             select {(atomno < nn) and thisModel and (chain=c)}
-             fix {(atomno >= nn) and (file=f) and (model=m) and (chain=c)}
+             fix {(atomno >= nn) and thisModel and (chain=c)}
              rotateselected @axis @aNn @{kPEPTIDE_ANGLE - 65.5}
@@ Line 402: / Line 400: @@
              # Make the old psi dihedral = kPSI (nominally -47)
-             select {(atomno < nn) and (file=f) and (model=m) and (chain=c)
+             select {(atomno < nn) and thisModel and (chain=c)
                  and not aPn2 and not aPn3}
              rotateselected @aPn1 @aPn2 @{kPSI + 33.4 + pb}
@@ Line 424: / Line 422: @@
      connect
-     var xx = {(element="Xx") and (file=f) and (model=m) and (chain=c)}
+     var xx = {(element="Xx") and thisModel and (chain=c)}
      for (var i = 1; i <= xx.size; i++) {
-           connect 1.8 {(atomindex=@{xx[i].atomIndex}) and (file=f)
+           connect 1.8 {(atomindex=@{xx[i].atomIndex}) and thisModel and (chain=c)}
+     }
      # Clean up
-     connect ([UNK].CA) ([UNK].Xx and within(group, _1) and (file=f)
+     connect ([UNK].CA) ([UNK].Xx and within(group, _1) and thisModel and (chain=c))
-        and (model=m) and (chain=c))
+     select (thisModel)
      fix none
      print format("%d atoms generated", gN-1)

@@ Line 453: / Line 453: @@
 === In a webpage ===
-The main script is a small adaptation of the one above.
+''(Updated to RIBOZOME v1.16 script, now works both in Jmol-Java and JSmol-HTML5)''
-The JSmol variant is not working yet. We need debugging the script, something in it fails to run properly in JSmol and no good helix is formed.
+Sequence input is managed from the webpage. In addition, the helix parameters (which are fixed in the original script) may be changed in the page by a user.
 See it [http://biomodel.uah.es/Jmol/helix_builder/ in action]

@@ Line 22: / Line 22: @@
 Copy and paste the following into a text editor and save in your scripts directory as ribozome.spt.
 <pre>#   RIBOZOME - Jmol script by Ron Mignery
-#   v1.15 beta    7/11/2014 -add frame option+
+#   v1.16 beta    7/13/2015 -minor edits
+#
 #   RIBOZOME takes a string message encoding an amino acid (aa) sequence
@@ Line 54: / Line 54: @@
 gCHAIN = 'A'    # The chain id
 gA = ""
-gPdbAddHydrogens = FALSE
+gPdbAddHydrogens = false
-gAppendNew = TRUE
+gAppendNew = true
-gNewFrame = FALSE
+gNewFrame = false
 # Lookup 3 letter code from 1 letter code
@@ Line 273: / Line 273: @@
 function plico_gen_alpha(gSeq) {
      gPdbAddHydrogens = pdbAddHydrogens
-     set pdbAddHydrogens FALSE
+     set pdbAddHydrogens false
      if (gPlicoRecord != "") {
          var g = format("show file \"%s\"", gPlicoRecord)
@@ Line 285: / Line 285: @@
      gSeq = gSeq%9999%0
-     gNewFrame = FALSE
+     gNewFrame = false
      if (gSeq[1] == '+') {
-         gNewFrame = TRUE
+         gNewFrame = true
          gSeq = gSeq[2][9999]
+     }
@@ Line 296: / Line 296: @@
      var f = (_frameID/1000000)
-     var m = (_frameID%100000)
+     var m = (_frameID%1000000)
      var c = gCHAIN
      gResno = 0    # global pre-existing AA count
@@ Line 303: / Line 303: @@
      gN = 1
      if (gNewFrame) {
-         appendNew = TRUE
+         appendNew = true
+     }
      else {
-         appendNew = FALSE
+         appendNew = false
-−
          # If not new
          if (m > 0) {
-−
              # Get the largest atomno in frame
              gN = {(file=f) and (model=m)}.atomno.max
-−
              # While there is an atom at the origin
-             while (TRUE) {
+             while (true) {
-                 ai = {within(0.1, {0 0 0}) and (file=f) and (model=m)}
+                 var ai = {within(0.1, {0 0 0}) and (file=f) and (model=m)}
                  if (ai.size > 0) {
-−
                      # If on the same chain
                      if (ai[1].chain = c) {
-−
                          # Delete OXT
                          delete {(atomName="OXT") and (file=f) and (model=m)
@@ Line 348: / Line 348: @@
          if ((m > 0) and not appendNew) {
-−
              # Move polypeptide C to bond distance from new AA N
              select {(file=f) and (model=m) and (chain=c)}
@@ Line 360: / Line 360: @@
          gA += "end \"append aa\""
          script inline @{gA}
-−
          f = (_frameID/1000000)
-         m = (_frameID%100000)
+         m = (_frameID%1000000)
-         appendNew = FALSE
+         appendNew = false
          # If PRO ahead
@@ Line 371: / Line 371: @@
                  pb = kPRO_BUMP
+             }
-−
+         }
          # If not first AA
@@ Line 422: / Line 422: @@
      gA += "end \"append aa\""
      script inline @{gA}
      connect
      var xx = {(element="Xx") and (file=f) and (model=m) and (chain=c)}
@@ Line 432: / Line 433: @@
      connect ([UNK].CA) ([UNK].Xx and within(group, _1) and (file=f)
          and (model=m) and (chain=c))
-     select all
+     select ((file=f) and (model=m))
      fix none
      print format("%d atoms generated", gN-1)