User:Remig/plico/toABnt - Revision history

Remig: Avoid "axis," a newly reserved word

2016-04-12T17:05:13Z

Avoid "axis," a newly reserved word

Remig at 14:26, 11 September 2015

2015-09-11T14:26:12Z

Remig: Add menu toggle

2015-07-24T18:52:41Z

Add menu toggle

Remig: Adjust constants

2014-11-18T21:33:05Z

Adjust constants

Remig: add single NT mode

2014-08-18T17:42:57Z

add single NT mode

Remig at 14:52, 16 July 2014

2014-07-16T14:52:43Z

Remig at 14:51, 16 July 2014

2014-07-16T14:51:57Z

Remig: Add multi-frame support

2014-07-16T14:09:36Z

Add multi-frame support

Show changes

Remig at 12:44, 11 June 2014

2014-06-11T12:44:24Z

Remig at 20:52, 10 June 2014

2014-06-10T20:52:18Z

@@ Line 14: / Line 14: @@
 Copy and paste the following into a text editor and save in your scripts directory as toABnt.spt.
 <pre>#   toABnt - Jmol script by Ron Mignery
-#   v1.12 beta    9/11/2015 -use thisModel
+#   v1.13 beta    4/12/2016 -require latest common includes
+#
 #   Convert a nucleotide or polynucleotide chain
@@ Line 35: / Line 35: @@
 function to_ab_single_nt(res, iChain) {
-     f = {atomIndex=_atomPicked}.file
+     var f = {atomIndex=_atomPicked}.file
-     m = {atomIndex=_atomPicked}.model
+     var m = {atomIndex=_atomPicked}.model
      var isForm = (is_form_a( res, iChain) ? "A" : "B")
      var p = prompt(format("Convert residue %d from %s-form to:",
@@ Line 65: / Line 65: @@
          var a0 = within(kDtolerance, {0 0 0})
          if (auto == false) {
-             f = {atomIndex=_atomPicked}.file
+             var f = {atomIndex=_atomPicked}.file
-             m = {atomIndex=_atomPicked}.model
+             var m = {atomIndex=_atomPicked}.model
              var isForm = (is_form_a( maxres, gChain1) ? "A" : "B")
              var p = prompt(format("Convert chain %s from %s-form to:",
@@ Line 130: / Line 130: @@
 # Load common functions if not already
 function load_common() {
-     if (kCommon < 6) {
+     if (kCommon < 7) {
          script $SCRIPT_PATH$plicoCommon.spt
-         if (kCommon < 6) {
+         if (kCommon < 7) {
              prompt ("A newer version of plicoCommon.SPT is required")
              quit
+         }
+     }
-     if (kNTcommon < 4) {
+     if (kNTcommon < 6) {
          script $SCRIPT_PATH$plicoNTcommon.spt
-         if (kNTcommon < 4) {
+         if (kNTcommon < 6) {
              prompt ("A newer version of plicoNTcommon.SPT is required")
              quit
@@ Line 150: / Line 150: @@
      # Load common functions if not already
-     if (kCommon < 6) {
+     if (kCommon < 7) {
          script $SCRIPT_PATH$plicoCommon.spt
-         if (kCommon < 6) {
+         if (kCommon < 7) {
              prompt ("A newer version of plicoCommon.SPT is required")
              quit
+         }
+     }
-     if (kNTCommon < 4) {
+     if (kNTCommon < 6) {
          script $SCRIPT_PATH$plicoCommon.spt
-         if (kCommon < 4) {
+         if (kCommon < 6) {
              prompt ("A newer version of plicoNTcommon.SPT is required")
              quit

@@ Line 14: / Line 14: @@
 Copy and paste the following into a text editor and save in your scripts directory as toABnt.spt.
 <pre>#   toABnt - Jmol script by Ron Mignery
-#   v1.11 beta    7/24/2015 -add menu toggle
+#   v1.12 beta    9/11/2015 -use thisModel
+#
 #   Convert a nucleotide or polynucleotide chain
@@ Line 54: / Line 54: @@
 function to_ab_nt(auto) {
      if (not gBusy) {
          gBusy = true
@@ Line 63: / Line 61: @@
          var s = (gToA ? 4.6 : 4.46)
-         var minres = {(chain=gChain1) and (file=f)and (model=m)}.resno.min
+         var minres = get_resno_min(gChain1)
-         var maxres = {(chain=gChain1) and (file=f)and (model=m)}.resno.max
+         var maxres = get_resno_max(gChain1)
          var a0 = within(kDtolerance, {0 0 0})
          if (auto == false) {
@@ Line 99: / Line 97: @@
          adjust_nts(minres, maxres, gChain1, toab, a, s)
-         select {(file=f) and (model=m)}
+         select {thisModel}
-         if (a0.size > 0) {
+         if (a0) {
              translateSelected @{-a0.xyz}
+         }
@@ Line 108: / Line 106: @@
          gBusy = false
+     }
+}
 # Bound to ALT-LEFT-CLICK by plicoto_ab_nt
 function to_ab_chain_mb() {
-     color {(file=f)and (model=m)} @gScheme
+     color {thisModel} @gScheme
      gChain1 = {atomIndex=_atomPicked}.chain
-     color {(chain=gChain1) and (file=f)and (model=m)} @gAltScheme
+     color {(chain=gChain1) and thisModel} @gAltScheme
      refresh
      to_ab_nt(false)
@@ Line 121: / Line 120: @@
 # Bound to SHIFT-LEFT-CLICK by plicoto_ab_nt
 function to_ab_res_mb() {
-     color {(file=f)and (model=m)} @gScheme
+     color {thisModel} @gScheme
      iChain = {atomIndex=_atomPicked}.chain
      res = {atomIndex=_atomPicked}.resno
-     color {(chain=iChain) and (file=f)and (model=m) and (resno=res)} @gAltScheme
+     color {(chain=iChain) and thisModel and (resno=res)} @gAltScheme
      refresh
      to_ab_single_nt(res, iChain)
@@ Line 151: / Line 150: @@
      # Load common functions if not already
-     load_common()
+     if (kCommon < 6) {
      gPlico = "TO A-FORM/B-FORM"
-     plico_prelim(false)
+     plico_prelim(false, true)
      gEcho = ("________A <==> B_______|ALT-CLICK=convert chain" +
-         "|SHIFT-CLICK=convert NT|DOUBLE-CLICK=exit")
+         "|SHIFT-CLICK=convert NT|SHIFT-DOUBLE-CLICK=exit")
      echo @gEcho
      bind "ALT-LEFT-CLICK" "_pickAtom";
@@ Line 167: / Line 176: @@
      bind "SHIFT-LEFT-CLICK" "_pickAtom";
      bind "SHIFT-LEFT-CLICK" "+:to_ab_res_mb";
-     bind "DOUBLE" "plico_exit";
+     bind "SHIFT-DOUBLE" "plico_exit(true)";
      bind "LEFT-CLICK" "+:plico_menu_toggle";
+}
 # End of to_ab_nt.SPT
 </pre>

@@ Line 14: / Line 14: @@
 Copy and paste the following into a text editor and save in your scripts directory as toABnt.spt.
 <pre>#   toABnt - Jmol script by Ron Mignery
-#   v1.10 beta    11/18/2014 -adjust constants
+#   v1.11 beta    7/24/2015 -add menu toggle
+#
 #   Convert a nucleotide or polynucleotide chain
@@ Line 131: / Line 131: @@
 # Load common functions if not already
 function load_common() {
-     if (kCommon < 3) {
+     if (kCommon < 6) {
          script $SCRIPT_PATH$plicoCommon.spt
-         if (kCommon < 3) {
+         if (kCommon < 6) {
              prompt ("A newer version of plicoCommon.SPT is required")
              quit
@@ Line 160: / Line 160: @@
      echo @gEcho
      gChain = ""
      unbind
@@ Line 167: / Line 168: @@
      bind "SHIFT-LEFT-CLICK" "+:to_ab_res_mb";
      bind "DOUBLE" "plico_exit";
+}
 # End of to_ab_nt.SPT
 </pre>

@@ Line 14: / Line 14: @@
 Copy and paste the following into a text editor and save in your scripts directory as toABnt.spt.
 <pre>#   toABnt - Jmol script by Ron Mignery
-#   v1.9 beta    8/18/2014 -add single NT mode
+#   v1.10 beta    11/18/2014 -adjust constants
+#
 #   Convert a nucleotide or polynucleotide chain
@@ Line 60: / Line 60: @@
          var toab = (gToA ? "A" : "B")
-         var a = (gToA ? 24.0 : 19.3)
+         var a = (gToA ? 24.0 : 33.3)
-         var s = (gToA ? 4.6 : 4.73)
+         var s = (gToA ? 4.6 : 4.46)
          var minres = {(chain=gChain1) and (file=f)and (model=m)}.resno.min
@@ Line 79: / Line 79: @@
              else if (p == "B-form") {
                  toab = "B"
-                 a = 19.3
+                 a = 33.3
-                 s = 4.73
+                 s = 4.46
+             }
              else {
@@ Line 86: / Line 86: @@
                  return # early exit
+             }
+         }
          set echo TOP LEFT

@@ Line 1: / Line 1: @@
-'''ToABnt''' allows the user to convert a polynucleotide chain or chain pair from A-form to B-form and ''vice versa''.  Both chains are converted in double helixes.
+'''ToABnt''' allows the user to convert a nucleotide or a polynucleotide chain or chain pair from A-form to B-form and ''vice versa''.
 When you ALT-CLICK on any atom, you are prompted to convert its chain from its current form to either the A-form or the B-form.  The two forms differ primarily in the pucker conformation of their sugar moieties. The A-form has its sugars in the C3'-endo conformation whereas the B-form has it in the C2'-endo conformation.  The A-form is characteristic of RNA while the B-form is characteristic of DNA.
 This routine is called automatically by the Plico routine [[Recycling_Corner/DNA_Generator|Polymeraze]] when a polynucleotide is generated.
@@ Line 11: / Line 14: @@
 Copy and paste the following into a text editor and save in your scripts directory as toABnt.spt.
 <pre>#   toABnt - Jmol script by Ron Mignery
-#   v1.8 beta    7/11/2014 -add multi-frame support
+#   v1.9 beta    8/18/2014 -add single NT mode
+#
-#   Convert a polynucleotide chain from A-form to B-form or vice versa
+#   Convert a nucleotide or polynucleotide chain
+#
-gToab = FALSE
+gToab = false
-gToabAlt = FALSE
+gToabAlt = false
-gToA = FALSE
+gToA = false
-gBusy = FALSE
+gBusy = false
 function to_ab_nt_auto(iChain, toA) {
@@ Line 27: / Line 31: @@
      gChain1 = iChain
      gToA = toA
-     to_ab_nt(TRUE)
+     to_ab_nt(true)
+}
 function to_ab_nt(auto) {
      if (not gBusy) {
-         gBusy = TRUE
+         gBusy = true
          var toab = (gToA ? "A" : "B")
-         var a = (gToA ? 20.8 : 19.3)
-         var s = (gToA ? 4.44 : 4.73)
+         var a = (gToA ? 24.0 : 19.3)
          var minres = {(chain=gChain1) and (file=f)and (model=m)}.resno.min
          var maxres = {(chain=gChain1) and (file=f)and (model=m)}.resno.max
-         var maxP = atom_rcn(maxres, gChain1, "P")
+         var a0 = within(kDtolerance, {0 0 0})
-         var cp = maxP.xyz
+         if (auto == false) {
-        var w = array()
+             f = {atomIndex=_atomPicked}.file
-        for (var i = maxres-1; i <= minres; i--) {
+            m = {atomIndex=_atomPicked}.model
              var isForm = (is_form_a( maxres, gChain1) ? "A" : "B")
              var p = prompt(format("Convert chain %s from %s-form to:",
-                 gChain1, isForm), "A-form|B-form", TRUE)
+                 gChain1, isForm), "A-form|B-form|Cancel", true)
              if (p == "A-form") {
                  toab = "A"
-                 a = 20.8
+                 a = 24.0
-                 s = 4.44
+                 s = 4.6
+             }
              else if (p == "B-form") {
@@ Line 65: / Line 86: @@
                  return # early exit
+             }
+         }
          adjust_nts(minres, maxres, gChain1, toab, a, s)
          select {(file=f)and (model=m)}
-         var v = cp - maxP.xyz
+         select {(file=f) and (model=m)}
-         translateSelected @v
+         if (a0.size > 0) {
+     }
+}
@@ Line 82: / Line 113: @@
      color {(chain=gChain1) and (file=f)and (model=m)} @gAltScheme
      refresh
-     to_ab_nt(FALSE)
+     to_ab_nt(false)
+}
@@ Line 110: / Line 151: @@
      gPlico = "TO A-FORM/B-FORM"
-     plico_prelim(FALSE)
+     plico_prelim(false)
-     gEcho = ("________A <==> B_______|ALT-CLICK=mark chain|DOUBLE-CLICK=exit")
+     gEcho = ("________A <==> B_______|ALT-CLICK=convert chain" +
      echo @gEcho
      gChain = ""
@@ Line 119: / Line 161: @@
      bind "ALT-LEFT-CLICK" "_pickAtom";
      bind "ALT-LEFT-CLICK" "+:to_ab_chain_mb";
      bind "DOUBLE" "plico_exit";
+}
 # End of to_ab_nt.SPT
 </pre>

@@ Line 11: / Line 11: @@
 Copy and paste the following into a text editor and save in your scripts directory as toABnt.spt.
 <pre>#   toABnt - Jmol script by Ron Mignery
-#   v1.6 beta    6/10/2014 -use who_pairs function
+#   v1.7 beta    6/11/2014 -bug fix
+#
 #   Convert a polynucleotide chain from A-form to B-form or vice versa
@@ Line 18: / Line 18: @@
 gToabAlt = FALSE
 gToA = FALSE
 function to_ab_nt_auto(iChain, toA) {
@@ Line 89: / Line 90: @@
                  # If paired
                  var w = who_pairs(i, gChain1)
                  k = w[1]
                  kmax = k
+             }
              pSet = {(resno=k) and (chain=gChain2)}