User:Remig/plico/adjustNT - Revision history

Remig at 17:26, 12 April 2016

2016-04-12T17:26:43Z

Remig at 16:27, 11 September 2015

2015-09-11T16:27:33Z

Remig at 15:14, 11 September 2015

2015-09-11T15:14:57Z

Remig: Add menu toggle

2015-07-24T18:53:53Z

Add menu toggle

Remig: Handle multiple frames

2014-07-21T16:02:17Z

Handle multiple frames

Remig: Jmol script to adjust spacing and twist of a portion of a single or double-stranded polynucleotide

2014-06-10T21:37:36Z

Jmol script to adjust spacing and twist of a portion of a single or double-stranded polynucleotide

New page

'''AdjustNT''' allows the user to change the spacing and twist of a portion of a polynucleotide chain or chain pair. When you ALT-CLICK on any atom, its residue is marked with halos and its entire chain is highlighted and selected. You may then ALT-CTRL-CLICK on another residue in the same chain and its residue will then be marked with halos; the stretch of just the polynucleotides between the two residues will then be selected and highlighted. If you then SHIFT-CLICK anywhere, you are prompted to enter a new interbase spacing, ''i. e.'' the distance in angstroms between the proximal base atom (the one connected to C1') of one base and the next. Next you will be prompted for the desired angle between the bases measured as the dihedral between the previously described atoms and the distal ring nitrogens. The selected polynucleotide stretch will then be so adjusted. Note that this may take some time and that the legend background color will go pink for the duration of processing. Note that unusual values entered may produce unusual results with atom collisions. When you DOUBLE-CLICK to exit, however, you are given the chance to undo if desired.

AdjustNT 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 Adjust polynucleotide
Script=script <path to your script directory>/adjustNT.spt;plico_adjust_nt
</pre>saved as adjustNT.macro in your .jmol/macros directory as described in [[Macro]].

Copy and paste the following into a text editor and save in your scripts directory as adjustNT.spt.

<pre># adjustNT - Jmol script by Ron Mignery
# v1.0 beta 6/9/2014
#
# Adjust the twist and spacing of a polynucleotide chain
#
g5res = -1
g3res = -1
g5chain = ""
g3chain = ""

function highlight_selection() {
if ((g3res >= 0) and ((g3res < g5res) or (g5res < 0))) {
i = g5res
g5res = g3res
g3res = i
i = g5chain
g5chain = g3chain
g3chain = i
}

select all
color jmol
halo off
if (g3res < 0) {
if (g5res >= 0) {
select {chain=g5chain}
color rasmol
select {(resno=g5res) and (chain=g5chain)}
halo on
}
}
else if (g5chain == g3chain) {
select {(resno >= g5res) and (resno <= g3res) and chain=iChain}
color rasmol
select {((resno=g5res) or (resno=g3res)) and (chain=g5chain)}
halo on
}
}

function mark_nt_1_mb() {
r = {atomIndex=_atomPicked}.resno
iChain = {atomIndex=_atomPicked}.chain
if ((g5res == r) and (g5chain = iChain)) {
g5res = -1
g5chain = ""
}
else {
g5res = r
g5chain = iChain
if (g3chain != g5chain) {
g3res = -1
g3chain = ""
}
}
highlight_selection()
}

function mark_nt_2_mb() {
r = {atomIndex=_atomPicked}.resno
iChain = {atomIndex=_atomPicked}.chain
if ((g3res == r) and (g3chain = iChain)) {
g3res = -1
g3chain = ""
}
else {
g3res = r
g3chain = iChain
if (g5chain != g3chain) {
g5res = -1
g5chain = ""
}
}
highlight_selection()
}

function adjust_mb() {
print "adjust_mb"
if ((not gBusy) and (g5res >= 0)) {
var s = 0.0 + prompt("Enter base separation in angstroms", "4.8")%9999%0
if (s != "NaN") {
var a = 0.0 + prompt("Enter base angle in degrees", "23.7")%9999%0
if (a != "NaN") {
if ((s.type != "decimal") or (a.type != "decimal")
or (s < 2.0) or (s > 10) or (a < -180) or (a > 180)) {
prompt (format("Parameters (s=%s a=%s) out of range", s, a))
}
else {
gBusy = TRUE
background ECHO pink
refresh
var savemt = useMinimizationThread
set useMinimizationThread FALSE
var min5 = {chain=g5chain}.resno.min
var max5 = {chain=g5chain}.resno.max
if (g3res < 0) {
g5res = min5
g3res = max5
}

# Collect any pairing
var w = array()
for (var i = min5; i < max5; i++) {
w = w + [who_pairs(i, g5chain)]
}

# Twist and turn
for (var i = g5res; i < g3res; i++) {
base_stack_a(i, i+1, g5chain, g5chain, s, a)
}

# Restore pairings
var j = 1
for (var i = min5; i < max5; i++) {
if ((w[j])[1] >= 0) {
pair_it_res((w[j])[1], i, (w[j])[2], g5chain)
}
j++
}

# Clean up
for (var i = g5res; i < g3res; i++) {
fix_p_res(i, g5chain)
}
set useMinimizationThread savemt
gBusy = FALSE
background ECHO yellow
refresh
}
}
}
}
}

# Top level of adjustNT
function plico_adjust_nt() {

# Load common functions if not already
if (kCommon < 2) {
script $SCRIPT_PATH$plicoCommon.spt
if (kCommon < 2) {
prompt ("A newer version of plicoCommon.SPT is required")
quit
}
}
if (kNTcommon < 3) {
script $SCRIPT_PATH$plicoNTcommon.spt
if (kNTcommon < 3) {
prompt ("A newer version of plicoNTcommon.SPT is required")
quit
}
}
gPlico = "Adjust NT"
plico_prelim(FALSE)

gEcho = ("______Adjust NT______|ALT-CLICK=mark 1" +
"|ALT-CTRL-CLICK=mark 2|SHIFT-CLICK=adjust" + "|DOUBLE-CLICK=exit")
echo @gEcho
g5res = -1
g3res = -1
g5chain = ""
g3chain = ""
unbind

bind "ALT-LEFT-CLICK" "_pickAtom";
bind "ALT-LEFT-CLICK" "+:mark_nt_1_mb";
bind "ALT-CTRL-LEFT-CLICK" "_pickAtom";
bind "ALT-CTRL-LEFT-CLICK" "+:mark_nt_2_mb";
bind "SHIFT-LEFT-CLICK" "_pickAtom";
bind "SHIFT-LEFT-CLICK" "+:adjust_mb";
bind "DOUBLE" "plico_exit";
}
# End of adjustNT.SPT
</pre>

@@ Line 9: / Line 9: @@
 <pre>#   adjustNT - Jmol script by Ron Mignery
-#   v1.3 beta    9/11/2015 -use thisModel
+#   v1.4 beta    4/12/2016 -require latest common includes
+#
 #   Adjust the twist and spacing of  a polynucleotide chain
@@ Line 90: / Line 90: @@
      if ((not gBusy) and (g5res >= 0)) {
          var s = 0.0 + prompt("Enter base separation in angstroms", "4.8")%9999%0//4.68
-         if (s != "NaN") {
+         if (abs(s).type == "decimal") {
              var a = 0.0 + prompt("Enter base angle in degrees", "23.7")%9999%0//24.2
-             if (a != "NaN") {
+             if (abs(a).type == "string") {
                  if ((s.type != "decimal") or (a.type != "decimal")
                      or (s < 2.0) or (s > 10) or (a < -180) or (a > 180)) {
@@ Line 145: / Line 145: @@
      # 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 $SCRIPT_PATH$plicoNTcommon.spt
-         if (kNTcommon < 4) {
+         if (kNTcommon < 6) {
              prompt ("A newer version of plicoNTcommon.SPT is required")
              quit

@@ Line 1: / Line 1: @@
-'''AdjustNT''' allows the user to change the spacing and twist of a portion of a polynucleotide chain or chain pair. When you ALT-CLICK on any atom, its residue is marked with halos and its entire chain is highlighted and selected.  You may then ALT-CTRL-CLICK on another residue in the same chain and its residue will then be marked with halos; the stretch of just the polynucleotides between the two residues will then be selected and highlighted.  If you then SHIFT-CLICK anywhere, you are prompted to enter a new interbase spacing, ''i. e.'' the distance in angstroms between the proximal base atom (the one connected to C1') of one base and the next.  Next you will be prompted for the desired angle between the bases measured as the dihedral between the previously described atoms and the distal ring nitrogens.  The selected polynucleotide stretch will then be so adjusted.  Note that this may take some time and that the legend background color will go pink for the duration of processing.  Note that unusual values entered may produce unusual results with atom collisions.  When you DOUBLE-CLICK to exit, however, you are given the chance to undo if desired.
+'''AdjustNT''' allows the user to change the spacing and twist of a portion of a polynucleotide chain or chain pair. When you ALT-CLICK on any atom, its residue is marked with halos and its entire chain is highlighted and selected.  You may then ALT-CTRL-CLICK on another residue in the same chain and its residue will then be marked with halos; the stretch of just the polynucleotides between the two residues will then be selected and highlighted.  If you then ALT-SHIFT-CLICK anywhere, you are prompted to enter a new interbase spacing, ''i. e.'' the distance in angstroms between the proximal base atom (the one connected to C1') of one base and the next.  Next you will be prompted for the desired angle between the bases measured as the dihedral between the previously described atoms and the distal ring nitrogens.  The selected polynucleotide stretch will then be so adjusted.  Note that this may take some time and that the legend background color will go pink for the duration of processing.  Note that unusual values entered may produce unusual results with atom collisions.  When you SHIFT-DOUBLE-CLICK to exit, however, you are given the chance to undo if desired.
 AdjustNT 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:
@@ Line 164: / Line 164: @@
      gEcho = ("______Adjust NT______|ALT-CLICK=mark 1" +
-         "|ALT-CTRL-CLICK=mark 2|SHIFT-CLICK=adjust" + "|SHIFT-DOUBLE-CLICK=exit")
+         "|ALT-CTRL-CLICK=mark 2|ALT-SHIFT-CLICK=adjust" + "|SHIFT-DOUBLE-CLICK=exit")
      echo @gEcho
      g5res = -1
@@ Line 175: / Line 175: @@
      bind "ALT-CTRL-LEFT-CLICK" "_pickAtom";
      bind "ALT-CTRL-LEFT-CLICK" "+:mark_nt_2_mb";
-     bind "SHIFT-LEFT-CLICK" "_pickAtom";
+     bind "ALT-SHIFT-LEFT-CLICK" "_pickAtom";
-     bind "SHIFT-LEFT-CLICK" "+:adjust_mb";
+     bind "ALT-SHIFT-LEFT-CLICK" "+:adjust_mb";
      bind "SHIFT-DOUBLE" "plico_exit";
      bind "LEFT-CLICK" "+:plico_menu_toggle";

@@ Line 9: / Line 9: @@
 <pre>#   adjustNT - Jmol script by Ron Mignery
-#   v1.2 beta    7/24/2015 -add menu toggle
+#   v1.3 beta    9/11/2015 -use thisModel
+#
 #   Adjust the twist and spacing of  a polynucleotide chain
@@ Line 20: / Line 20: @@
 function highlight_selection() {
      if ((g3res >= 0) and ((g3res < g5res) or  (g5res < 0))) {
@@ Line 32: / Line 30: @@
+     }
-     select ((file=f) and (model=m))
+     select (thisModel)
      color {selected} @gScheme
      halo off
      if (g3res < 0) {
          if (g5res >= 0) {
-             select {(chain=g5chain) and (file=f) and (model=m)}
+             select {(chain=g5chain) and thisModel}
              color {selected} @gAltScheme
-             select {(resno=g5res) and (chain=g5chain) and (file=f) and (model=m)}
+             select {(resno=g5res) and (chain=g5chain) and thisModel}
              halo on
+         }
@@ Line 45: / Line 43: @@
      else if (g5chain == g3chain)  {
          select {(resno >= g5res) and (resno <= g3res)
-             and (chain=g5Chain) and (file=f) and (model=m)}
+             and (chain=g5Chain) and thisModel}
          color {selected} @gAltScheme
          select {((resno=g5res) or (resno=g3res)) and (chain=g5chain)
-             and (file=f) and (model=m)}
+             and thisModel}
          halo on
+     }
@@ Line 103: / Line 101: @@
                      background ECHO pink
                      refresh
-                     min5 = {chain=g5chain}.resno.min
+                     min5 = get_resno_min(g5chain)
-                     max5 = {chain=g5chain}.resno.max
+                     max5 = get_resno_max(g5chain)
                      if (g3res < 0) {
                          g5res = min5
@@ Line 161: / Line 159: @@
+         }
+     }
      gPlico = "Adjust NT"
-     plico_prelim(false)
+     plico_prelim(false, true)
      gEcho = ("______Adjust NT______|ALT-CLICK=mark 1" +
-         "|ALT-CTRL-CLICK=mark 2|SHIFT-CLICK=adjust" + "|DOUBLE-CLICK=exit")
+         "|ALT-CTRL-CLICK=mark 2|SHIFT-CLICK=adjust" + "|SHIFT-DOUBLE-CLICK=exit")
      echo @gEcho
      g5res = -1
@@ Line 171: / Line 170: @@
      g5chain = ""
      g3chain = ""
      bind "ALT-LEFT-CLICK" "_pickAtom";
@@ Line 180: / Line 177: @@
      bind "SHIFT-LEFT-CLICK" "_pickAtom";
      bind "SHIFT-LEFT-CLICK" "+:adjust_mb";
-     bind "DOUBLE" "plico_exit";
+     bind "SHIFT-DOUBLE" "plico_exit";
      bind "LEFT-CLICK" "+:plico_menu_toggle";
+}
 # End of adjustNT.SPT
 </pre>

@@ Line 9: / Line 9: @@
 <pre>#   adjustNT - Jmol script by Ron Mignery
-#   v1.1 beta    7/9/2014 -handle multiple frames
+#   v1.2 beta    7/24/2015 -add menu toggle
+#
 #   Adjust the twist and spacing of  a polynucleotide chain
@@ Line 17: / Line 17: @@
 g5chain = ""
 g3chain = ""
-gBusy = FALSE
+gBusy = false
 function highlight_selection() {
@@ Line 90: / Line 90: @@
 function adjust_mb() {
      if ((not gBusy) and (g5res >= 0)) {
          var s = 0.0 + prompt("Enter base separation in angstroms", "4.8")%9999%0//4.68
@@ Line 101: / Line 100: @@
+                 }
                  else {
-                     gBusy = TRUE
+                     gBusy = true
                      background ECHO pink
                      refresh
                      min5 = {chain=g5chain}.resno.min
                      max5 = {chain=g5chain}.resno.max
@@ Line 135: / Line 132: @@
                      # Clean up
                      for (var i = g5res; i < g3res; i++) {
-                         fix_p_res(i, g5chain, TRUE)
+                         fix_p_res(i, g5chain, true)
+                     }
-                    set useMinimizationThread savemt
+                     gBusy = false
                      background ECHO yellow
                      refresh
@@ Line 151: / Line 147: @@
      # Load common functions if not already
-     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 166: / Line 162: @@
+     }
      gPlico = "Adjust NT"
-     plico_prelim(FALSE)
+     plico_prelim(false)
      gEcho = ("______Adjust NT______|ALT-CLICK=mark 1" +
@@ Line 175: / Line 171: @@
      g5chain = ""
      g3chain = ""
      unbind
@@ Line 184: / Line 181: @@
      bind "SHIFT-LEFT-CLICK" "+:adjust_mb";
      bind "DOUBLE" "plico_exit";
+}
 # End of adjustNT.SPT
 </pre>