User:Remig/plico/turn - Revision history

Remig at 17:24, 12 April 2016

2016-04-12T17:24:41Z

Remig at 14:43, 11 September 2015

2015-09-11T14:43:49Z

Show changes

Remig: Add menu toggle

2015-07-24T18:46:10Z

Add menu toggle

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Remig at 16:33, 16 May 2014

2014-05-16T16:33:55Z

Remig: lc all functions

2014-05-16T16:25:16Z

lc all functions

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Remig at 13:45, 2 April 2014

2014-04-02T13:45:25Z

Remig: Add proline cis/trans

2014-02-26T16:15:45Z

Add proline cis/trans

Remig: Plico turn module

2014-02-15T23:43:01Z

Plico turn module

New page

'''Turn''' allows the user to make type I and II reverse turns and beta-hairpins in polypeptides with a single mouse click on the corner oxygen where you want the turn. ALT-CLICK creates a type I turn and SHIFT-CLICK makes a type II.

'''Turn''' 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 Turn
Script=script <path to your scripts folder>/turn.spt;plicoTurn
</pre>
saved as plicoTurn.macro in your .jmol/macros folder as described in [[Macro]].

Copy and paste the following to a text editor and save to your scripts folder as turn.spt, replacing the text "<SCRIPT_PATH>" with the path to your scripts:
<pre># turn - Jmol script by Ron Mignery
#*****Replace <SCRIPT_PATH> with path to your scripts folder before use***
# v1.0 beta 2/14/2014 for Jmol 14
#
# Apply a type I or type II turn to a polypeptide
#

# Bound to ALT-LEFT-CLICK by plicoTurn
function turnCargo1MB() {
print "turnCargo1MB()"#TBD

# If O atom picked
if ({atomIndex=_atomPicked}.atomName = "O") {
gChain = {atomIndex=_atomPicked}.chain
var cMidx = getScBBidx (_atomPicked, gChain)

var caMidx = getNwardBBidx (cMidx, gChain)
var nMidx = getNwardBBidx (caMidx, gChain)
var ncMidx = getNwardBBidx (nMidx, gChain)
var nPidx = getCwardBBidx (cMidx, gChain)
var caPidx = getCwardBBidx (nPidx, gChain)
var cPidx = getCwardBBidx (caPidx, gChain)
var cnPidx = getCwardBBidx (cPidx, gChain)

save state gState
selectNwardIdx(caPidx, 0)
setDihedralIdx(cnPidx, cPidx, caPidx, nPidx, 0) # cWard Psi
selectNwardIdx(nPidx, 0)
setDihedralIdx(cPidx, caPidx, nPidx, cMidx, -90) # cWard Phi
selectNwardIdx(caMidx, 0)
setDihedralIdx(nPidx, cMidx, caMidx, nMidx, -60) # nWard Psi
selectNwardIdx(nMidx, 0)
setDihedralIdx(cMidx, caMidx, nMidx, ncMidx, -40) # nWard Phi

handleCollisions2( 0)
if (countcollisions(({})) > 0) {
var p = prompt("Unable to handle all collisions!")
restore state gState
}
}
}

# Bound to SHIFT-LEFT-CLICK by plicoTurn
function turnCargo2MB() {
print "turnCargo2MB()"#TBD

# If O atom picked
if ({atomIndex=_atomPicked}.atomName = "O") {
gChain = {atomIndex=_atomPicked}.chain
var cMidx = getScBBidx (_atomPicked, gChain)

save state gState
var caMidx = getNwardBBidx (cMidx, gChain)
var nMidx = getNwardBBidx (caMidx, gChain)
var ncMidx = getNwardBBidx (nMidx, gChain)
var nPidx = getCwardBBidx (cMidx, gChain)
var caPidx = getCwardBBidx (nPidx, gChain)
var cPidx = getCwardBBidx (caPidx, gChain)
var cnPidx = getCwardBBidx (cPidx, gChain)

# Hi to lo since N-terminal is to move
selectNwardIdx(caPidx, 0)
setDihedralIdx(cnPidx, cPidx, caPidx, nPidx, 0) # cWard Psi
selectNwardIdx(nPidx, 0)
setDihedralIdx(cPidx, caPidx, nPidx, cMidx, 90) # cWard Phi
selectNwardIdx(caMidx, 0)
setDihedralIdx(nPidx, cMidx, caMidx, nMidx, 120) # nWard Psi
selectNwardIdx(nMidx, 0)
setDihedralIdx(cMidx, caMidx, nMidx, ncMidx, -70) # nWard Phi

handleCollisions2( 0)
if (countcollisions(({})) > 0) {
var p = prompt("Unable to handle all collisions!")
restore state gState
}
}
}

# Top level of Turn
function plicoTurn() {

# Load tug functions if not already
if (kTug < 3) {
script "<SCRIPT_PATH>tug.spt"
if (kTug < 3) {
prompt ("A newer version of TUG.SPT is required")
quit
}
}

gPlico = "TURN"
plicoPrelim()

select GLY and Oxygen
halo on
select all
gEcho = ("_______TURN_______| *** Click on O ***|ALT-CLICK=Type I" +
"|SHIFT-CLICK=Type II|DOUBLE-CLICK=exit")
echo @gEcho
gChain = ""
unbind

bind "ALT-LEFT-CLICK" "_pickAtom";
bind "ALT-LEFT-CLICK" "+:turnCargo1MB";
bind "SHIFT-LEFT-CLICK" "_pickAtom";
bind "SHIFT-LEFT-CLICK" "+:turnCargo2MB";
bind "DOUBLE" "plicoExit";
}

# End of TURN.SPT
</pre>

@@ Line 12: / Line 12: @@
 <pre>#   turn - Jmol script by Ron Mignery
+#
-#   v1.5 beta    9/11/2015 -use thisModel
+#   v1.6 beta    4/12/2016 -require latest common includes
+#
 #   Apply a type I or type II turn to a polypeptide
@@ Line 132: / Line 132: @@
      # 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
@@ Line 140: / Line 140: @@
+     }
-     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 3: / Line 3: @@
 '''Turn''' 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 Turn
-Script=script <path to your scripts folder>/turn.spt;plicoTurn
+Script=script <path to your scripts folder>/turn.spt;plico_turn
 </pre>
 saved as plicoTurn.macro in your .jmol/macros folder as described in [[Macro]].

@@ Line 7: / Line 7: @@
 saved as plicoTurn.macro in your .jmol/macros folder as described in [[Macro]].
-Copy and paste the following to a text editor and save to your scripts folder as turn.spt, replacing the text "<SCRIPT_PATH>" with the path to your scripts:
+A copy of the Plico script [[User:Remig/plico/tug|tug.spt]] must be in the same directory as this script.
 <pre>#   turn - Jmol script by Ron Mignery
-#*****Replace <SCRIPT_PATH> with path to your scripts folder before use***
-#   v1.1 beta    2/14/2014 for Jmol 14 - add proline cis/trans
+#   v1.2 beta    4/2/2014 for Jmol 14
+#
 #   Apply a type I or type II turn to a polypeptide
@@ Line 17: / Line 19: @@
 # Bound to ALT-LEFT-CLICK by plicoTurn
 function turnCargo1MB() {
      # If O atom picked
@@ Line 72: / Line 73: @@
 # Bound to SHIFT-LEFT-CLICK by plicoTurn
 function turnCargo2MB() {
      # If O atom picked
@@ Line 130: / Line 130: @@
 function plicoTurn() {
-     # Load tug functions if not already
+     # Load common functions if not already
-     if (kTug < 3) {
+     if (kCommon < 1) {
-         script "<SCRIPT_PATH>tug.spt"
+         script $SCRIPT_PATH$tug.spt
-         if (kTug < 3) {
+         if (kCommon < 1) {
-             prompt ("A newer version of TUG.SPT is required")
+             prompt ("A newer version of plicoCommon.SPT is required")
              quit
+         }

@@ Line 1: / Line 1: @@
-'''Turn''' allows the user to make type I and II reverse turns and beta-hairpins in polypeptides with a single mouse click on the corner oxygen where you want the turn.  ALT-CLICK creates a type I turn and SHIFT-CLICK makes a type II.
+'''Turn''' allows the user to make type I and II reverse turns and beta-hairpins in polypeptides with a single mouse click on the corner oxygen where you want the turn.  ALT-CLICK creates a type I turn and SHIFT-CLICK makes a type II.  Either on a proline N rotates the omega bond 180 for a cis/trans transition.
 '''Turn''' 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 10: / Line 10: @@
 <pre>#   turn - Jmol script by Ron Mignery
 #*****Replace <SCRIPT_PATH> with path to your scripts folder before use***
-#   v1.0 beta    2/14/2014 for Jmol 14
+#   v1.1 beta    2/14/2014 for Jmol 14 - add proline cis/trans
+#
 #   Apply a type I or type II turn to a polypeptide
@@ Line 46: / Line 46: @@
              var p = prompt("Unable to handle all collisions!")
              restore state gState
+         }
+     }
@@ Line 57: / Line 77: @@
      if ({atomIndex=_atomPicked}.atomName = "O") {
          gChain = {atomIndex=_atomPicked}.chain
-         var cMidx = getScBBidx (_atomPicked, gChain)
+        var caMidx = getNwardBBidx (_atomPicked, gChain)
          save state gState
@@ Line 82: / Line 103: @@
              var p = prompt("Unable to handle all collisions!")
              restore state gState
+         }
+     }
@@ Line 101: / Line 142: @@
      plicoPrelim()
-     select GLY and Oxygen
+     select (GLY and Oxygen) or (PRO and Nitrogen)
      halo on
      select all
-     gEcho = ("_______TURN_______|  *** Click on O ***|ALT-CLICK=Type I" +
+     gEcho = ("_______TURN_______|  *** Click on O ***|      (or proline N)|ALT-CLICK=Type I" +
          "|SHIFT-CLICK=Type II|DOUBLE-CLICK=exit")
      echo @gEcho