User:Remig/plico/modify - Revision history

Remig at 15:12, 11 September 2015

2015-09-11T15:12:05Z

Show changes

Remig: Add dragSelected=true

2015-07-27T15:04:47Z

Add dragSelected=true

Remig: Add menu toggle

2015-07-24T18:51:28Z

Add menu toggle

Remig: Clear hover labels on exit

2015-07-13T19:03:48Z

Clear hover labels on exit

Remig: Use get_atom_rcn

2014-11-18T21:34:56Z

Use get_atom_rcn

Remig at 17:40, 3 October 2014

2014-10-03T17:40:01Z

Remig: Fix connect bug

2014-10-03T17:31:36Z

Fix connect bug

Remig at 16:22, 23 July 2014

2014-07-23T16:22:48Z

Remig at 15:08, 21 July 2014

2014-07-21T15:08:32Z

Remig: Handle multi-frame environment

2014-07-21T14:56:37Z

Handle multi-frame environment

Show changes

@@ Line 1: / Line 1: @@
-'''Modify''' allows the user to make common amino acid and nucleotide modification by mouse actions.  Hover text above each atom gives the available options including methylation on nucleosides, single-bond oxygens, and nitrogens, hydroxylation of PRO, formylation of MET, ribose/deoxyribose interconversion, phosphorylation of SER, THR, TYR and HIS, and nucleotide modifications to generate pseudouridine, dihyrouridine, inosine, and xanthine.
+'''Modify''' allows the user to make common amino acid and nucleotide modifications by mouse actions.  Hover text above each atom gives the available options if any including methylation on nucleosides, single-bond oxygens, and nitrogens, hydroxylation of PRO, formylation of MET, ribose/deoxyribose interconversion, phosphorylation of SER, THR, TYR and HIS, and nucleotide modifications to generate pseudouridine, dihyrouridine, inosine, and xanthine.
 See [[User:Remig/plico/convert|Convert]] for a script to replace one amino-acid with another or one nucleotide with another.
 After a modification adding atoms, the hover text on those atoms includes 'X' to remove the modification.  Note also that the desired modification may be presented in the hover text on only just one or a few of the atoms of the residue to be modified and you may have to look around to find it.
-Some features unrelated to modification have been placed here as well to serve other Plico functions.  Water molecules may be added and moved around to serve as pivot points for Tug when no other atoms are where the pivot point is wanted.  Also the Jmol parameters allowMoveAtoms and allowRotateSelected are set true while modify is active to allow free rotation and translation of selected atoms.
+Some features unrelated to modification have been placed here as well to serve other Plico functions.  Water molecules may be added and moved around perhaps to serve as pivot points for Tug when no other atoms are where the pivot point is wanted.
 '''Modify''' 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 15: / Line 20: @@
 Copy and paste the following to a text editor and save to your scripts directory as modify.spt:
 <pre>#   modify - Jmol script by Ron Mignery
-#   v1.9 beta    7/24/2015 -add menu toggle
+#   v1.10 beta    7/27/2015 -add dragSelected
+#
 # See atom hover text for options:
@@ Line 26: / Line 31: @@
 gAllowMoveAtoms = allowMoveAtoms
 gAllowRotateSelected = allowRotateSelected
 gSelsave = ({})
 gScheme = defaultColorScheme
@@ Line 588: / Line 594: @@
+     }
      color {selected} @gAltScheme
+}
@@ Line 596: / Line 603: @@
      set allowRotateSelected gAllowRotateSelected
      set allowMoveAtoms gAllowMoveAtoms
      set hoverDelay gHoverDelay
      set AnimFrameCallback none
@@ Line 612: / Line 620: @@
      gAllowMoveAtoms = allowMoveAtoms
      gAllowRotateSelected = allowRotateSelected
      gHoverDelay = hoverDelay
      gHoverLabel = hoverLabel
      set allowMoveAtoms true
      set allowRotateSelected true
      set AnimFrameCallback "jmolscript:set_hover_labels"

@@ Line 15: / Line 15: @@
 Copy and paste the following to a text editor and save to your scripts directory as modify.spt:
 <pre>#   modify - Jmol script by Ron Mignery
-#   v1.8 beta    6/18/2015 -clear hover labels on exit
+#   v1.9 beta    7/24/2015 -add menu toggle
+#
 # See atom hover text for options:
@@ Line 35: / Line 35: @@
 # Return L tetrahedron point if i1<i2<i3, else R point
 function get_tet(i1, i2, i3, dist) {
      var v1 = {atomIndex=i3}.xyz - {atomIndex=i2}.xyz
      var v2 = {atomIndex=i1}.xyz - {atomIndex=i2}.xyz
@@ Line 307: / Line 306: @@
          axis = (c2.xyz - c6.xyz + n1.xyz)
          select c2 or o2 or n3 or c4 or o4 or c5 or c6
-#quit
          rotateSelected @n1 @axis 40
          select o2 or n3 or c4 or o4 or c5
@@ Line 631: / Line 630: @@
      echo @gEcho
      gChain = ""
      unbind
@@ Line 642: / Line 642: @@
      bind "ALT-CTRL-LEFT-CLICK" "+:add_water_mb";
      bind "DOUBLE" "modify_exit_mb";
      set hoverDelay 0.001

@@ Line 15: / Line 15: @@
 Copy and paste the following to a text editor and save to your scripts directory as modify.spt:
 <pre>#   modify - Jmol script by Ron Mignery
-#   v1.7 beta    11/18/2014 -use get_atom_rcn
+#   v1.8 beta    6/18/2015 -clear hover labels on exit
+#
 # See atom hover text for options:
@@ Line 24: / Line 24: @@
 # Enable jmol move for duration
 gAllowMoveAtoms = allowMoveAtoms
 gAllowRotateSelected = allowRotateSelected
@@ Line 604: / Line 603: @@
      select ((file=f) and (model=m))
      hoverLabel = gHoverLabel
      color {selected} @gScheme
      select {gSelsave}

@@ Line 15: / Line 15: @@
 Copy and paste the following to a text editor and save to your scripts directory as modify.spt:
 <pre>#   modify - Jmol script by Ron Mignery
-#   v1.6 beta    10/3/2014 -fix for multiframe
+#   v1.7 beta    11/18/2014 -use get_atom_rcn
+#
 # See atom hover text for options:
@@ Line 189: / Line 189: @@
      appendNew = gAppendNew
-     var aP = atom_rcn(r, iChain, "P")
+     var aP = get_atom_rcn(r, iChain, "P")
-     var aO3p = atom_rcn(r-1, iChain, "O3\'")
+     var aO3p = get_atom_rcn(r-1, iChain, "O3\'")
      connect @aP @aO3p
-     var aO3 = atom_rcn(r, iChain, "O3\'")
+     var aO3 = get_atom_rcn(r, iChain, "O3\'")
-     var aPn = atom_rcn(r+1, iChain, "P")
+     var aPn = get_atom_rcn(r+1, iChain, "P")
      connect @aO3 @aPn
+}
@@ Line 200: / Line 200: @@
      var iResno = {atomIndex=idx}.resno
      var iChain = {atomIndex=idx}.chain
-     var a1 = atom_rcn(iResno, iChain, "O2")
+     var a1 = get_atom_rcn(iResno, iChain, "O2")
-     var a2 = atom_rcn(iResno, iChain, "O4")
+     var a2 = get_atom_rcn(iResno, iChain, "O4")
      var xyz = {0 0 0} + a1.xyz
      a1.xyz = {0 0 0} + a2.xyz
      a2.xyz = xyz
-     a1 = atom_rcn(iResno, iChain, "C2")
+     a1 = get_atom_rcn(iResno, iChain, "C2")
-     a2 = atom_rcn(iResno, iChain, "C4")
+     a2 = get_atom_rcn(iResno, iChain, "C4")
      xyz = {0 0 0} + a1.xyz
      a1.xyz = {0 0 0} + a2.xyz
      a2.xyz = xyz
-     a1 = atom_rcn(iResno, iChain, "N1")
+     a1 = get_atom_rcn(iResno, iChain, "N1")
-     a2 = atom_rcn(iResno, iChain, "C5")
+     a2 = get_atom_rcn(iResno, iChain, "C5")
      xyz = {0 0 0} + a1.xyz
      a1.xyz = {0 0 0} + a2.xyz
      a2.xyz = xyz
-     var a3 = atom_rcn(iResno, iChain, "C1\'")
+     var a3 = get_atom_rcn(iResno, iChain, "C1\'")
      connect @a3 @a1 DELETE
      connect @a3 @a2
@@ Line 235: / Line 235: @@
      var iResno = {atomIndex=idx}.resno
      var iChain = {atomIndex=idx}.chain
-     var n1 = atom_rcn(iResno, iChain, "N1")
+     var n1 = get_atom_rcn(iResno, iChain, "N1")
-     var c2 = atom_rcn(iResno, iChain, "C2")
+     var c2 = get_atom_rcn(iResno, iChain, "C2")
-     var o2 = atom_rcn(iResno, iChain, "O2")
+     var o2 = get_atom_rcn(iResno, iChain, "O2")
-     var n3 = atom_rcn(iResno, iChain, "N3")
+     var n3 = get_atom_rcn(iResno, iChain, "N3")
-     var c4 = atom_rcn(iResno, iChain, "C4")
+     var c4 = get_atom_rcn(iResno, iChain, "C4")
-     var o4 = atom_rcn(iResno, iChain, "O4")
+     var o4 = get_atom_rcn(iResno, iChain, "O4")
-     var c5 = atom_rcn(iResno, iChain, "C5")
+     var c5 = get_atom_rcn(iResno, iChain, "C5")
-     var c6 = atom_rcn(iResno, iChain, "C6")
+     var c6 = get_atom_rcn(iResno, iChain, "C6")
      var a1 = angle(n1, c6, c5, c4)\10
@@ Line 475: / Line 475: @@
+         }
          else {
-              delete atom_rcn(iResno, iChain, "CF")
+              delete get_atom_rcn(iResno, iChain, "CF")
-              delete atom_rcn(iResno, iChain, "OC1")
+              delete get_atom_rcn(iResno, iChain, "OC1")
+         }
+     }
@@ Line 536: / Line 536: @@
+     }
      else if ((iGroup="T") and (iName="c5")) {
-         delete atom_rcn(iResno, iChain, "C7")
+         delete get_atom_rcn(iResno, iChain, "C7")
          to_x_idx(idx, "C", "U")
+     }

@@ Line 1: / Line 1: @@
-'''Modify''' allows the user to make common amino acid and nucleotide modification by mouse actions.  Hover text above each atom gives the available options including methylation on nucleosides, single-bond oxygens, and nitrogens, hydroxylation of PRO, formylation of MET, ribose/deoxyribose interconversion, phosphorylation of SER, THR, TYR and HIS, and nucleotide modifications to pseudouridine, dihyrouridine, inosine, and xanthine.
+'''Modify''' allows the user to make common amino acid and nucleotide modification by mouse actions.  Hover text above each atom gives the available options including methylation on nucleosides, single-bond oxygens, and nitrogens, hydroxylation of PRO, formylation of MET, ribose/deoxyribose interconversion, phosphorylation of SER, THR, TYR and HIS, and nucleotide modifications to generate pseudouridine, dihyrouridine, inosine, and xanthine.
 See [[User:Remig/plico/convert|Convert]] for a script to replace one amino-acid with another or one nucleotide with another.
 Some features unrelated to modification have been placed here as well to serve other Plico functions.  Water molecules may be added and moved around to serve as pivot points for Tug when no other atoms are where the pivot point is wanted.  Also the Jmol parameters allowMoveAtoms and allowRotateSelected are set true while modify is active to allow free rotation and translation of selected atoms.

@@ Line 1: / Line 1: @@
-'''Modify''' allows the user to make common amino acid and nucleotide modification by mouse actions.  Hover text above each atom gives the available options including methylation on nucleosides, single-bond oxygens, and nitrogens, hydroxylation of PRO, formylation of MET, ribose/deoxyribose interconversion, phosphorylation of SER, THR, TYR and HIS, and conversions to pseudouridine, dihyrouridine, inosine, and xanthine.
+'''Modify''' allows the user to make common amino acid and nucleotide modification by mouse actions.  Hover text above each atom gives the available options including methylation on nucleosides, single-bond oxygens, and nitrogens, hydroxylation of PRO, formylation of MET, ribose/deoxyribose interconversion, phosphorylation of SER, THR, TYR and HIS, and nucleotide modifications to pseudouridine, dihyrouridine, inosine, and xanthine.
 Some features unrelated to modification have been placed here as well to serve other Plico functions.  Water molecules may be added and moved around to serve as pivot points for Tug when no other atoms are where the pivot point is wanted.  Also the Jmol parameters allowMoveAtoms and allowRotateSelected are set true while modify is active to allow free rotation and translation of selected atoms.
@@ Line 11: / Line 13: @@
 Copy and paste the following to a text editor and save to your scripts directory as modify.spt:
 <pre>#   modify - Jmol script by Ron Mignery
-#   v1.5 beta    7/23/2014 -fixes
+#   v1.6 beta    10/3/2014 -fix for multiframe
+#
 # See atom hover text for options:
@@ Line 50: / Line 52: @@
 # return vector parallel to previous bond
 function get_tet_1(pIdx, idx) {
      var cset = connected({atomIndex=pIdx}) and not {atomIndex=idx}
      return {atomIndex=idx}.xyz + {atomIndex=pIdx}.xyz - cset[1].xyz
@@ Line 56: / Line 57: @@
 function get_trigonal(i1, i2, i3, dist) {
      var v1 = {atomIndex=i1}.xyz - {atomIndex=i2}.xyz
      var v2 = {atomIndex=i3}.xyz - {atomIndex=i2}.xyz
@@ Line 70: / Line 70: @@
 function add_to_idx(idx, aElement, greek, addOs) {
      var iGroup = {atomIndex=idx}.group
      var iResno = {atomIndex=idx}.resno
@@ Line 166: / Line 165: @@
 function to_x_idx(idx, newElement, newGroup) {
-     var cSet = {resno=@{{atomIndex=idx}.resno}}
+     var f = {atomIndex=idx}.file
      var ls = "data \"append toX\"\n"
      for (var i = 1; i <= cSet.size; i++) {
@@ Line 184: / Line 186: @@
      script inline @{ls}
      appendNew = gAppendNew
+}

@@ Line 361: / Line 361: @@
      select ??.?2' and (file=f) and (model=m)
      set hoverLabel "%U|1:  -CH3|2: X <--> DX"
      refresh
+  }