User:Remig/plico/convert - Revision history

Remig at 17:28, 12 April 2016

2016-04-12T17:28:22Z

Remig at 15:18, 11 September 2015

2015-09-11T15:18:21Z

Remig at 15:16, 11 September 2015

2015-09-11T15:16:55Z

Remig: Add toggle menu

2015-07-24T18:55:12Z

Add toggle menu

Remig: Add double-bonding options

2015-07-13T18:29:04Z

Add double-bonding options

Show changes

Remig at 16:23, 23 July 2014

2014-07-23T16:23:58Z

Remig: Jmol script to convert residues

2014-07-16T14:04:57Z

Jmol script to convert residues

New page

'''Convert_residue''' allows the user to change polypeptide or polynucleotide residues from one type to another. When the residue to change is selected with a mouse click, the user is prompted for the amino-acid or nucleotide to replace the selected residue.

'''Convert_residue''' 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 Convert residue
Script=script <path to your scripts directory>/convert_residue.spt;plico_convert
</pre>
saved as plicoConvert.macro in your .jmol/macros directory as described in [[Macro]].

Copy and paste the following to a text editor and save to your scripts directory as convert_residue.spt:

<pre># convert_residue - Jmol script by Ron Mignery
# v1.0 beta 7/15/2014
#
# Converts a selected residue base from one form to another.
# Click to select a residue
# Then enter new residue type:
# One of ACDEFGHIKLMNPQRSTUVWXY for polypeptide or
# One of ACGUT for nucleotides
gAppendNew = TRUE
g1from3 = {"ALA":"A", "GLX":"B","CYS":"C", "ASP":"D","GLU":"E", "PHE":"F",
"GLY":"G", "HIS":"H","ILE":"I", "LYS":"K","LEU":"L", "MET":"M",
"ASN":"N", "PYL":"O","PRO":"P", "GLN":"Q","ARG":"R", "SER":"S",
"THR":"T", "SEC":"U","VAL":"V", "TRP":"W","UNK":"X", "TYR":"Y", "ASX":"Z"}

function convert_aa(iResno, iChain, newres) {
gBusy = TRUE
background ECHO pink
refresh
gCHAIN = iChain

# Collect data
var f = _frameID/1000000
var m = _frameID%1000000
var topno = {(resno=iResno) and (chain=iChain)
and (file=f) and (model=m)}.atomno.max + 0
var idmax = {(file=f) and (model=m)}.atomIndex.max
var aN = atom_rcn(iResno, iChain, "N")
var aCA = atom_rcn(iResno, iChain, "CA")
var aC = atom_rcn(iResno, iChain, "C")
var aO = atom_rcn(iResno, iChain, "O")
var aNxyz = aN.xyz + {0 0 0}
var aCAxyz = aCA.xyz + {0 0 0}
var aCxyz = aC.xyz + {0 0 0}
var aOxyz = aO.xyz + {0 0 0}
gN = aN.atomno

# Delete the original
delete {(resno=iResno) and (chain=iChain) and (file=f) and (model=m)}

# Gen AA ==================================================
gAppendNew = appendNew
set appendNew FALSE
gA = "data \"append aa\"\n"
gA += gen_aa(iResno, newres);
gA += "end \"append aa\""
script inline @{gA}
appendNew = gAppendNew

# Recollect data and move backbone to coords of old aa
aN = atom_rcn(iResno, iChain, "N")
aCA = atom_rcn(iResno, iChain, "CA")
aC = atom_rcn(iResno, iChain, "C")
aO = atom_rcn(iResno, iChain, "O")
var aCB = atom_rcn(iResno, iChain, "CB")
aN.xyz = aNxyz
aCA.xyz = aCAxyz
aC.xyz = aCxyz
aO.xyz = aOxyz

# Reconstruct side-chain position on backbone
select ((atomIndex > idmax) and sidechain and (file=f) and (model=m))
color rasmol
if (aCB.size > 0) {
set_distance_atoms( aCA, aCB, 1.5)
set_angle_atoms( aC, aCA, aCB, 115.9)
set_dihedral_atoms( aO, aC, aCA, aCB, -100.2)
var aCG = atom_rcn(iResno, iChain, "*G*")
if (aCG.size > 0) {
var nno = aCG[0].atomno+1
set_dihedral_atoms( aC, aCA, aCB, aCG[1], -172.9)
set_angle_atoms( aCA, aCB, aCG[1], 113.2)
aCD = {(atomno=nno) and (chain=iChain) and (file=f) and (model=m)}
if (aCD.size > 0) {
set_dihedral_atoms( aCA, aCB, aCG[1], aCD, 179.4)
}
}
}

# Connect the new AA
var aCm = atom_rcn(iResno-1, iChain, "C")
var aNp = atom_rcn(iResno+1, iChain, "N")
connect @aN @aCm
connect @aC @aNp

# Update atomnos
var topdif = {(resno=iResno) and (chain=iChain)
and (file=f) and (model=m)}.atomno.max - topno
if (topdif != 0) {
topmax = {(chain=iChain) and (file=f) and (model=m)}.atomno.max
for (var i=(topno+1); i <= topmax; i++) {
{(atomno=i) and (chain=iChain) and (file=f) and (model=m)}.atomno += topdif
}
}

set echo TOP LEFT
background ECHO yellow
refresh
gBusy = FALSE
}

function atom_rcn_xyz(iResno, iChain, iName, xyz) {
var a = atom_rcn(iResno, iChain, iName)
a.xyz = xyz
}

function convert_nt(iResno, iChain, newres) {
gBusy = TRUE
background ECHO pink
refresh
gChain1 = iChain
var f = (_frameID/1000000)
var m = (_frameID%1000000)

# Collect data
var topno = {(resno=iResno) and (chain=iChain)
and (file=f) and (model=m)}.atomno.max + 0
var idmax = {(file=f) and (model=m)}.atomIndex.max
var aO4 = atom_rcn(iResno, iChain, "O4\'")
var aC1 = atom_rcn(iResno, iChain, "C1\'")
var aC4 = atom_rcn(iResno, iChain, "C4\'")
var aP = atom_rcn(iResno, iChain, "P")
var aPxyz = aP.xyz + {0 0 0}
var aOP1xyz = atom_rcn(iResno, iChain, "OP1").xyz + {0 0 0}
var aOP2xyz = atom_rcn(iResno, iChain, "OP2").xyz + {0 0 0}
var aC1xyz = aC1.xyz + {0 0 0}
var aO4xyz = aO4.xyz + {0 0 0}
var aO3xyz = atom_rcn(iResno, iChain, "O3\'").xyz + {0 0 0}
var aC3xyz = atom_rcn(iResno, iChain, "C3\'").xyz + {0 0 0}
var aC2xyz = atom_rcn(iResno, iChain, "C2\'").xyz + {0 0 0}
var aO2xyz = atom_rcn(iResno, iChain, "O2\'").xyz + {0 0 0}
var aC4xyz = aC4.xyz + {0 0 0}
var aC5xyz = atom_rcn(iResno, iChain, "C5\'").xyz + {0 0 0}
var aO5xyz = atom_rcn(iResno, iChain, "O5\'").xyz + {0 0 0}
var isR = ((aC1 and {purine}).size > 0)
var N1or9 = (isR ? "N9" : "N1")
var C6or8 = (isR ? "C8" : "C6")
var aN = atom_rcn(iResno, iChain, N1or9)
var aC = atom_rcn(iResno, iChain, C6or8)
var chi = angle(aO4, aC1, aN, aC)
var dist = distance( aC1, aN)
var bang = angle( aO4, aC1, aN)
var bdh = angle( aC4, aO4, aC1, aN)
gNa = aP.atomno

# Delete the original
delete {(resno=iResno) and (chain=iChain) and (file=f) and (model=m)}

# Gen NT ==================================================
var isRna = (aC1.group.size == 1)
set appendNew FALSE
gA = "data \"append nt\"\n"
gA += gen_nt(iResno, newres, isRna, FALSE);
gA += "end \"append nt\""
script inline @{gA}

# Recollect data and move new NT to coords of old
isR = ((newres="A") or (newres="G"))
N1or9 = (isR ? "N9" : "N1")
C6or8 = (isR ? "C8" : "C6")
N3or7 = (isR ? "N7" : "N3")
aN = atom_rcn(iResno, iChain, N1or9)
aC = atom_rcn(iResno, iChain, C6or8)
var aN3or7 = atom_rcn(iResno, iChain, N3or7)
var aC4 = atom_rcn(iResno, iChain, "C4\'")
aO4 = atom_rcn(iResno, iChain, "O4\'")
aC1 = atom_rcn(iResno, iChain, "C1\'")
aP = atom_rcn(iResno, iChain, "P")
var aO3 = atom_rcn(iResno, iChain, "O3\'")
aP.xyz = aPxyz
atom_rcn_xyz(iResno, iChain, "OP1", aOP1xyz)
atom_rcn_xyz(iResno, iChain, "OP2", aOP2xyz)
aC1.xyz = aC1xyz
aO4.xyz = aO4xyz
aO3.xyz = aO3xyz
atom_rcn_xyz(iResno, iChain, "C3\'", aC3xyz)
atom_rcn_xyz(iResno, iChain, "C2\'", aC2xyz)
atom_rcn_xyz(iResno, iChain, "O2\'", aO2xyz)
aC4.xyz = aC4xyz
atom_rcn_xyz(iResno, iChain, "C5\'", aC5xyz)
atom_rcn_xyz(iResno, iChain, "O5\'", aO5xyz)

# Reconstruct base position on backbone
select ((atomIndex > idmax) and base and (file=f) and (model=m))
color rasmol
set_distance_atoms( aC1, aN, dist)
set_angle_atoms( aO4, aC1, aN, bang)
set_dihedral_atoms( aC4, aO4, aC1, aN, bdh)

set_angle_atoms( aC1, aN, aC, (isR ? 128.5 : 121.4))
set_dihedral_atoms( aC1, aN, aC, aN3or7, 180.0)
set_dihedral_atoms( aO4, aC1, aN, aC, chi)

# Connect the new NT
var aO3m = atom_rcn(iResno-1, iChain, "O3\'")
var aPp = atom_rcn(iResno+1, iChain, "P")
connect @aP @aO3m
connect @aO3 @aPp

# Update atomnos
topdif = {(resno=iResno) and (chain=iChain)
and (file=f) and (model=m)}.atomno.max - topno
if (topdif != 0) {
topmax = {(chain=iChain) and (file=f) and (model=m)}.atomno.max
for (var i=(topno+1); i <= topmax; i++) {
{(atomno=i) and (chain=iChain) and (file=f)
and (model=m)}.atomno += topdif
}
}

set echo TOP LEFT
background ECHO yellow
refresh
gBusy = FALSE
}

function convert_mb() {
var f = (_frameID/1000000)
var m = (_frameID%1000000)
if (gBusy == FALSE) {
var idx = _atomPicked
var isAmino = (({(atomIndex=idx) and amino}.size > 0)
or ({atomIndex=idx}.group="SEC")
or ({atomIndex=idx}.group="PYL"))
var isNT = ({(atomIndex=idx) and (rna or dna)}.size > 0)
var iResno = {atomIndex=idx}.resno
var iGroup = {atomIndex=idx}.group
var iChain = {atomIndex=idx}.chain
var sels = ""
select {(resno=iResno) and (chain=iChain) and (file=f) and (model=m)}
halo on
refresh

if (isAmino) {
if (kPHI.size == 0) {
script $SCRIPT_PATH$ribozome.spt
if (kPHI.size == 0) {
prompt ("The Plico script ribozome.spt is required")
quit
}
}
sels = "ABCDEFGHIKLMNOPQRSTUVWXYZ"
selp = " (enter 1 or 3 characters)"
}
else if (isNT) {
if (kPu.size == 0) {
script $SCRIPT_PATH$polymeraze.spt
if (kPu.size == 0) {
prompt ("The Plico script polymeraze.spt is required")
quit
}
}
sels = "ACGTU"
selp = " (enter A, C, G, T, or U)"
}
if (sels.size > 0) {
var ps = format("Change residue %d from %s to ?\n%s",
iResno, iGroup, selp)
newres = prompt(ps, "")%9999%0
if (isAmino and (newres.size==3)) {
newres = g1from3[newres]
}
else if (newres.size==2) {
newres = newres[2]
}
if ((newres != "") and (newres != "NULL")) {
if (sels.find(newres[1]) > 0) {
if (isAmino) {
convert_aa(iResno, iChain, newres[1])
}
else {
convert_nt(iResno, iChain, newres[1])
}
}
else {
prompt("Invalid entry")
}
}
}
else {
prompt("Not a polypeptide or polynucleotide")
}
select {(resno=iResno) and (chain=iChain) and (file=f) and (model=m)}
halo off
}
}

function convert_exit_mb() {
var f = (_frameID/1000000)
var m = (_frameID%1000000)
unbind
set echo TOP LEFT
echo
set allowRotateSelected gAllowRotateSelected
set allowMoveAtoms gAllowMoveAtoms
select ((file=f) and (model=m))
color {selected} @gScheme
select {gSelsave}
}

# Top level of Modify
function plico_convert() {
gBusy = FALSE
gSelsave = {selected}
gPlico = "CONVERT RESIDUE"

# Load common functions if not already
if (kCommon < 3) {
script $SCRIPT_PATH$plicoCommon.spt
if (kCommon < 3) {
prompt ("A newer version of plicoCommon.SPT is required")
quit
}
}
if (kNTcommon < 4) {
script $SCRIPT_PATH$plicoNTcommon.spt
if (kNTcommon < 4) {
prompt ("A newer version of plicoNTcommon.SPT is required")
quit
}
}

set echo TOP LEFT
background ECHO yellow

gEcho = ("____CONVERT_RESIDUE____|ALT-CLICK=select|DOUBLE-CLICK=exit")
echo @gEcho
gChain = ""
unbind

bind "ALT-LEFT-CLICK" "_pickAtom";
bind "ALT-LEFT-CLICK" "+:convert_mb";
bind "DOUBLE" "convert_exit_mb";

}

# End of CONVERT_RESIDUE.SPT
</pre>

@@ Line 12: / Line 12: @@
 <pre>#   convert_residue - Jmol script by Ron Mignery
-#   v1.4 beta    9/11/2015 -use thisModel
+#   v1.5 beta    4/12/2016 -require latest common includes
+#
 # Converts a selected residue base from one form to another.
@@ Line 73: / Line 73: @@
      var v1=aNp.xyz - aC.xyz
      var v2=aCA.xyz - aC.xyz
-     var axis = cross(v1, v2) + aC.xyz
+     var caxis = cross(v1, v2) + aC.xyz
      var curangle =  angle(aNp, aC, aCA)
-     rotateselected @aC @axis @{angC-curangle}
+     rotateselected @aC @caxis @{angC-curangle}
      curangle =  angle(aCAp, aNp, aC, aCA)
      rotateselected @aNp @aC @{dihedralC-curangle}
@@ Line 233: / Line 233: @@
          if (isAmino) {
-             if (kPHI) {
+             if (not kPHI) {
                  script $SCRIPT_PATH$ribozome.spt
-                 if (kPHI) {
+                 if (not kPHI) {
                      prompt ("The Plico script ribozome.spt is required")
                      quit
@@ Line 327: / Line 327: @@
      # 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: @@
 '''Convert_residue''' allows the user to change polypeptide or polynucleotide residues from one type to another.  When the residue to change is selected with a mouse click, the user is prompted for the amino-acid or nucleotide to replace the selected residue.
-The script also allows the user to double-bond or single bond all planars (aromatics, amides, etc) in an amino-acid or nucletotide chain by a shift-click or alt-shift-click respectively.  Double-bonding is useful to prevent certain distortions introduced by minimization.
+The script also allows the user to double-bond or single bond all planars (aromatics, amides, etc) in an amino-acid or nucletotide chain by a shift-click or alt-shift-click respectively.  Double-bonding is useful to prevent certain distortions introduced by minimization and allows proper placement of hydrogens with the 'calculate hydrogens' command.
 '''Convert_residue''' 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 12: / Line 12: @@
 <pre>#   convert_residue - Jmol script by Ron Mignery
-#   v1.3 beta    7/24/2015 -add menu toggle
+#   v1.4 beta    9/11/2015 -use thisModel
+#
 # Converts a selected residue base from one form to another.
@@ Line 29: / Line 29: @@
 function convert_aa(iResno, iChain, newres) {
      gBusy = true
      background ECHO pink
@@ Line 51: / Line 49: @@
      # Delete the original
-     delete {(resno=iResno) and (chain=iChain) and (file=f) and (model=m)}
+     delete {(resno=iResno) and (chain=iChain) and thisModel}
      # Make a new AA
@@ Line 70: / Line 68: @@
      aN = get_atom_rcn(iResno, iChain, "N")
-     select {(chain=iChain) and (resno=iResno) and (file=f) and (model=m)}
+     select {(chain=iChain) and (resno=iResno) and thisModel}
      var v = aCxyz - aC.xyz
      translate Selected @v
@@ Line 91: / Line 89: @@
      # Update atomnos
      var topdif = {(resno=iResno) and (chain=iChain)
-         and (file=f) and (model=m)}.atomno.max - topno
+         and thisModel}.atomno.max - topno
      if (topdif != 0) {
-         topmax = {(chain=iChain) and (file=f) and (model=m)}.atomno.max
+         topmax = {(chain=iChain) and thisModel}.atomno.max
          for (var i=(topno+1); i <= topmax; i++) {
-             {(atomno=i) and (chain=iChain) and (file=f) and (model=m)}.atomno += topdif
+             {(atomno=i) and (chain=iChain) and thisModel}.atomno += topdif
+         }
+     }
@@ Line 113: / Line 111: @@
 function convert_nt(iResno, iChain, newres) {
      gChain1 = iChain
      # Collect data
      var topno = {(resno=iResno) and (chain=iChain)
-         and (file=f) and (model=m)}.atomno.max + 0
+         and thisModel}.atomno.max + 0
-     var idmax = {(file=f) and (model=m)}.atomIndex.max
+     var idmax = {thisModel}.atomIndex.max
      var aO4 = get_atom_rcn(iResno, iChain, "O4\'")
      if (newres = "") {
@@ Line 139: / Line 135: @@
      var aC5xyz = get_atom_rcn(iResno, iChain, "C5\'").xyz + {0 0 0}
      var aO5xyz = get_atom_rcn(iResno, iChain, "O5\'").xyz + {0 0 0}
-     var isR  = ((aC1 and {purine}).size > 0)
+     var isR  = (aC1 and {purine})
      var N1or9 = (isR ? "N9" : "N1")
      var C6or8 = (isR ? "C8" : "C6")
@@ Line 153: / Line 149: @@
      gNa = aP.atomno
      # Delete the original
-     delete {(resno=iResno) and (chain=iChain) and (file=f) and (model=m)}
+     delete {(resno=iResno) and (chain=iChain) and thisModel}
      # Gen NT ==================================================
@@ Line 201: / Line 197: @@
      # Reconstruct base position on backbone
-     select ((atomIndex > idmax) and base and (file=f) and (model=m))
+     select ((atomIndex > idmax) and base and thisModel)
      color {selected} @gAltScheme
      set_distance_atoms( aC1, aN, dist)
@@ Line 224: / Line 220: @@
      if (gBusy == false) {
          var idx = _atomPicked
-         var isAmino = (({(atomIndex=idx) and amino}.size > 0)
+         var isAmino = ({(atomIndex=idx) and amino}
              or ({atomIndex=idx}.group="SEC")
              or ({atomIndex=idx}.group="PYL"))
-         var isNT = ({(atomIndex=idx) and (rna or dna)}.size > 0)
+         var isNT = {(atomIndex=idx) and (rna or dna)}
          var iResno = {atomIndex=idx}.resno
          var iGroup = {atomIndex=idx}.group
          var iChain = {atomIndex=idx}.chain
          var sels = ""
-         select {(resno=iResno) and (chain=iChain) and (file=f) and (model=m)}
+         select {(resno=iResno) and (chain=iChain) and thisModel}
          halo on
          refresh
          if (isAmino) {
-             if (kPHI.size == 0) {
+             if (kPHI) {
                  script $SCRIPT_PATH$ribozome.spt
-                 if (kPHI.size == 0) {
+                 if (kPHI) {
                      prompt ("The Plico script ribozome.spt is required")
                      quit
@@ Line 260: / Line 254: @@
              selp = "   (enter A, C, G, T, or U)"
+         }
-         if (sels.size > 0) {
+         if (sels) {
              var ps = format("Change residue %d from %s to ?\n%s",
                  iResno, iGroup, selp)
@@ Line 294: / Line 288: @@
              prompt("Not a polypeptide or polynucleotide")
+         }
-         select {(resno=iResno) and (chain=iChain) and (file=f) and (model=m)}
+         select {(resno=iResno) and (chain=iChain) and thisModel}
          halo off
+     }
@@ Line 320: / Line 314: @@
 function convert_exit_mb() {
-     var f = (_frameID/1000000)
+     if (plico_exit()) {
-    var m = (_frameID%1000000)
+        set allowRotateSelected gAllowRotateSelected
-    unbind
+        set allowMoveAtoms gAllowMoveAtoms
-    set echo TOP LEFT
+}
@@ Line 360: / Line 348: @@
      gEcho = ("____CONVERT_RESIDUE____|ALT-CLICK=select residue"+
          "|SHIFT-CLICK=add double bonds to chain"+
-         "|ALT-SHIFT-CLICK=remove double bonds|DOUBLE-CLICK=exit")
+         "|ALT-SHIFT-CLICK=remove double bonds|SHIFT-DOUBLE-CLICK=exit")
      echo @gEcho
      gChain = ""
@@ Line 373: / Line 361: @@
      bind "ALT-SHIFT-LEFT-CLICK" "+:undouble_mb";
      bind "ALT-CTRL-LEFT-CLICK" "align_trna";
-     bind "DOUBLE" "convert_exit_mb";
+     bind "SHIFT-DOUBLE" "convert_exit_mb";
      bind "LEFT-CLICK" "+:plico_menu_toggle";

@@ Line 10: / Line 10: @@
 <pre>#   convert_residue - Jmol script by Ron Mignery
-#   v1.0 beta    7/15/2014
+#   v1.1 beta    7/23/2014 -better rna detection
+#
 # Converts a selected residue base from one form to another.
@@ Line 17: / Line 17: @@
 #   One of ACDEFGHIKLMNPQRSTUVWXY for polypeptide or
 #   One of ACGUT for nucleotides
-gAppendNew = TRUE
+gAppendNew = true
 g1from3 = {"ALA":"A", "GLX":"B","CYS":"C", "ASP":"D","GLU":"E", "PHE":"F",
      "GLY":"G", "HIS":"H","ILE":"I", "LYS":"K","LEU":"L", "MET":"M",
@@ Line 24: / Line 24: @@
 function convert_aa(iResno, iChain, newres) {
-     gBusy = TRUE
+     gBusy = true
      background ECHO pink
      refresh
@@ Line 30: / Line 30: @@
      # Collect data
-     var f = _frameID/1000000
+     var f = {atomIndex=_atomPicked}.file
-     var m = _frameID%1000000
+     var m = {atomIndex=_atomPicked}.model
      var topno = {(resno=iResno) and (chain=iChain)
          and (file=f) and (model=m)}.atomno.max + 0
@@ Line 50: / Line 50: @@
      # Gen AA ==================================================
      gAppendNew = appendNew
-     set appendNew FALSE
+     set appendNew false
      gA = "data \"append aa\"\n"
      gA += gen_aa(iResno, newres);
@@ Line 70: / Line 70: @@
      # Reconstruct side-chain position on backbone
      select ((atomIndex > idmax) and sidechain and (file=f) and (model=m))
-     color rasmol
+     color {selected} @gAltScheme
      if (aCB.size > 0) {
          set_distance_atoms( aCA, aCB, 1.5)
@@ Line 106: / Line 106: @@
      background ECHO yellow
      refresh
-     gBusy = FALSE
+     gBusy = false
+}
@@ Line 115: / Line 115: @@
 function convert_nt(iResno, iChain, newres) {
-     gBusy = TRUE
+     gBusy = true
      background ECHO pink
      refresh
      gChain1 = iChain
-     var f = (_frameID/1000000)
+     var f = {atomIndex=_atomPicked}.file
-     var m = (_frameID%1000000)
+     var m = {atomIndex=_atomPicked}.model
      # Collect data
@@ Line 145: / Line 145: @@
      var N1or9 = (isR ? "N9" : "N1")
      var C6or8 = (isR ? "C8" : "C6")
      var aN = atom_rcn(iResno, iChain, N1or9)
      var aC = atom_rcn(iResno, iChain, C6or8)
@@ Line 155: / Line 158: @@
      # Delete the original
      delete {(resno=iResno) and (chain=iChain) and (file=f) and (model=m)}
+    refresh
      # Gen NT ==================================================
-     var isRna = (aC1.group.size == 1)
+     var isRna = (aO2xyz != {0 0 0})
-     set appendNew FALSE
+    gAppendNew = appendNew
      gA = "data \"append nt\"\n"
-     gA += gen_nt(iResno, newres, isRna, FALSE);
+     gA += gen_nt(iResno, newres, isRna, false);
      gA += "end \"append nt\""
      script inline @{gA}
      # Recollect data and move new NT to coords of old
@@ Line 192: / Line 198: @@
      # Reconstruct base position on backbone
      select ((atomIndex > idmax) and base and (file=f) and (model=m))
-     color rasmol
+     color {selected} @gAltScheme
      set_distance_atoms( aC1, aN, dist)
      set_angle_atoms( aO4, aC1, aN, bang)
@@ Line 221: / Line 227: @@
      background ECHO yellow
      refresh
-     gBusy = FALSE
+     gBusy = false
+}
 function convert_mb() {
-    var f = (_frameID/1000000)
+     if (gBusy == false) {
          var idx = _atomPicked
          var isAmino = (({(atomIndex=idx) and amino}.size > 0)
@@ Line 236: / Line 240: @@
          var iGroup = {atomIndex=idx}.group
          var iChain = {atomIndex=idx}.chain
          var sels = ""
          select {(resno=iResno) and (chain=iChain) and (file=f) and (model=m)}
@@ Line 310: / Line 316: @@
 # Top level of Modify
 function plico_convert() {
-     gBusy = FALSE
+     gBusy = false
      gSelsave = {selected}
      gPlico = "CONVERT RESIDUE"