User:Remig/plico/remapNT - Revision history

Remig at 17:22, 12 April 2016

2016-04-12T17:22:47Z

Show changes

Remig at 14:41, 11 September 2015

2015-09-11T14:41:06Z

Show changes

Remig: Add menu toggle

2015-07-24T18:41:25Z

Add menu toggle

Remig: handle OMG

2015-07-13T18:58:53Z

handle OMG

Show changes

Remig: lc all functions

2014-05-16T15:23:52Z

lc all functions

Show changes

Remig: Do not var globals

2014-04-03T15:43:21Z

Do not var globals

Remig: Fix bug with arrays

2014-03-31T17:20:15Z

Fix bug with arrays

Remig: Handle chains missing terminal PO4s.

2014-03-19T16:56:31Z

Handle chains missing terminal PO4s.

Remig at 13:45, 18 March 2014

2014-03-18T13:45:27Z

Remig: Jmol script to remap polynucleotides

2014-02-18T22:02:01Z

Jmol script to remap polynucleotides

New page

'''RemapNT''' allows you to change the chain ID, atom numbers and/or residue numbers of a polynucleotide chain by mouse actions. It also calculates group values [nucleotide names (DU, A, etc.)].

Note that it will also remove all waters, ligands, hydrogens and %B alternates when any chain is updated.

'''RemapNT''' 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 Remap Polynucleotide
Script=script <path to your scripts folder>/remapNT.spt;plicoRemapNT
</pre>saved as plicoRemapNT.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 remapNT.spt:
<pre># remapNT - Jmol script by Ron Mignery
# v1.0 beta 2/16/2014 for Jmol 14
#
# Calculate or change polynucleotide chain, atom number, residue names
# and/or residue numbers
#

function find5prime(pIdx) {
while (pIdx >= 0) {

# Find C3'
var c3pIdx = -1
select {atomIndex=pIdx}
var cSet = {selected}
for (var i = 1; i <= cSet.size; i++) {
var ocSet = connected(cSet[i])
for (var j = 1; j <= ocSet.size; j++) {
var occSet = connected(ocSet[j]) and not {atomIndex=pIdx}
for (var k = 1; k <= occSet.size; k++) {
if (connected(occSet[k]).size > 2) {
c3pIdx = occSet[k].atomIndex
}
}
}
}

if (c3pIdx < 0) {
return pIdx
}

# Find C4'
var endIdx = -1
cSet = connected({atomIndex=c3pIdx}) and not {oxygen}
for (var i = 1; i <= cSet.size; i++) {
var ocSet = connected(cSet[i]) and {oxygen}
for (var j = 1; j <= ocSet.size; j++) {
if (connected(ocSet[j]).size > 1) {
endIdx = cSet[i].atomIndex
}
}
}

# Find C5'
var c5idx = -1
cSet = (connected({atomIndex=endIdx}) and not {atomIndex=c3pIdx}
and not {oxygen})
if (cSet.size > 0) {
c5idx = cSet[1].atomIndex
}

# Find O5'
var o5idx = -1
cSet = connected({atomIndex=c5idx}) and {oxygen}
if (cSet.size > 0) {
o5idx = cSet[1].atomIndex
}

if (o5idx < 0) {
return c5idx
}

# Find P
pIdx = -1
cSet = connected({atomIndex=o5idx}) and {phosphorus}
if (cSet.size > 0) {
pIdx = cSet[1].atomIndex
}
}

return -1
}

function findPidx(idx) {
select {atomIndex=idx}
var cSet = {selected}
while (cSet.size > 0) {
for (var i = 1; i <= cSet.size; i++) {
if (cSet[i].element == "P") {
return cSet[i].atomIndex
}
}
cSet = connected({selected}) and not {selected} and not {hydrogen}
select {selected} or cset
}
return -1
}

# cSet, s, and newGreek are arrays and thus passed by reference
function ringCommon(cSet, nIdx, s, newGreek, nextGreek) {
if (cSet.size > 2) {
print format("Unrecognized structure with set %s", cSet)
}
var oldGreek = 0 + newGreek[1]
newGreek[1] = nextGreek
for (var i = 1; i <= cSet.size; i++) {
var ccSet = connected(cSet[i])
if (ccSet.size == 1) {
if (cSet[i].element == ccSet[1].element) {
s[2] = i
s[1] = ((i > 1) ? 1 : 2)
newGreek[i] = 1 + nextGreek
newGreek[s[1]] = nextGreek
return cSet[s[1]].atomIndex
}
else {
s[1] = i
s[2] = ((i > 1) ? 1 : 2)
newGreek[i] = oldGreek
newGreek[s[2]] = nextGreek
return cSet[s[2]].atomIndex
}
}
}
return cSet[1].atomIndex
}

# Bound to ALT-LEFT-CLICK by plicoRemapNT
function remapNTcargoMB() {

var idx =_atomPicked
if ({atomIndex=idx}.element == "H") {
idx = connected({atomIndex=idx})[1].atomIndex
}

# If P can be found
var pIdx = findPidx(idx)
var isValid = FALSE
var newResno = 1
var newChain = "A"
var newAtomno = 1
var t5idx = -1
if (pIdx >= 0) {

t5idx = find5prime(pIdx)

if (t5idx >= 0) {
c5resno = {atomIndex=t5idx}.resno
c5chain = {atomIndex=t5idx}.chain
c5atomno = {atomIndex=t5idx}.atomno
select {atomIndex=t5idx}
halo on
refresh

# Prompt for new designators
var p = prompt(("Enter 5\'-terminal atom designator as\n"
+ " <resno>:<chain>#<atomno>"),
format("%d:%s#%d", c5resno, c5chain, c5atomno))%0
# If valid
if (p != "null") {
var iColon = p.find(":")
if (iColon > 0) {
var iHash = p.find("#")
if (iHash > 0) {
newResno = 0 + (p[1][iColon-1])
newChain = p[iColon+1][iHash-1]
newAtomno = 0 + (p[iHash+1][0])
if ((newResno > 0)
and (newChain.size == 1)
and (newAtomno > 0)) {
isValid = TRUE
}
}
}
if (not isValid) {
prompt ("Entry not valid!")
}
}
}
}

if (isValid) {
background ECHO pink
refresh

delete {hydrogen}
delete {hoh}
delete %B
delete ligands

# Build inline pdb file
var ls = "data \"append remap\"\n" # global PDB atom record
var rs = ""

select {atomIndex=t5idx}
var cSet = {selected}
var nextAtomName = {atomIndex=t5idx}.element
var newGroup = "UNK"
var newGreek = array()
var nIdx = t5idx
var c1pIdx = -1
var o3pIdx = -1
var stopIdx = -1
var endIdx = -1
var isRNA = FALSE
while (cSet.size > 0) {
var s = array(1, 2, 3)
var iKeep = -1
var iDrop = -1
switch( nextAtomName) {
case "O" :
newGreek[1] = "P3\'"
nextAtomName = "P"
nIdx = cSet[1].atomIndex
break
case "P" :
newGreek[1] = ""
nextAtomName = "OP"
nIdx = cSet[1].atomIndex
break
case "OP" :
var oc5set = ({})
for (var i = 1; i <= cSet.size; i++) {
if (connected(cSet[i]).size > 1) {
s[3] = i
newGreek[i] = "5\'"
oc5set = connected(cSet[i]) and {carbon}
nIdx = cSet[i].atomIndex
}
}
for (var i = 1; i <= cSet.size; i++) {
if (i != s[3]) {
if (abs(angle(cSet[i], {atomIndex=pIdx}, cSet[s[3]],
oc5set[1])) < 90.0) {
s[1] = i
newGreek[i] = "P1"
}
else {
s[2] = i
newGreek[i] = "P2"
}
}
}
#nIdx = pIdx
nextAtomName = "C5\'"
break
case "C5\'" :
nIdx = cSet[1].atomIndex
newGreek[1] = "5\'"
nextAtomName = "C4\'"
break
case "C4\'" :
nIdx = cSet[1].atomIndex
newGreek[1] = "4\'"
nextAtomName = "C3\'"
break
case "C3\'" :
for (var i = 1; i <= cSet.size; i++) {
if (cSet[i].element == "O") {
s[1] = i
newGreek[1] = "4\'"
cSet[i].selected = FALSE
stopIdx = cSet[i].atomIndex
}
else {
s[2] = i
newGreek[2] = "3\'"
nIdx = cSet[i].atomIndex

}
}
nextAtomName = "O3\'"
break
case "O3\'" :
for (var i = 1; i <= cSet.size; i++) {
if (cSet[i].element == "O") {
s[1] = i
newGreek[1] = "3\'"
o3pIdx = cSet[i].atomIndex
}
else {
s[2] = i
newGreek[2] = "2\'"
nIdx = cSet[i].atomIndex
}
}
nextAtomName = "C2\'"
break
case "C2\'" :
pIdx = -1
for (var i = 1; i <= cSet.size; i++) {
if (cSet[i].element == "P") {
pIdx = cSet[i].atomIndex
cSet = cSet and not cSet[i]
break
}
}
for (var i = 1; i <= cSet.size; i++) {
if (cSet[i].element == "O") {
s[2] = i
newGreek[2] = "2\'"
isRNA = TRUE
}
else {
s[1] = i
newGreek[1] = "1\'"
c1pIdx = cSet[i].atomIndex
nIdx = cSet[i].atomIndex
}
}
nextAtomName = "C1\'"
break
case "C1\'" :
for (var i = 1; i <= cSet.size; i++) {
if (cSet[i].element == "N") {
iKeep = i
nIdx = cSet[i].atomIndex
}
else {
cSet[i].selected = FALSE
}
}
cSet = cSet[iKeep]
var ccSet = connected(cSet[1]) and not {atomIndex=c1pIdx}
newGreek[1] = "9"
nextAtomName = "N9u"
newGroup = "PU"
for (var j = 1; j <= ccSet.size; j++) {
if ((connected(ccSet[j]) and {oxygen}) > 0) {
newGreek[1] = "1"
nextAtomName = "N1y"
newGroup = "PY"
}
}
break
case "N1y" :
for (var i = 1; i <= cSet.size; i++) {
if (connected(cSet[i]) > 2) {
iKeep = i
nIdx = cSet[i].atomIndex
}
else {
stopIdx = cSet[i].atomIndex
}
}
cSet = cSet[iKeep]
newGreek[1] = "2"
nextAtomName = "C2"
break
case "N9u" :
# Find N-C-N-C-N
for (var i = 1; i <= cSet.size; i++) {
n1atom = (connected(cSet[i]) and {nitrogen}
and not {atomIndex=nIdx})
c2set = connected(n1atom) and {carbon} and not cSet[i]
for (var j = 1; j <= c2set.size; j++) {
if ((connected(c2set[j]) and {nitrogen}) > 1) {
iDrop = i
}
}
}
stopIdx = cSet[iDrop].atomIndex
cSet = cSet and not cSet[iDrop]
nIdx = cSet[1].atomIndex
newGreek[1] = "8"
nextAtomName = "C8"
break
case "C8" :
nIdx = ringCommon( cSet, nIdx, s, newGreek, "7")
nextAtomName = "N7"
break
case "N7" :
nIdx = ringCommon( cSet, nIdx, s, newGreek, "5")
nextAtomName = "C5"
break
case "C5" :
nIdx = ringCommon( cSet, nIdx, s, newGreek, "6")
if ((newGroup == "DU ") and (cSet.size > 1)) {
newGroup = "DT "
}
nextAtomName = "C6"
break
case "C6" :
if (newGroup == "PU") {
nIdx = ringCommon( cSet, nIdx, s, newGreek, "1")
newGroup = ((cSet[1].element == "O") ? "DG " : "DA ")
nextAtomName = "N1"
}
else {
cSet = ({})
}
break
case "N1" :
nIdx = ringCommon( cSet, nIdx, s, newGreek, "2")
nextAtomName = "C2"
break
case "C2" :
nIdx = ringCommon( cSet, nIdx, s, newGreek, "3")
nextAtomName = "N3"
stopIdx = -1
break
case "N3" :
nIdx = ringCommon( cSet, nIdx, s, newGreek, "4")
nextAtomName = "C4"
break
case "C4" :
if (newGroup != "PY") {
cSet = ({})
}
else {
nIdx = ringCommon( cSet, nIdx, s, newGreek, "5")
newGroup = ((cSet[1].element == "N") ? "DC " : "DU ")
nextAtomName = "C5"
}
break
}

for (var i = 1; i <= cSet.size; i++) {
rs += format("ATOM %5d %-4sUNK ", newAtomNo,
(cSet[s[i]].element + newGreek[s[i]]))
rs += format("%s%4d %8.3f", newChain, newResno, cSet[s[i]].x)
rs += format("%8.3f%8.3f\n", cSet[s[i]].y, cSet[s[i]].z)
newAtomno++
}
cSet = (connected(cSet and not {atomIndex=stopIdx})
and not cSet and not {atomIndex=stopIdx} and not {atomIndex=endIdx})
endIdx = nIdx

if (cSet.size == 0) {
if (isRNA) {
newGroup = (newGroup.replace("DA ","A ").replace("DG ","G ")
.replace("DC ","C ").replace("DT ","T ").replace("DU ","U "))
}
ls += rs.replace("UNK", newGroup)
rs = ""
newResno++

if (pIdx >= 0) {
cSet = {atomIndex=pIdx}
nextAtomName = "P"
newGroup = "UNK"
greek = ""
newGreek[1] = greek
c1pIdx = -1
stopIdx = o3pIdx
endIdx = -1
isRNA = FALSE
}
else {
break
}
}
} # endwhile

# Replace chain with new chain
cset = {atomIndex=idx}
select cSet
while (cSet.size > 0) {
cSet = connected({selected}) and not {selected}
select {selected} or cSet
}
delete {selected}

ls += "end \"append remap\""
script inline @{ls}
gEcho += format("|Chain %s has been rebuilt", newChain)
set echo TOP LEFT
echo @gEcho
background ECHO yellow
refresh
}
}

# Top level of Remap
function plicoRemapNT() {

# Push selected
gSelSaves = {selected}

gAppendNew = appendNew
set appendNew FALSE
gScheme = defaultColorScheme
gAltScheme = ((gScheme == "Jmol") ? "Rasmol" : "Jmol")
set echo TOP LEFT
background ECHO yellow
gEcho = "_____REMAP NT_____|ALT-CLICK=select NT chain|DOUBLE-CLICK=exit"
echo @gEcho
gChain = ""
unbind

set picking ON
bind "ALT-LEFT-CLICK" "_pickAtom";
bind "ALT-LEFT-CLICK" "+:remapNTcargoMB";
bind "DOUBLE" "remapNTexit";
}

# Bound to DOUBLE by plicoRemap
function remapNTexit() {
unbind
halo off
echo
select all
color {selected} @gScheme
gBusy = FALSE
set appendNew gAppendNew

# Pop selected
select gSelSaves
}

# End of REMAPNT.SPT
</pre>

@@ Line 13: / Line 13: @@
 Copy and paste the following to a text editor and save to your scripts directory as remapNT.spt:
 <pre>#   remapNT - Jmol script by Ron Mignery
-#   v1.5  beta    2/6/2015 -handle OMG
+#   v1.6  beta     7/24/2015 -add menu toggle
+#
 #   Calculate or change polynucleotide chain, atom number, residue names
@@ Line 594: / Line 594: @@
      echo @gEcho
      gChain = ""
      unbind
@@ Line 600: / Line 601: @@
      bind "ALT-LEFT-CLICK" "+:remap_nt_cargo_mb";
      bind "DOUBLE" "remap_nt_exit";
+}

@@ Line 7: / Line 7: @@
 <pre>Title=PLICO Remap Polynucleotide
 Script=script <path to your scripts folder>/remapNT.spt;plicoRemapNT
-</pre>saved as plicoRemapNT.macro in your .jmol/macros folder as described in [[Macro]].
+</pre>saved as plicoRemapNT.macro in your .jmol/macros directory as described in [[Macro]].
-Copy and paste the following to a text editor and save to your scripts folder as remapNT.spt:
+Copy and paste the following to a text editor and save to your scripts directory as remapNT.spt:
 <pre>#   remapNT - Jmol script by Ron Mignery
-#   v1.3 beta    3/31/2014 for Jmol 14.0.8
+#   v1.4 beta    4/3/2014 for Jmol 14 -do not var globals for Jmol 14.0.13+
+#
 #   Calculate or change polynucleotide chain, atom number, residue names

@@ Line 11: / Line 11: @@
 Copy and paste the following to a text editor and save to your scripts folder as remapNT.spt:
 <pre>#   remapNT - Jmol script by Ron Mignery
-#   v1.2 beta    3/19/2014 for Jmol 14
+#   v1.3 beta    3/31/2014 for Jmol 14.0.8
+#
 #   Calculate or change polynucleotide chain, atom number, residue names
@@ Line 192: / Line 192: @@
          delete %B
          delete ligands
          # Build inline pdb file
-         var ls = "data \"append remap\"\n"    # global PDB atom record
+         ls = "data \"append remap\"\n"    # global PDB atom record
          var rs = ""
@@ Line 201: / Line 202: @@
          var nextAtomName = {atomIndex=t5idx}.element
          var newGroup = "UNK"
-         var newGreek = array()
+         var newGreek = array("", "", "", "")
          var nIdx = t5idx
          var c1pIdx = -1
@@ Line 319: / Line 320: @@
                  for (var i = 1; i <= cSet.size; i++) {
                      if (cSet[i].element == "N") {
                          iKeep = i
                          nIdx = cSet[i].atomIndex

@@ Line 11: / Line 11: @@
 Copy and paste the following to a text editor and save to your scripts folder as remapNT.spt:
 <pre>#   remapNT - Jmol script by Ron Mignery
-#   v1.1 beta    3/18/2014 for Jmol 14
+#   v1.2 beta    3/19/2014 for Jmol 14
+#
 #   Calculate or change polynucleotide chain, atom number, residue names
@@ Line 75: / Line 75: @@
          cSet = connected({atomIndex=o5idx}) and {phosphorus}
          if (cSet.size > 0) {
-             pIdx = cSet[1].atomIndex
+             Pidx =  cSet[1].atomIndex
+         }
+     }
@@ Line 204: / Line 208: @@
          var endIdx = -1
          var isRNA = FALSE
          while (cSet.size > 0) {
              var s = array(1, 2, 3)
@@ Line 210: / Line 215: @@
              switch( nextAtomName) {
              case "O" :
-                 newGreek[1] = "P3\'"
+                 newGreek[1] = (first ? "5\'" : "P3")
-                 nextAtomName = "P"
+                 nextAtomName = (first ? "C5\'" : "P")
                  nIdx = cSet[1].atomIndex
                  break
@@ Line 415: / Line 420: @@
                  break
+             }
              for (var i = 1; i <= cSet.size; i++) {
@@ Line 423: / Line 429: @@
                  newAtomno++
+             }
              cSet = (connected(cSet and not {atomIndex=stopIdx})
                  and not cSet and not {atomIndex=stopIdx} and not {atomIndex=endIdx})

@@ Line 1: / Line 1: @@
-'''RemapNT''' allows you to change the chain ID, atom numbers and/or residue numbers of a polynucleotide chain by mouse actions.  It also calculates group values [nucleotide names (DU, A, etc.)].
+'''RemapNT''' allows you to change the chain ID, atom numbers and/or residue numbers of a polynucleotide chain by mouse actions.  It also calculates group values [nucleotide names (DU, A, etc.)].  Finally it prints the resultant 1 char string to the console.
 Note that it will also remove all waters, ligands, hydrogens and %B alternates when any chain is updated.
@@ Line 11: / Line 11: @@
 Copy and paste the following to a text editor and save to your scripts folder as remapNT.spt:
 <pre>#   remapNT - Jmol script by Ron Mignery
-#   v1.0 beta    2/16/2014 for Jmol 14
+#   v1.1 beta    3/18/2014 for Jmol 14
+#
 #   Calculate or change polynucleotide chain, atom number, residue names
-#    and/or residue numbers
+#    and/or residue numbers and print the resultant 1 char string
+#
@@ Line 469: / Line 469: @@
          background ECHO yellow
          refresh
+     }
+}