User:Remig/plico/remapNT
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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.
RemapNT is a member of the Plico suite of protein folding tools described here. It may be installed and accessed as a macro with the file:
Title=PLICO Remap Polynucleotide Script=script <path to your scripts folder>/remapNT.spt;plicoRemapNT
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:
# remapNT - Jmol script by Ron Mignery
# v1.1 beta 3/18/2014 for Jmol 14
#
# Calculate or change polynucleotide chain, atom number, residue names
# and/or residue numbers and print the resultant 1 char string
#
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
print1cChain( newChain)
}
}
function print1cChain(iChain) {
var resmin = {chain=iChain}.resno.min
var resmax = {chain=iChain}.resno.max
var rchar = (({(resno=resmin) and (chain=iChain)}.group[0].size > 1) ? "" : "R")
var lcAtoms = (within(3.1, FALSE, {(resno=resmin) and (chain=iChain) and base})
and not {(resno=resmin) and (chain=iChain)})
var chain2 = ""
var schar = "S"
if (lcAtoms.size > 0) {
chain2 = lcAtoms[1].chain
if (((rchar == "R") and (lcAtoms[1].group.size > 1))
or ((rchar == "") and (lcAtoms[1].group.size == 1))) {
schar = "M"
}
else {
schar = ""
}
}
var ls = format("%s%s:%s", iChain, chain2, format("%s%s", rchar, schar))
for (var i = {chain=iChain}.resno.min; i <= {chain=iChain}.resno.max; i++) {
ls += ({(resno=i) and (chain=iChain)}.group[0])[0]
}
print ls
}
# 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
