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.
When you click on a polynucleotide chain, it gives the current chain ID, residue, residue number and atom number of the most 5'ward atom in that chain. You may then edit any value (except residue). Remap then remaps the entire chain based on those values by conventional increments and identifies each nucleotide residue.
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;plico_remap_nt
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 directory as remapNT.spt:
# remapNT - Jmol script by Ron Mignery
# v1.6 beta 7/24/2015 -add menu toggle
#
# Calculate or change polynucleotide chain, atom number, residue names
# and/or residue numbers and print the resultant 1 char string
#
gBusy = false
kRemapNT=2
function find_5_prime(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 = 0 + 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) {
if (endIdx = -1) {
endIdx = 0 + cSet[i].atomIndex
}
else {
var Ox = connected(ocSet[j]) and not {atomindex=@{cset[i].atomIndex}}
if (connected(Ox) > 1) {
endIdx = 0 + cSet[i].atomIndex
}
}
}
}
}
# Find C5'
var c5idx = -1
cSet = (connected({atomIndex=endIdx}) and not {atomIndex=c3pIdx}
and not {oxygen})
if (cSet.size > 0) {
c5idx = 0 + cSet[1].atomIndex
}
# Find O5'
var o5idx = -1
cSet = connected({atomIndex=c5idx}) and {oxygen}
if (cSet.size > 0) {
o5idx = 0 + cSet[1].atomIndex
}
if (o5idx < 0) {
return c5idx
}
# Find P
pIdx = -1
cSet = connected({atomIndex=o5idx}) and {phosphorus}
if (cSet.size > 0) {
Pidx = 0 + cSet[1].atomIndex
}
if (Pidx < 0) {
return o5idx
}
}
return -1
}
function find_p_idx(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 ring_common(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 plico_remap_nt
function remap_nt_cargo_mb() {
var idx =_atomPicked
if ({atomIndex=idx}.element == "H") {
idx = connected({atomIndex=idx})[1].atomIndex
}
delete {hydrogen}
delete {hoh}
delete %B
delete ligands
connect
remap_nt( idx, false, 0)
set echo TOP LEFT
echo @gEcho
background ECHO yellow
refresh
print_1c_chain( newChain)
}
function remap_nt(idx, auto, base) {
var f = (_frameID/1000000)
var m = (_frameID%1000000)
# If P can be found
var pIdx = find_p_idx(idx)
var isValid = false
var newResno = 1
var newChain = "A"
var newAtomno = 1
var t5idx = -1
if (pIdx >= 0) {
t5idx = find_5_prime(pIdx)
if (t5idx >= 0) {
f = {atomIndex=t5idx}.file
m = {atomIndex=t5idx}.model
newResno = {atomIndex=t5idx}.resno
newChain = {atomIndex=t5idx}.chain
newAtomno = {atomIndex=t5idx}.atomno
select {(file=f) and (model=m)}
color {selected} @gScheme
select {(chain=newChain) and (file=f) and (model=m)}
color {selected} @gAltScheme
refresh
if (auto) {
newResno = base
isValid = true
newChain = gChain1
}
else {
# Prompt for new designators
var p = prompt(("Enter 5\'-terminal atom designator as\n"
+ " <resno>:<chain>#<atomno>"),
format("%d:%s#%d", newResno, newChain, newAtomno))%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
# Build inline pdb file
var ls = "data \"append remapNT\"\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
var first = true
var psu = false
while (cSet.size > 0) {
var s = array(1, 2, 3, 4)
var iKeep = -1
var iDrop = -1
switch( nextAtomName) {
case "O" :
newGreek[1] = (first ? "5\'" : "P3")
nextAtomName = (first ? "C5\'" : "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++) {
newGreek[i] = ""
if (connected(cSet[i]).size > 1) {
s[cSet.size] = i
newGreek[cSet.size] = "5\'"
oc5set = connected(cSet[i]) and {carbon}
nIdx = cSet[i].atomIndex
}
}
var isP1 = false
if (cSet.size > 3) {
newGreek[1] = "P1"
newGreek[2] = "P2"
newGreek[3] = "P3"
s[1] = 1
s[2] = 2
s[3] = 3
}
else {
for (var i = 1; i <= cSet.size; i++) {
if (i != s[cSet.size]) {
if ((isP1 == false)
and (abs(angle(cSet[i], {atomIndex=pIdx},
cSet[s[cSet.size]], oc5set[1])) < 90.0)) {
s[1] = i
newGreek[1] = "P1"
isP1 = true
}
else {
s[2] = i
newGreek[2] = "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[1] = i
newGreek[1] = "2\'"
isRNA = true
}
else {
s[2] = i
newGreek[2] = "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 if ((cSet[i].element == "C") and
((connected(cSet[i]) and {oxygen}).size == 0)) { #PSU
psu = true
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++) {
var n1atom = (connected(cSet[i]) and {nitrogen}
and not {atomIndex=nIdx})
var 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 = ring_common( cSet, nIdx, s, newGreek, "7")
nextAtomName = "N7"
break
case "N7" :
nIdx = ring_common( cSet, nIdx, s, newGreek, "5")
nextAtomName = "C5"
break
case "C5" :
if (isRNA and (newGroup == "DU ")) {
var c5set = {atomIndex=nIdx} or connected({atomIndex=nIdx})
if (angle(c5set[1], c5set[2], c5set[3]) < 114.0) {
newGroup = "D "
}
}
nIdx = ring_common( cSet, nIdx, s, newGreek, "6")
if ((newGroup == "DU ") and (cSet.size > 1)) {
newGroup = "DT "
}
nextAtomName = "C6"
break
case "C6" :
if (newGroup == "PU") {
nIdx = ring_common( cSet, nIdx, s, newGreek, "1")
newGroup = ((cSet[1].element == "O") ? "DG " : "DA ")
nextAtomName = "N1"
}
else {
if (psu) {
psu = false
newGroup = "DU "
}
cSet = ({})
}
break
case "N1" :
if (connected({atomIndex=nIdx}).size > 2) { # YG
newGroup = "X "
}
nIdx = ring_common( cSet, nIdx, s, newGreek, "2")
nextAtomName = "C2"
break
case "C2" :
nIdx = ring_common( cSet, nIdx, s, newGreek, "3")
nextAtomName = "N3"
stopIdx = -1
break
case "N3" :
nIdx = ring_common( cSet, nIdx, s, newGreek, "4")
nextAtomName = "C4"
break
case "C4" :
if (newGroup != "PY") {
cSet = ({})
}
else {
nIdx = ring_common( cSet, nIdx, s, newGreek, "5")
newGroup = ((cSet[1].element == "N") ? "DC " : "DU ")
nextAtomName = "C5"
}
break
}
first = false
for (var i = 1; i <= cSet.size; i++) {
rs += format("ATOM %5d %-4sUNK ", newAtomNo,
(cSet[i].element + newGreek[s[i]]))
rs += format("%s%4d %8.3f", newChain, newResno, cSet[i].x)
rs += format("%8.3f%8.3f\n", cSet[i].y, cSet[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"
newGreek[1] = ""
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 remapNT\""
gAppendNew = appendNew
set appendNew false
script inline @{ls}
set appendNew gAppendNew
}
else {
color {selected} @gScheme
}
print_1c_chain( newChain)
}
function print_1c_chain(iChain) {
var f = (_frameID/1000000)
var m = (_frameID%1000000)
var resmin = {(chain=iChain) and (file=f) and (model=m)}.resno.min
var resmax = {(chain=iChain) and (file=f) and (model=m)}.resno.max
var rchar = (({(resno=resmin) and (chain=iChain) and (file=f)
and (model=m)}.group[0].size > 1) ? "" : "R")
var lcAtoms = (within(3.1, false, {(resno=resmin) and (chain=iChain)
and (file=f) and (model=m) and base})
and not {(resno=resmin) and (chain=iChain) and (file=f) and (model=m)})
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 = "S"
chain2 = ""
}
}
var ls = format("%s%s:%s", iChain, chain2, format("%s%s", rchar, schar))
for (var i = {(chain=iChain) and (file=f) and (model=m)}.resno.min;
i <= {(chain=iChain) and (file=f) and (model=m)}.resno.max; i++) {
ls += ({(resno=i) and (chain=iChain) and (file=f) and (model=m)}.group[0])[0]
}
print ls
}
# Top level of Remap
function plico_remap_nt() {
# 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 = ""
gMenuMin = false
unbind
set picking ON
bind "ALT-LEFT-CLICK" "_pickAtom";
bind "ALT-LEFT-CLICK" "+:remap_nt_cargo_mb";
bind "DOUBLE" "remap_nt_exit";
bind "LEFT-CLICK" "+:plico_menu_toggle";
}
# Bound to DOUBLE by plicoRemap
function remap_nt_exit() {
unbind
halo off
echo
var f = (_frameID/1000000)
var m = (_frameID%1000000)
select ((file=f) and (model=m))
color {selected} @gScheme
gBusy = false
set appendNew gAppendNew
# Pop selected
select gSelSaves
}
# End of REMAPNT.SPT
