User:Remig/plico/remap
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Remap allows you to change the chain ID, atom numbers and/or residue numbers of a polypeptide chain by mouse actions. It also calculates group values [amino acid names (GLY, THR, etc.)]. Finally it prints the 1 char resultant string to the console.
When you click on a polypeptide chain, it gives the current chain ID, residue, residue number and atom number of the most nward 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 amino acid residue.
Note that it will also remove all waters, hydrogens and %B alternates when any chain is updated.
Remap 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 Script=script <path to your scripts folder>/remap.spt;plico_remap
saved as plicoRemap.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 remap.spt:
# remap - Jmol script by Ron Mignery
# v1.3 beta 5/16/2014 -lc all functions
#
# Calculate or change polypeptide chain, atom number, residue names and/or residue
# numbers and print the resultant 1 char string
#
var gAppendNew = TRUE
# Search for N-C-C-0
function get_bb_nward_ca_idx(idx) {
if ({atomIndex=idx}.element == "N") {
var c1 = (connected({atomIndex=idx}) and not {hydrogen})
for (var i1 = 1; i1 <= c1.size; i1++) {
if (c1[i1].element == "C") {
var c2 = (connected({atomIndex=@{c1[i1].atomIndex}}) and not {hydrogen})
for (var i2 = 1; i2 <= c2.size; i2++) {
if (c2[i2].element == "C") {
var c3 = (connected({atomIndex=@{c2[i2].atomIndex}})
and not {hydrogen})
for (var i3 = 1; i3 <= c3.size; i3++) {
if (c3[i3].element == "O") {
return c1[i1].atomIndex
}
}
}
}
}
}
}
return -1
}
# Find N-terminal N
function find_n0_idx(aIdx) {
select {atomIndex=aIdx}
var cSet = {selected}
while (cSet.size > 0) {
for (var i = 1; i <= cSet.size; i++) {
var idx = cSet[i].atomIndex
var caIdx = get_bb_nward_ca_idx(idx)
if (caIdx >= 0) {
if ({connected({atomIndex=idx}) and not {hydrogen}}.size < 2) {
return idx
}
}
}
cSet = connected({selected}) and not {selected} and not {hydrogen}
select {selected} or cset
}
return -1
}
# Bound to ALT-LEFT-CLICK by plico_remap
function remap_cargo_mb() {
var idx =_atomPicked
if ({atomIndex=idx}.element == "H") {
idx = connected({atomIndex=idx})[1].atomIndex
}
# If n-terminal N can be found
var n0idx = find_n0_idx(idx)
var isValid = FALSE
var newResno = 1
var newChain = "A"
var newAtomno = 1
if (n0idx >= 0) {
# Prompt for new designators
var p = prompt("Enter n-terminal atom designator as\n"
+ " <resno>:<chain>.N#<atomno>", "1:A.N#1")%0
# If valid
var iColon = p.find(":")
if (iColon > 0) {
var iDot = p.find(".")
if (iDot > 0) {
var iHash = p.find("#")
if (iHash > 0) {
newResno = 0 + (p[1][iColon-1])
newChain = p[iColon+1][iDot-1]
newAtomno = 0 + (p[iHash+1][0])
if ((newResno > 0)
and (newChain.size == 1)
and (newAtomno > 0)) {
isValid = TRUE
}
}
}
}
}
if (isValid) {
delete {hydrogen}
delete {hoh}
delete %B
ssbonds off
# Build inline pdb file
var ls = "data \"append remap\"\n"
var rs = ""
var ls1 = format("%s:", newChain)
select {atomIndex=n0idx}
var cSet = {selected}
var newAtomName = "N"
var newGroup = "UNK"
var s1 = "X"
var newGreek = ""
var newCount = ""
var isCB = FALSE
var nIdx = n0idx
var proDidx = -1
var oxtIdx = -1
while ((nIdx >= n0idx) or (cSet.size > 0)) {
var s = array(1, 2, 3)
var pTrp = 0
if (cSet.size == 0) {
ls += rs.replace("UNK", newGroup).replace(" SeG" , " SeG ")
ls1 += s1
rs = ""
newResno++
nIdx = -1
proIdx = -1
newGroup = "UNK"
s1 = "X"
newAtomName = "N"
isCB = FALSE
}
else if (cSet.size == 1) {
if (newAtomName == "N") {
newGreek = ""
newAtomName = "CA"
}
else if (newAtomName == "CA") {
newGreek = "A"
newAtomName = "C"
}
else if (newAtomName == "C") {
newGroup = "GLY"
s1 = "G"
newGreek = ""
newAtomName = "O"
}
else if (newAtomName == "CB") {
if (cSet[1].element == "C") {
newGroup = "ALA" # for now
s1 = "A"
newGreek = "B"
}
newAtomName = "XG"
}
else if (newAtomName == "XG") {
if (proDidx >= 0) {
newGroup = "PRO"
s1 = "P"
proDidx = -1
}
if (cSet[1].element == "O") { # SER CYS SEC
newGroup = "SER"
s1 = "S"
}
else if (cSet[1].element == "S") {
newGroup = "CYS"
s1 = "C"
}
else if (cSet[1].element == "Se") {
newGroup = "SEC"
s1 = "U"
}
newGreek = "G"
newAtomName = "XD"
}
else if (newAtomName == "XD") {
if (newGroup == "VAL") {
newGroup = "ILE"
s1 = "I"
newCount = "1"
}
newGreek = "D"
newAtomName = "XE"
}
else if (newAtomName == "XE") {
newGroup = "MET"
s1 = "M"
newGreek = "E"
newAtomName = "XZ"
}
else if (newAtomName == "XZ") {
if (cSet[1].element == "N") {
newGroup = "LYS"
s1 = "K"
}
else {
newGroup = "PHE" # for now
s1 = "F"
}
newGreek = "Z"
newAtomName = "XH"
}
else if (newAtomName == "XH") {
if (cSet[1].element == "O") {
newGroup = "TYR"
s1 = "Y"
}
else {
newGroup = "TRP" # for now
s1 = "W"
newCount = "2"
}
newGreek = "H"
newAtomName = "N"
}
}
else if (cSet.size == 2) {
var hasN = ((cSet[1].element == "N") or (cSet[2].element == "N"))
var hasO = ((cSet[1].element == "O") or (cSet[2].element == "O"))
# If CA 2
if (newAtomName == "CA") {
var iKeep = -1
for (var i = 1; i <= cSet.size; i++) {
if (connected(cSet[i]) > 2) {
iKeep = i
}
else {
proDidx = cSet[i].atomIndex
cSet[i].selected = FALSE
}
}
cSet = cSet[iKeep]
newGroup = "PRO"
s1 = "P"
newGreek = "A"
newAtomName = "C"
}
# Else if C or CB 2
else if (newAtomName == "C") {
for (var i = 1; i <= cSet.size; i++) {
# If it connects O and (N or O)
var tSet = (connected(cSet[i]) and not {selected})
var oCount = 0
var nCount = 0
for (var j = 1; j <= tSet.size; j++) {
oCount += ((tSet[j].element == "O") ? 1 : 0)
nCount += ((tSet[j].element == "N") ? 1 : 0)
}
if ((nCount > 0) or (oCount > 1)) { # C
newGreek = ""
newAtomName = "O"
}
else { # CB
isCB = TRUE
cSet[i].selected = FALSE
cSet = (cSet and not cSet[i])
continue
}
} # endfor
}
# Else if O or N 2
else if (newAtomName == "O") {
var iKeep = -1
for (var i = 1; i <= cSet.size; i++) {
if (cSet[i].element != "O") {
if (cSet[i].element == "N") {
nIdx = cSet[i].atomIndex
}
cSet[i].selected = FALSE
}
else {
iKeep = i
}
}
cSet = cSet[iKeep]
newGreek = ""
newAtomName = (isCB ? "CB" : "N")
}
# Else if N or CB 2
else if (newAtomName == "CB") {
for (var i = 1; i <= cSet.size; i++) {
if (cSet[i].element != "C") {
nIdx = cSet[i].atomIndex
cSet[i].selected = FALSE
continue
}
newGreek = "B"
newAtomName = "XG"
} # endfor
}
# Else if XG or XGn 2
else if (newAtomName == "XG") { # VAL THR ILE
newGroup = (hasO ? "THR" : "VAL")
s1 = (hasO ? "T" : "V")
newGreek = "G"
newAtomName = "XD"
}
# Else if XD or XDn 2
else if (newAtomName == "XD") { # LEU ASP ASN
var cTrp = (connected(cSet[2]) and not {selected})
var sTrp = ((trp.size > 0) ? (trp[1].element=="N") : FALSE)
if ((cSet[2].element != "C") or sTrp
or ((connected(cSet[1]) and not {selected}).size == 0)) {
bRev = TRUE
}
if ((cSet[2].element == "O") or (cSet[1].element == "N")
or ((cSet[1].element == "C") and (cSet[2].element != "C"))) {
bRev = TRUE
}
if (hasN) {
if (hasO) {
newGroup = "ASN"
s1 = "N"
}
else {
newGroup = "HIS"
s1 = "H"
}
}
else if (hasO) {
newGroup = "ASP"
s1 = "D"
}
else {
newGroup = "LEU" # for now
s1 = "L"
}
newGreek = "D"
newAtomName = "XE"
}
# Else if XE or XEn 2
else if (newAtomName == "XE") { # GLU GLN HIS
if ((cSet[2].element == "O") or (cSet[1].element == "N")
or ((cSet[1].element == "C") and (cSet[2].element != "C"))) {
bRev = TRUE
}
if (hasO) {
if (hasN) {
newGroup = "GLN"
s1 = "Q"
}
else {
newGroup = "GLU"
s1 = "E"
}
}
newGreek = "E"
newAtomName = "XZ"
}
# Else if XZ 2
else if (newAtomName == "XZ") { # ARG
if (newGroup == "TRP") {
pTrp = 1
}
newGreek = "Z"
newAtomName = "XH"
}
# Else if XH 2
else if (newAtomName == "XH") { # ARG
newGroup = "ARG"
s1 = "R"
newGreek = "H"
newAtomName = "N"
}
}
# Else cSet.size = 3
else {
# If O
if (newAtomName == "O") {
var oCount = 0
var iKeep = -1
for (var i = 1; i <= cSet.size; i++) {
if (cSet[i].element != "O") {
if (cSet[i].element == "N") {
nIdx = cSet[i].atomIndex
}
cSet[i].selected = FALSE
}
else {
oCount++
if (iKeep < 0) {
iKeep = i
}
else {
oxtIdx = cSet[i].atomIndex
}
}
}
cset = cSet[iKeep[1]]
newGreek = ""
newAtomName = (isCB ? "CB" : "N")
}
else if (newAtomName == "CA") { # PRO
var iKeep = -1
for (var i = 1; i <= cSet.size; i++) {
if (connected(cSet[i]) > 2) {
iKeep = i
}
}
cSet = cSet[iKeep]
newGreek = "A"
newAtomName = "C"
}
else if (newAtomName == "XE") { # TRP
for (var i = 1; i <= cSet.size; i++) {
if (cSet[i].element == "N") {
s[1] = i
}
else if (connected(cSet[i]) > 2) {
s[2] = i
}
else {
s[3] = i
}
}
newGroup = "TRP"
s1 = "W"
newGreek = "E"
newAtomName = "XZ"
}
else {
}
}
for (var i = 1; i <= cSet.size; i++) {
rs += format("ATOM %5d %-4sUNK ", newAtomNo,
(cSet[s[i]].element + newGreek
+ ((cSet.size > 1) ? (i+pTrp) : newCount)))
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)
if (newGreek == "XT") {
newGreek == ""
}
newAtomno++
}
newCount = ""
cSet = (connected({selected}) and not {selected}
and not {atomIndex=@nIdx} and not {atomIndex=proDidx})
select ({selected} or cSet and not {atomIndex=nIdx}
and not {atomIndex=proDidx})
} # endwhile
# Replace chain with new chain
if (oxtIdx >= 0) {
rs += format("ATOM %5d OXT UNK %s", newAtomNo, newChain)
rs += format("%4d %8.3f", newResno, {atomIndex=oxtIdx}.x)
rs += format("%8.3f%8.3f\n", {atomIndex=oxtIdx}.y, {atomIndex=oxtIdx}.z)
}
ls += rs.replace("UNK", newGroup).replace(" SeG" , " SeG ")
ls1 += s1
delete {selected}
ls += "end \"append remap\""
script inline @{ls}
var xx = {element="Xx"}
for (var i = 1; i <= xx.size; i++) {
connect 1.8 {atomindex=@{xx[i].atomIndex}}
}
ssbonds on
gEcho += format("|Chain %s has been rebuilt", newChain)
set echo TOP LEFT
echo @gEcho
print ls1
}
}
# Top level of Remap
function plico_remap() {
# 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_______|ALT-CLICK=select chain|DOUBLE-CLICK=exit"
echo @gEcho
gChain = ""
unbind
set picking ON
bind "ALT-LEFT-CLICK" "_pickAtom";
bind "ALT-LEFT-CLICK" "+:remap_cargo_mb";
bind "DOUBLE" "remap_exit";
}
# Bound to DOUBLE by plico_remap
function remap_exit() {
unbind
halo off
echo
select all
color {selected} @gScheme
gBusy = FALSE
set appendNew gAppendNew
# Pop selected
select gSelSaves
}
# End of REMAP.SPT
