Difference between revisions of "User:Remig/plico/remap"
< User:Remig | plico
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(A Jmol application macro and script to edit polypeptide chains) |
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| Line 3: | Line 3: | ||
Note that it will also remove all waters, hydrogens and %B alternates when any chain is updated. | 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 | + | '''Remap''' 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 | <pre>Title=PLICO Remap | ||
| Line 11: | Line 11: | ||
Copy and paste the following to a text editor and save to your scripts folder as remap.spt: | Copy and paste the following to a text editor and save to your scripts folder as remap.spt: | ||
<pre># remap - Jmol script by Ron Mignery | <pre># remap - Jmol script by Ron Mignery | ||
| − | # v1. | + | # v1.1 beta 2/12/2014 for Jmol 14 |
# | # | ||
# Calculate or change chain, atom number, residue names and/or residue numbers | # Calculate or change chain, atom number, residue names and/or residue numbers | ||
| Line 79: | Line 79: | ||
# Prompt for new designators | # Prompt for new designators | ||
| − | var p = prompt("Enter n-terminal atom designator as | + | var p = prompt("Enter n-terminal atom designator as\n" |
| + | + " <resno>:<chain>.N#<atomno>", "1:A.N#1")%0 | ||
# If valid | # If valid | ||
| Line 472: | Line 473: | ||
set echo TOP LEFT | set echo TOP LEFT | ||
background ECHO yellow | background ECHO yellow | ||
| − | gEcho = "ALT-CLICK=select chain|DOUBLE-CLICK=exit" | + | gEcho = "_______REMAP_______|ALT-CLICK=select chain|DOUBLE-CLICK=exit" |
echo @gEcho | echo @gEcho | ||
gChain = "" | gChain = "" | ||
| Line 485: | Line 486: | ||
# Bound to DOUBLE by plicoRemap | # Bound to DOUBLE by plicoRemap | ||
function remapExit() { | function remapExit() { | ||
| − | + | unbind | |
| − | + | halo off | |
| − | + | echo | |
| − | + | select all | |
| − | + | color {selected} @gScheme | |
| − | + | gBusy = FALSE | |
| − | + | set appendNew gAppendNew | |
| − | + | ||
| − | + | # Pop selected | |
| − | + | select gSelSaves | |
| − | |||
| − | |||
| − | |||
} | } | ||
| − | # End of TUG.SPT | + | # End of TUG.SPT</pre> |
| − | </pre> | ||
Revision as of 00:15, 16 February 2014
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.)].
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;plicoRemap
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
# v1.1 beta 2/12/2014 for Jmol 14
#
# Calculate or change chain, atom number, residue names and/or residue numbers
#
var gAppendNew = TRUE
# Search for N-C-C-0
function getBBnCAidx(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 findN0idx(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 = getBBnCAidx(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 plicoRemap
function remapCargoMB() {
var idx =_atomPicked
if ({atomIndex=idx}.element == "H") {
idx = connected({atomIndex=idx})[1].atomIndex
}
# If n-terminal N can be found
var n0idx = findN0idx(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" # global PDB atom record
var rs = ""
select {atomIndex=n0idx}
var cSet = {selected}
var newAtomName = "N"
var newGroup = "UNK"
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 ")
rs = ""
newResno++
nIdx = -1
proIdx = -1
newGroup = "UNK"
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"
newGreek = ""
newAtomName = "O"
}
else if (newAtomName == "CB") {
if (cSet[1].element == "C") {
newGroup = "ALA" # for now
newGreek = "B"
}
newAtomName = "XG"
}
else if (newAtomName == "XG") {
if (proDidx >= 0) {
newGroup = "PRO"
proDidx = -1
}
if (cSet[1].element == "O") { # SER CYS SEC
newGroup = "SER"
}
else if (cSet[1].element == "S") {
newGroup = "CYS"
}
else if (cSet[1].element == "Se") {
newGroup = "SEC"
}
newGreek = "G"
newAtomName = "XD"
}
else if (newAtomName == "XD") {
if (newGroup == "VAL") {
newGroup = "ILE"
newCount = "1"
}
newGreek = "D"
newAtomName = "XE"
}
else if (newAtomName == "XE") {
newGroup = "MET"
newGreek = "E"
newAtomName = "XZ"
}
else if (newAtomName == "XZ") {
if (cSet[1].element == "N") {
newGroup = "LYS"
}
else {
newGroup = "PHE" # for now
}
newGreek = "Z"
newAtomName = "XH"
}
else if (newAtomName == "XH") {
if (cSet[1].element == "O") {
newGroup = "TYR"
}
else {
newGroup = "TRP" # for now
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"
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")
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"
}
else {
newGroup = "HIS"
}
}
else if (hasO) {
newGroup = "ASP"
}
else {
newGroup = "LEU" # for now
}
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"
}
else {
newGroup = "GLU"
}
}
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"
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"
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 ")
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
}
}
# Top level of Remap
function plicoRemap() {
# 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" "+:remapCargoMB";
bind "DOUBLE" "remapExit";
}
# Bound to DOUBLE by plicoRemap
function remapExit() {
unbind
halo off
echo
select all
color {selected} @gScheme
gBusy = FALSE
set appendNew gAppendNew
# Pop selected
select gSelSaves
}
# End of TUG.SPT
