Difference between revisions of "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. | '''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. | Note that it will also remove all waters, hydrogens and %B alternates when any chain is updated. | ||
| Line 6: | Line 8: | ||
<pre>Title=PLICO Remap | <pre>Title=PLICO Remap | ||
| − | Script=script <path to your scripts | + | Script=script <path to your scripts directory>/remap.spt;plico_remap |
| − | </pre>saved as plicoRemap.macro in your .jmol/macros | + | </pre>saved as plicoRemap.macro in your .jmol/macros directory as described in [[Macro]]. |
| − | Copy and paste the following to a text editor and save to your scripts | + | Copy and paste the following to a text editor and save to your scripts directory as remap.spt: |
<pre># remap - Jmol script by Ron Mignery | <pre># remap - Jmol script by Ron Mignery | ||
| − | # v1. | + | # v1.10 beta 4/12/2016 -require latest common includes |
# | # | ||
# Calculate or change polypeptide chain, atom number, residue names and/or residue | # Calculate or change polypeptide chain, atom number, residue names and/or residue | ||
# numbers and print the resultant 1 char string | # numbers and print the resultant 1 char string | ||
# | # | ||
| − | + | gAppendNew = false | |
| + | gBusy = false | ||
# Search for N-C-C-0 | # Search for N-C-C-0 | ||
| − | function | + | function get_bb_nward_ca_idx(idx) { |
if ({atomIndex=idx}.element == "N") { | if ({atomIndex=idx}.element == "N") { | ||
var c1 = (connected({atomIndex=idx}) and not {hydrogen}) | var c1 = (connected({atomIndex=idx}) and not {hydrogen}) | ||
| Line 34: | Line 37: | ||
} | } | ||
} | } | ||
| − | } | + | } |
} | } | ||
} | } | ||
| Line 43: | Line 46: | ||
# Find N-terminal N | # Find N-terminal N | ||
| − | function | + | function find_n0_idx(aIdx) { |
select {atomIndex=aIdx} | select {atomIndex=aIdx} | ||
| − | var | + | var sSet = {selected} |
| − | while ( | + | while (sSet) { |
| − | for (var i = 1; i <= | + | for (var i = 1; i <= sSet.size; i++) { |
| − | var idx = | + | var idx = sSet[i].atomIndex |
| − | var caIdx = | + | var caIdx = get_bb_nward_ca_idx(idx) |
if (caIdx >= 0) { | if (caIdx >= 0) { | ||
| − | + | var cset = connected({atomIndex=idx}) and not {hydrogen} | |
| − | return idx | + | var ccset = connected(cset) and not {hydrogen} |
| − | } | + | if (cset.size < 2) { |
| + | return idx #*** | ||
| + | } | ||
| + | else if (({ccset and {carbon}}.size = 3) and (ccset.size == 4)) { | ||
| + | return idx #*** | ||
| + | } | ||
} | } | ||
| − | } | + | } # endfor |
| − | + | ||
| − | select {selected} or | + | sSet = connected({selected}) and not {selected} and not {hydrogen} |
| − | } | + | select {selected} or sSet |
| + | } # endwhile | ||
| + | |||
return -1 | return -1 | ||
} | } | ||
| − | # Bound to ALT-LEFT-CLICK by | + | # Bound to ALT-LEFT-CLICK by plico_remap |
| − | function | + | function remap_cargo_mb() { |
var idx =_atomPicked | var idx =_atomPicked | ||
| − | + | ||
if ({atomIndex=idx}.element == "H") { | if ({atomIndex=idx}.element == "H") { | ||
idx = connected({atomIndex=idx})[1].atomIndex | idx = connected({atomIndex=idx})[1].atomIndex | ||
} | } | ||
| − | + | ||
# If n-terminal N can be found | # If n-terminal N can be found | ||
| − | var n0idx = | + | var n0idx = find_n0_idx(idx) |
| − | var isValid = | + | var isValid = false |
var newResno = 1 | var newResno = 1 | ||
var newChain = "A" | var newChain = "A" | ||
var newAtomno = 1 | var newAtomno = 1 | ||
if (n0idx >= 0) { | if (n0idx >= 0) { | ||
| − | + | ||
# Prompt for new designators | # Prompt for new designators | ||
| + | var f = {atomIndex=n0idx}.file | ||
| + | var m = {atomIndex=n0idx}.model | ||
| + | var iResno = {atomIndex=n0idx}.resno | ||
| + | var iChain = {atomIndex=n0idx}.chain | ||
| + | var iNo = {atomIndex=n0idx}.atomno | ||
| + | select {thisModel} | ||
| + | color {selected} @gScheme | ||
| + | select {(chain=iChain) and thisModel} | ||
| + | color {selected} @gAltScheme | ||
| + | refresh | ||
var p = prompt("Enter n-terminal atom designator as\n" | var p = prompt("Enter n-terminal atom designator as\n" | ||
| − | + " <resno>:<chain>.N#<atomno>", " | + | + " <resno>:<chain>.N#<atomno>", |
| + | format("%d:%s.N#%d", iResno, iChain, iNo)%0) | ||
# If valid | # If valid | ||
| Line 96: | Line 117: | ||
and (newChain.size == 1) | and (newChain.size == 1) | ||
and (newAtomno > 0)) { | and (newAtomno > 0)) { | ||
| − | isValid = | + | isValid = true |
} | } | ||
} | } | ||
| Line 103: | Line 124: | ||
} | } | ||
if (isValid) { | if (isValid) { | ||
| − | + | ||
| − | delete {hydrogen} | + | delete {hydrogen and thisModel} |
| − | delete {hoh} | + | delete {hoh and thisModel} |
| − | delete %B | + | delete %B and thisModel |
ssbonds off | ssbonds off | ||
| − | + | ||
# Build inline pdb file | # Build inline pdb file | ||
var ls = "data \"append remap\"\n" | var ls = "data \"append remap\"\n" | ||
var rs = "" | var rs = "" | ||
var ls1 = format("%s:", newChain) | var ls1 = format("%s:", newChain) | ||
| − | + | ||
select {atomIndex=n0idx} | select {atomIndex=n0idx} | ||
var cSet = {selected} | var cSet = {selected} | ||
| Line 121: | Line 142: | ||
var newGreek = "" | var newGreek = "" | ||
var newCount = "" | var newCount = "" | ||
| − | var isCB = | + | var isCB = false |
var nIdx = n0idx | var nIdx = n0idx | ||
var proDidx = -1 | var proDidx = -1 | ||
var oxtIdx = -1 | var oxtIdx = -1 | ||
| − | while ((nIdx >= n0idx) or (cSet | + | while ((nIdx >= n0idx) or (cSet)) { |
var s = array(1, 2, 3) | var s = array(1, 2, 3) | ||
var pTrp = 0 | var pTrp = 0 | ||
| Line 138: | Line 159: | ||
s1 = "X" | s1 = "X" | ||
newAtomName = "N" | newAtomName = "N" | ||
| − | isCB = | + | isCB = false |
} | } | ||
else if (cSet.size == 1) { | else if (cSet.size == 1) { | ||
| Line 238: | Line 259: | ||
else { | else { | ||
proDidx = cSet[i].atomIndex | proDidx = cSet[i].atomIndex | ||
| − | cSet[i].selected = | + | cSet[i].selected = false |
} | } | ||
} | } | ||
| Line 247: | Line 268: | ||
newAtomName = "C" | newAtomName = "C" | ||
} | } | ||
| − | + | ||
# Else if C or CB 2 | # Else if C or CB 2 | ||
else if (newAtomName == "C") { | else if (newAtomName == "C") { | ||
for (var i = 1; i <= cSet.size; i++) { | for (var i = 1; i <= cSet.size; i++) { | ||
| − | + | ||
# If it connects O and (N or O) | # If it connects O and (N or O) | ||
var tSet = (connected(cSet[i]) and not {selected}) | var tSet = (connected(cSet[i]) and not {selected}) | ||
| Line 265: | Line 286: | ||
} | } | ||
else { # CB | else { # CB | ||
| − | isCB = | + | isCB = true |
| − | cSet[i].selected = | + | cSet[i].selected = false |
cSet = (cSet and not cSet[i]) | cSet = (cSet and not cSet[i]) | ||
continue | continue | ||
| − | } | + | } |
} # endfor | } # endfor | ||
} | } | ||
| − | + | ||
# Else if O or N 2 | # Else if O or N 2 | ||
else if (newAtomName == "O") { | else if (newAtomName == "O") { | ||
| Line 281: | Line 302: | ||
nIdx = cSet[i].atomIndex | nIdx = cSet[i].atomIndex | ||
} | } | ||
| − | cSet[i].selected = | + | cSet[i].selected = false |
} | } | ||
else { | else { | ||
| Line 291: | Line 312: | ||
newAtomName = (isCB ? "CB" : "N") | newAtomName = (isCB ? "CB" : "N") | ||
} | } | ||
| − | + | ||
# Else if N or CB 2 | # Else if N or CB 2 | ||
else if (newAtomName == "CB") { | else if (newAtomName == "CB") { | ||
| Line 297: | Line 318: | ||
if (cSet[i].element != "C") { | if (cSet[i].element != "C") { | ||
nIdx = cSet[i].atomIndex | nIdx = cSet[i].atomIndex | ||
| − | cSet[i].selected = | + | cSet[i].selected = false |
continue | continue | ||
} | } | ||
| Line 304: | Line 325: | ||
} # endfor | } # endfor | ||
} | } | ||
| − | + | ||
| − | + | ||
# Else if XG or XGn 2 | # Else if XG or XGn 2 | ||
else if (newAtomName == "XG") { # VAL THR ILE | else if (newAtomName == "XG") { # VAL THR ILE | ||
| Line 313: | Line 334: | ||
newAtomName = "XD" | newAtomName = "XD" | ||
} | } | ||
| − | + | ||
| − | + | ||
# Else if XD or XDn 2 | # Else if XD or XDn 2 | ||
else if (newAtomName == "XD") { # LEU ASP ASN | else if (newAtomName == "XD") { # LEU ASP ASN | ||
var cTrp = (connected(cSet[2]) and not {selected}) | var cTrp = (connected(cSet[2]) and not {selected}) | ||
| − | var sTrp = ((trp | + | var sTrp = ((trp) ? (trp[1].element=="N") : false) |
if ((cSet[2].element != "C") or sTrp | if ((cSet[2].element != "C") or sTrp | ||
or ((connected(cSet[1]) and not {selected}).size == 0)) { | or ((connected(cSet[1]) and not {selected}).size == 0)) { | ||
| − | bRev = | + | bRev = true |
} | } | ||
if ((cSet[2].element == "O") or (cSet[1].element == "N") | if ((cSet[2].element == "O") or (cSet[1].element == "N") | ||
or ((cSet[1].element == "C") and (cSet[2].element != "C"))) { | or ((cSet[1].element == "C") and (cSet[2].element != "C"))) { | ||
| − | bRev = | + | bRev = true |
} | } | ||
if (hasN) { | if (hasN) { | ||
| Line 348: | Line 369: | ||
newAtomName = "XE" | newAtomName = "XE" | ||
} | } | ||
| − | + | ||
# Else if XE or XEn 2 | # Else if XE or XEn 2 | ||
else if (newAtomName == "XE") { # GLU GLN HIS | else if (newAtomName == "XE") { # GLU GLN HIS | ||
if ((cSet[2].element == "O") or (cSet[1].element == "N") | if ((cSet[2].element == "O") or (cSet[1].element == "N") | ||
or ((cSet[1].element == "C") and (cSet[2].element != "C"))) { | or ((cSet[1].element == "C") and (cSet[2].element != "C"))) { | ||
| − | bRev = | + | bRev = true |
} | } | ||
if (hasO) { | if (hasO) { | ||
| Line 368: | Line 389: | ||
newAtomName = "XZ" | newAtomName = "XZ" | ||
} | } | ||
| − | + | ||
# Else if XZ 2 | # Else if XZ 2 | ||
else if (newAtomName == "XZ") { # ARG | else if (newAtomName == "XZ") { # ARG | ||
| Line 377: | Line 398: | ||
newAtomName = "XH" | newAtomName = "XH" | ||
} | } | ||
| − | + | ||
# Else if XH 2 | # Else if XH 2 | ||
else if (newAtomName == "XH") { # ARG | else if (newAtomName == "XH") { # ARG | ||
| Line 386: | Line 407: | ||
} | } | ||
} | } | ||
| − | + | ||
# Else cSet.size = 3 | # Else cSet.size = 3 | ||
else { | else { | ||
| Line 398: | Line 419: | ||
nIdx = cSet[i].atomIndex | nIdx = cSet[i].atomIndex | ||
} | } | ||
| − | cSet[i].selected = | + | cSet[i].selected = false |
} | } | ||
else { | else { | ||
| Line 446: | Line 467: | ||
} | } | ||
} | } | ||
| − | + | ||
for (var i = 1; i <= cSet.size; i++) { | for (var i = 1; i <= cSet.size; i++) { | ||
rs += format("ATOM %5d %-4sUNK ", newAtomNo, | rs += format("ATOM %5d %-4sUNK ", newAtomNo, | ||
(cSet[s[i]].element + newGreek | (cSet[s[i]].element + newGreek | ||
+ ((cSet.size > 1) ? (i+pTrp) : newCount))) | + ((cSet.size > 1) ? (i+pTrp) : newCount))) | ||
| − | rs += format("%s%4d %8.3f", newChain, newResno, cSet[s[i]].x) | + | 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) | rs += format("%8.3f%8.3f\n", cSet[s[i]].y, cSet[s[i]].z) | ||
if (newGreek == "XT") { | if (newGreek == "XT") { | ||
| Line 463: | Line 484: | ||
select ({selected} or cSet and not {atomIndex=nIdx} | select ({selected} or cSet and not {atomIndex=nIdx} | ||
and not {atomIndex=proDidx}) | and not {atomIndex=proDidx}) | ||
| − | + | ||
| − | } # endwhile | + | } # endwhile |
| − | + | ||
# Replace chain with new chain | # Replace chain with new chain | ||
if (oxtIdx >= 0) { | if (oxtIdx >= 0) { | ||
rs += format("ATOM %5d OXT UNK %s", newAtomNo, newChain) | rs += format("ATOM %5d OXT UNK %s", newAtomNo, newChain) | ||
| − | rs += format("%4d %8.3f", newResno, {atomIndex=oxtIdx}.x) | + | rs += format("%4d %8.3f", newResno, {atomIndex=oxtIdx}.x) |
rs += format("%8.3f%8.3f\n", {atomIndex=oxtIdx}.y, {atomIndex=oxtIdx}.z) | rs += format("%8.3f%8.3f\n", {atomIndex=oxtIdx}.y, {atomIndex=oxtIdx}.z) | ||
} | } | ||
| Line 476: | Line 497: | ||
delete {selected} | delete {selected} | ||
ls += "end \"append remap\"" | ls += "end \"append remap\"" | ||
| + | gAppendNew = appendNew | ||
| + | set appendNew false | ||
script inline @{ls} | script inline @{ls} | ||
| + | set appendNew gAppendNew | ||
var xx = {element="Xx"} | var xx = {element="Xx"} | ||
for (var i = 1; i <= xx.size; i++) { | for (var i = 1; i <= xx.size; i++) { | ||
| Line 486: | Line 510: | ||
echo @gEcho | echo @gEcho | ||
print ls1 | print ls1 | ||
| − | + | ||
| − | } | + | } |
| + | else { | ||
| + | color {selected} @gScheme | ||
| + | } | ||
} | } | ||
# Top level of Remap | # Top level of Remap | ||
| − | function | + | function plico_remap() { |
| + | |||
| + | # Load common functions if not already | ||
| + | if (kCommon < 7) { | ||
| + | script $SCRIPT_PATH$plicoCommon.spt | ||
| + | if (kCommon < 7) { | ||
| + | prompt ("A newer version of plicoCommon.SPT is required") | ||
| + | quit | ||
| + | } | ||
| + | } | ||
| + | |||
| + | gPlico = "Remap" | ||
| + | plico_prelim(false, true) | ||
| − | + | gEcho = "_______REMAP_______|ALT-CLICK=select chain|SHIFT-DOUBLE-CLICK=exit" | |
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | gEcho = "_______REMAP_______|ALT-CLICK=select chain|DOUBLE-CLICK=exit" | ||
echo @gEcho | echo @gEcho | ||
| − | |||
| − | |||
set picking ON | set picking ON | ||
bind "ALT-LEFT-CLICK" "_pickAtom"; | bind "ALT-LEFT-CLICK" "_pickAtom"; | ||
| − | bind "ALT-LEFT-CLICK" "+: | + | bind "ALT-LEFT-CLICK" "+:remap_cargo_mb"; |
| − | bind "DOUBLE" " | + | bind "SHIFT-DOUBLE" "plico_exit(true)"; |
| + | bind "LEFT-CLICK" "+:plico_menu_toggle"; | ||
} | } | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
# End of REMAP.SPT</pre> | # End of REMAP.SPT</pre> | ||
Latest revision as of 17:17, 12 April 2016
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 directory>/remap.spt;plico_remap
saved as plicoRemap.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 remap.spt:
# remap - Jmol script by Ron Mignery
# v1.10 beta 4/12/2016 -require latest common includes
#
# Calculate or change polypeptide chain, atom number, residue names and/or residue
# numbers and print the resultant 1 char string
#
gAppendNew = false
gBusy = false
# 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 sSet = {selected}
while (sSet) {
for (var i = 1; i <= sSet.size; i++) {
var idx = sSet[i].atomIndex
var caIdx = get_bb_nward_ca_idx(idx)
if (caIdx >= 0) {
var cset = connected({atomIndex=idx}) and not {hydrogen}
var ccset = connected(cset) and not {hydrogen}
if (cset.size < 2) {
return idx #***
}
else if (({ccset and {carbon}}.size = 3) and (ccset.size == 4)) {
return idx #***
}
}
} # endfor
sSet = connected({selected}) and not {selected} and not {hydrogen}
select {selected} or sSet
} # endwhile
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 f = {atomIndex=n0idx}.file
var m = {atomIndex=n0idx}.model
var iResno = {atomIndex=n0idx}.resno
var iChain = {atomIndex=n0idx}.chain
var iNo = {atomIndex=n0idx}.atomno
select {thisModel}
color {selected} @gScheme
select {(chain=iChain) and thisModel}
color {selected} @gAltScheme
refresh
var p = prompt("Enter n-terminal atom designator as\n"
+ " <resno>:<chain>.N#<atomno>",
format("%d:%s.N#%d", iResno, iChain, iNo)%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 and thisModel}
delete {hoh and thisModel}
delete %B and thisModel
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)) {
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) ? (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\""
gAppendNew = appendNew
set appendNew false
script inline @{ls}
set appendNew gAppendNew
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
}
else {
color {selected} @gScheme
}
}
# Top level of Remap
function plico_remap() {
# Load common functions if not already
if (kCommon < 7) {
script $SCRIPT_PATH$plicoCommon.spt
if (kCommon < 7) {
prompt ("A newer version of plicoCommon.SPT is required")
quit
}
}
gPlico = "Remap"
plico_prelim(false, true)
gEcho = "_______REMAP_______|ALT-CLICK=select chain|SHIFT-DOUBLE-CLICK=exit"
echo @gEcho
set picking ON
bind "ALT-LEFT-CLICK" "_pickAtom";
bind "ALT-LEFT-CLICK" "+:remap_cargo_mb";
bind "SHIFT-DOUBLE" "plico_exit(true)";
bind "LEFT-CLICK" "+:plico_menu_toggle";
}
# End of REMAP.SPT
