Difference between revisions of "User:Remig/plico/remap"

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Line 1: Line 1:
 
'''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 folder>/remap.spt;plicoRemap
+
Script=script <path to your scripts directory>/remap.spt;plico_remap
</pre>saved as plicoRemap.macro in your .jmol/macros folder as described in [[Macro]].
+
</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 folder as remap.spt:
+
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
#  v1.2 beta    3/18/2014 for Jmol 14
+
#  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
 
#
 
#
var gAppendNew = TRUE
+
gAppendNew = false
 +
gBusy = false
  
 
# Search for N-C-C-0
 
# Search for N-C-C-0
function getBBnCAidx(idx) {
+
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 findN0idx(aIdx) {
+
function find_n0_idx(aIdx) {
  
 
     select {atomIndex=aIdx}
 
     select {atomIndex=aIdx}
     var cSet = {selected}
+
     var sSet = {selected}
     while (cSet.size > 0) {
+
     while (sSet) {
         for (var i = 1; i <= cSet.size; i++) {
+
         for (var i = 1; i <= sSet.size; i++) {
             var idx = cSet[i].atomIndex
+
             var idx = sSet[i].atomIndex
             var caIdx = getBBnCAidx(idx)
+
             var caIdx = get_bb_nward_ca_idx(idx)
 
             if (caIdx >= 0) {
 
             if (caIdx >= 0) {
                 if ({connected({atomIndex=idx}) and not {hydrogen}}.size < 2) {
+
                 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
         cSet = connected({selected}) and not {selected} and not {hydrogen}
+
          
         select {selected} or cset
+
        sSet = connected({selected}) and not {selected} and not {hydrogen}
     }
+
         select {selected} or sSet
 +
     } # endwhile
 +
   
 
     return -1
 
     return -1
 
}
 
}
  
# Bound to ALT-LEFT-CLICK by plicoRemap
+
# Bound to ALT-LEFT-CLICK by plico_remap
function remapCargoMB() {
+
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 = findN0idx(idx)
+
     var n0idx = find_n0_idx(idx)
     var isValid = FALSE
+
     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>", "1:A.N#1")%0
+
             + "  <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 = TRUE
+
                             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 = FALSE
+
         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.size > 0)) {
+
         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 = FALSE
+
                     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 = FALSE
+
                             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 = TRUE
+
                             isCB = true
                             cSet[i].selected = FALSE
+
                             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 = FALSE
+
                             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 = FALSE
+
                             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.size > 0) ? (trp[1].element=="N") : FALSE)
+
                     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 = TRUE
+
                         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 = TRUE
+
                         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 = TRUE
+
                         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 = FALSE
+
                             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 plicoRemap() {
+
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)
 
      
 
      
    # Push selected
+
     gEcho = "_______REMAP_______|ALT-CLICK=select chain|SHIFT-DOUBLE-CLICK=exit"
    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
 
     echo @gEcho
    gChain = ""
 
    unbind
 
  
 
     set picking ON
 
     set picking ON
 
     bind "ALT-LEFT-CLICK" "_pickAtom";
 
     bind "ALT-LEFT-CLICK" "_pickAtom";
     bind "ALT-LEFT-CLICK" "+:remapCargoMB";
+
     bind "ALT-LEFT-CLICK" "+:remap_cargo_mb";
     bind "DOUBLE" "remapExit";
+
     bind "SHIFT-DOUBLE" "plico_exit(true)";
 +
    bind "LEFT-CLICK" "+:plico_menu_toggle";
 
}
 
}
  
# 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 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

Contributors

Remig