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

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(lc all functions)
(Handle multiple frames)
Line 8: Line 8:
  
 
<pre>Title=PLICO Remap
 
<pre>Title=PLICO Remap
Script=script <path to your scripts folder>/remap.spt;plico_remap
+
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
#  v1.3 beta    5/16/2014 -lc all functions
+
#  v1.5 beta    6/17/2014 -handle multiple frames
 
#
 
#
 
#  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
Line 36: Line 37:
 
                             }
 
                             }
 
                         }
 
                         }
                     }              
+
                     }
 
                 }
 
                 }
 
             }
 
             }
Line 56: Line 57:
 
                 if ({connected({atomIndex=idx}) and not {hydrogen}}.size < 2) {
 
                 if ({connected({atomIndex=idx}) and not {hydrogen}}.size < 2) {
 
                     return idx
 
                     return idx
                 }          
+
                 }
 
             }
 
             }
 
         }
 
         }
Line 67: Line 68:
 
# Bound to ALT-LEFT-CLICK by plico_remap
 
# Bound to ALT-LEFT-CLICK by plico_remap
 
function remap_cargo_mb() {
 
function remap_cargo_mb() {
 +
    var f = (_frameID/1000000)
 +
    var m = (_frameID%1000000)
 
     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 = find_n0_idx(idx)
 
     var n0idx = find_n0_idx(idx)
Line 80: Line 83:
 
     var newAtomno = 1
 
     var newAtomno = 1
 
     if (n0idx >= 0) {
 
     if (n0idx >= 0) {
   
+
 
 
         # Prompt for new designators
 
         # Prompt for new designators
 +
        var iResno = {atomIndex=n0idx}.resno
 +
        var iChain = {atomIndex=n0idx}.chain
 +
        var iNo = {atomIndex=n0idx}.atomno
 +
        select {(chain=iChain) and (file=f) and (model=m)}
 +
        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 105: Line 115:
 
     }
 
     }
 
     if (isValid) {
 
     if (isValid) {
+
 
         delete {hydrogen}
+
         delete {hydrogen and (file=f) and (model=m)}
         delete {hoh}
+
         delete {hoh and (file=f) and (model=m)}
         delete %B
+
         delete %B and (file=f) and (model=m)
 
         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 249: Line 259:
 
                     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 271: Line 281:
 
                             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 293: Line 303:
 
                     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 306: Line 316:
 
                     } # 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 315: Line 325:
 
                     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
Line 350: Line 360:
 
                     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
Line 370: Line 380:
 
                     newAtomName = "XZ"
 
                     newAtomName = "XZ"
 
                 }
 
                 }
                   
+
 
 
                 # Else if XZ 2
 
                 # Else if XZ 2
 
                 else if (newAtomName == "XZ") { # ARG
 
                 else if (newAtomName == "XZ") { # ARG
Line 379: Line 389:
 
                     newAtomName = "XH"
 
                     newAtomName = "XH"
 
                 }
 
                 }
                   
+
 
 
                 # Else if XH 2
 
                 # Else if XH 2
 
                 else if (newAtomName == "XH") { # ARG
 
                 else if (newAtomName == "XH") { # ARG
Line 388: Line 398:
 
                 }
 
                 }
 
             }
 
             }
           
+
 
 
             # Else cSet.size = 3
 
             # Else cSet.size = 3
 
             else {
 
             else {
Line 448: Line 458:
 
                 }
 
                 }
 
             }
 
             }
           
+
 
 
             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 465: Line 475:
 
             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 488: Line 498:
 
         echo @gEcho
 
         echo @gEcho
 
         print ls1
 
         print ls1
                       
+
 
     }  
+
     }
 
}
 
}
  
 
# Top level of Remap
 
# Top level of Remap
 
function plico_remap() {
 
function plico_remap() {
   
+
 
 
     # Push selected
 
     # Push selected
 
     gSelSaves = {selected}
 
     gSelSaves = {selected}
   
+
 
 
     gAppendNew = appendNew
 
     gAppendNew = appendNew
 
     set appendNew FALSE
 
     set appendNew FALSE
Line 518: Line 528:
 
function remap_exit() {
 
function remap_exit() {
 
     unbind
 
     unbind
     halo off  
+
     halo off
 
     echo
 
     echo
     select all
+
    var f = (_frameID/1000000)
 +
    var m = (_frameID%1000000)
 +
     select ((file=f) and (model=m))
 
     color {selected} @gScheme
 
     color {selected} @gScheme
 
     gBusy = FALSE
 
     gBusy = FALSE
 
     set appendNew gAppendNew
 
     set appendNew gAppendNew
   
+
 
 
     # Pop selected
 
     # Pop selected
 
     select gSelSaves
 
     select gSelSaves
 
}
 
}
 
# End of REMAP.SPT</pre>
 
# End of REMAP.SPT</pre>

Revision as of 15:13, 17 July 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.)]. 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
#   v1.5 beta    6/17/2014 -handle multiple frames
#
#   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 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 f = (_frameID/1000000)
    var m = (_frameID%1000000)
    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 iResno = {atomIndex=n0idx}.resno
        var iChain = {atomIndex=n0idx}.chain
        var iNo = {atomIndex=n0idx}.atomno
        select {(chain=iChain) and (file=f) and (model=m)}
        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 (file=f) and (model=m)}
        delete {hoh and (file=f) and (model=m)}
        delete %B and (file=f) and (model=m)
        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
    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 REMAP.SPT

Contributors

Remig