User:Remig/plico/convert

Convert_residue allows the user to change polypeptide or polynucleotide residues from one type to another. When the residue to change is selected with a mouse click, the user is prompted for the amino-acid or nucleotide to replace the selected residue.

Convert_residue 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 Convert residue
Script=script <path to your scripts directory>/convert_residue.spt;plico_convert

saved as plicoConvert.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 convert_residue.spt:

#   convert_residue - Jmol script by Ron Mignery
#   v1.1 beta    7/23/2014 -better rna detection
#
# Converts a selected residue base from one form to another.
# Click to select a residue
# Then enter new residue type:
#   One of ACDEFGHIKLMNPQRSTUVWXY for polypeptide or
#   One of ACGUT for nucleotides
gAppendNew = true
g1from3 = {"ALA":"A", "GLX":"B","CYS":"C", "ASP":"D","GLU":"E", "PHE":"F",
    "GLY":"G", "HIS":"H","ILE":"I", "LYS":"K","LEU":"L", "MET":"M",
    "ASN":"N", "PYL":"O","PRO":"P", "GLN":"Q","ARG":"R", "SER":"S",
    "THR":"T", "SEC":"U","VAL":"V", "TRP":"W","UNK":"X", "TYR":"Y", "ASX":"Z"}

function convert_aa(iResno, iChain, newres) {
    gBusy = true
    background ECHO pink
    refresh
    gCHAIN = iChain

    # Collect data
    var f = {atomIndex=_atomPicked}.file
    var m = {atomIndex=_atomPicked}.model
    var topno = {(resno=iResno) and (chain=iChain)
        and (file=f) and (model=m)}.atomno.max + 0
    var idmax = {(file=f) and (model=m)}.atomIndex.max
    var aN = atom_rcn(iResno, iChain, "N")
    var aCA = atom_rcn(iResno, iChain, "CA")
    var aC = atom_rcn(iResno, iChain, "C")
    var aO = atom_rcn(iResno, iChain, "O")
    var aNxyz = aN.xyz + {0 0 0}
    var aCAxyz = aCA.xyz + {0 0 0}
    var aCxyz = aC.xyz + {0 0 0}
    var aOxyz = aO.xyz + {0 0 0}
    gN = aN.atomno

    # Delete the original
    delete {(resno=iResno) and (chain=iChain) and (file=f) and (model=m)}

    # Gen AA ==================================================
    gAppendNew = appendNew
    set appendNew false
    gA = "data \"append aa\"\n"
    gA += gen_aa(iResno, newres);
    gA += "end \"append aa\""
    script inline @{gA}
    appendNew = gAppendNew

    # Recollect data and move backbone to coords of old aa
    aN = atom_rcn(iResno, iChain, "N")
    aCA = atom_rcn(iResno, iChain, "CA")
    aC = atom_rcn(iResno, iChain, "C")
    aO = atom_rcn(iResno, iChain, "O")
    var aCB = atom_rcn(iResno, iChain, "CB")
    aN.xyz = aNxyz
    aCA.xyz = aCAxyz
    aC.xyz = aCxyz
    aO.xyz = aOxyz

    # Reconstruct side-chain position on backbone
    select ((atomIndex > idmax) and sidechain and (file=f) and (model=m))
    color {selected} @gAltScheme
    if (aCB.size > 0) {
        set_distance_atoms( aCA, aCB, 1.5)
        set_angle_atoms( aC, aCA, aCB, 115.9)
        set_dihedral_atoms( aO, aC, aCA, aCB, -100.2)
        var aCG = atom_rcn(iResno, iChain, "*G*")
        if (aCG.size > 0) {
            var nno = aCG[0].atomno+1
            set_dihedral_atoms( aC, aCA, aCB, aCG[1], -172.9)
            set_angle_atoms( aCA, aCB, aCG[1], 113.2)
            aCD = {(atomno=nno) and (chain=iChain) and (file=f) and (model=m)}
            if (aCD.size > 0) {
                set_dihedral_atoms( aCA, aCB, aCG[1], aCD, 179.4)
            }
        }
    }

    # Connect the new AA
    var aCm = atom_rcn(iResno-1, iChain, "C")
    var aNp = atom_rcn(iResno+1, iChain, "N")
    connect @aN @aCm
    connect @aC @aNp

    # Update atomnos
    var topdif = {(resno=iResno) and (chain=iChain)
        and (file=f) and (model=m)}.atomno.max - topno
    if (topdif != 0) {
        topmax = {(chain=iChain) and (file=f) and (model=m)}.atomno.max
        for (var i=(topno+1); i <= topmax; i++) {
            {(atomno=i) and (chain=iChain) and (file=f) and (model=m)}.atomno += topdif
        }
    }

    set echo TOP LEFT
    background ECHO yellow
    refresh
    gBusy = false
}

function atom_rcn_xyz(iResno, iChain, iName, xyz) {
    var a = atom_rcn(iResno, iChain, iName)
    a.xyz = xyz
}

function convert_nt(iResno, iChain, newres) {
    gBusy = true
    background ECHO pink
    refresh
    gChain1 = iChain
    var f = {atomIndex=_atomPicked}.file
    var m = {atomIndex=_atomPicked}.model

    # Collect data
    var topno = {(resno=iResno) and (chain=iChain)
        and (file=f) and (model=m)}.atomno.max + 0
    var idmax = {(file=f) and (model=m)}.atomIndex.max
    var aO4 = atom_rcn(iResno, iChain, "O4\'")
    var aC1 = atom_rcn(iResno, iChain, "C1\'")
    var aC4 = atom_rcn(iResno, iChain, "C4\'")
    var aP = atom_rcn(iResno, iChain, "P")
    var aPxyz = aP.xyz + {0 0 0}
    var aOP1xyz = atom_rcn(iResno, iChain, "OP1").xyz + {0 0 0}
    var aOP2xyz = atom_rcn(iResno, iChain, "OP2").xyz + {0 0 0}
    var aC1xyz = aC1.xyz + {0 0 0}
    var aO4xyz = aO4.xyz + {0 0 0}
    var aO3xyz = atom_rcn(iResno, iChain, "O3\'").xyz + {0 0 0}
    var aC3xyz = atom_rcn(iResno, iChain, "C3\'").xyz + {0 0 0}
    var aC2xyz = atom_rcn(iResno, iChain, "C2\'").xyz + {0 0 0}
    var aO2xyz = atom_rcn(iResno, iChain, "O2\'").xyz + {0 0 0}
    var aC4xyz = aC4.xyz + {0 0 0}
    var aC5xyz = atom_rcn(iResno, iChain, "C5\'").xyz + {0 0 0}
    var aO5xyz = atom_rcn(iResno, iChain, "O5\'").xyz + {0 0 0}
    var isR  = ((aC1 and {purine}).size > 0)
    var N1or9 = (isR ? "N9" : "N1")
    var C6or8 = (isR ? "C8" : "C6")
    if (aC1.group="PSU") {
        N1or9 = "C5"
    }
    var aN = atom_rcn(iResno, iChain, N1or9)
    var aC = atom_rcn(iResno, iChain, C6or8)
    var chi = angle(aO4, aC1, aN, aC)
    var dist = distance( aC1, aN)
    var bang = angle( aO4, aC1, aN)
    var bdh = angle( aC4, aO4, aC1, aN)
    gNa = aP.atomno

    # Delete the original
    delete {(resno=iResno) and (chain=iChain) and (file=f) and (model=m)}
    refresh
    
    # Gen NT ==================================================
    var isRna = (aO2xyz != {0 0 0})
    gAppendNew = appendNew
    set appendNew false
    gA = "data \"append nt\"\n"
    gA += gen_nt(iResno, newres, isRna, false);
    gA += "end \"append nt\""
    script inline @{gA}
    appendNew = gAppendNew

    # Recollect data and move new NT to coords of old
    isR  = ((newres="A") or (newres="G"))
    N1or9 = (isR ? "N9" : "N1")
    C6or8 = (isR ? "C8" : "C6")
    N3or7 = (isR ? "N7" : "N3")
    aN = atom_rcn(iResno, iChain, N1or9)
    aC = atom_rcn(iResno, iChain, C6or8)
    var aN3or7 = atom_rcn(iResno, iChain, N3or7)
    var aC4 = atom_rcn(iResno, iChain, "C4\'")
    aO4 = atom_rcn(iResno, iChain, "O4\'")
    aC1 = atom_rcn(iResno, iChain, "C1\'")
    aP = atom_rcn(iResno, iChain, "P")
    var aO3 = atom_rcn(iResno, iChain, "O3\'")
    aP.xyz = aPxyz
    atom_rcn_xyz(iResno, iChain, "OP1", aOP1xyz)
    atom_rcn_xyz(iResno, iChain, "OP2", aOP2xyz)
    aC1.xyz = aC1xyz
    aO4.xyz = aO4xyz
    aO3.xyz = aO3xyz
    atom_rcn_xyz(iResno, iChain, "C3\'", aC3xyz)
    atom_rcn_xyz(iResno, iChain, "C2\'", aC2xyz)
    atom_rcn_xyz(iResno, iChain, "O2\'", aO2xyz)
    aC4.xyz = aC4xyz
    atom_rcn_xyz(iResno, iChain, "C5\'", aC5xyz)
    atom_rcn_xyz(iResno, iChain, "O5\'", aO5xyz)

    # Reconstruct base position on backbone
    select ((atomIndex > idmax) and base and (file=f) and (model=m))
    color {selected} @gAltScheme
    set_distance_atoms( aC1, aN, dist)
    set_angle_atoms( aO4, aC1, aN, bang)
    set_dihedral_atoms( aC4, aO4, aC1, aN, bdh)

    set_angle_atoms( aC1, aN, aC, (isR ? 128.5 : 121.4))
    set_dihedral_atoms( aC1, aN, aC, aN3or7, 180.0)
    set_dihedral_atoms( aO4, aC1, aN, aC, chi)

    # Connect the new NT
    var aO3m = atom_rcn(iResno-1, iChain, "O3\'")
    var aPp = atom_rcn(iResno+1, iChain, "P")
    connect @aP @aO3m
    connect @aO3 @aPp

    # Update atomnos
    topdif = {(resno=iResno) and (chain=iChain)
        and (file=f) and (model=m)}.atomno.max - topno
    if (topdif != 0) {
        topmax = {(chain=iChain) and (file=f) and (model=m)}.atomno.max
        for (var i=(topno+1); i <= topmax; i++) {
            {(atomno=i) and (chain=iChain) and (file=f)
                and (model=m)}.atomno += topdif
        }
    }

    set echo TOP LEFT
    background ECHO yellow
    refresh
    gBusy = false
}

function convert_mb() {
    if (gBusy == false) {
        var idx = _atomPicked
        var isAmino = (({(atomIndex=idx) and amino}.size > 0)
            or ({atomIndex=idx}.group="SEC")
            or ({atomIndex=idx}.group="PYL"))
        var isNT = ({(atomIndex=idx) and (rna or dna)}.size > 0)
        var iResno = {atomIndex=idx}.resno
        var iGroup = {atomIndex=idx}.group
        var iChain = {atomIndex=idx}.chain
        var f = {atomIndex=idx}.file
        var m = {atomIndex=idx}.model
        var sels = ""
        select {(resno=iResno) and (chain=iChain) and (file=f) and (model=m)}
        halo on
        refresh

        if (isAmino) {
            if (kPHI.size == 0) {
                script $SCRIPT_PATH$ribozome.spt
                if (kPHI.size == 0) {
                    prompt ("The Plico script ribozome.spt is required")
                    quit
                }
            }
            sels = "ABCDEFGHIKLMNOPQRSTUVWXYZ"
            selp = "   (enter 1 or 3 characters)"
        }
        else if (isNT) {
            if (kPu.size == 0) {
                script $SCRIPT_PATH$polymeraze.spt
                if (kPu.size == 0) {
                    prompt ("The Plico script polymeraze.spt is required")
                    quit
                }
            }
            sels = "ACGTU"
            selp = "   (enter A, C, G, T, or U)"
        }
        if (sels.size > 0) {
            var ps = format("Change residue %d from %s to ?\n%s",
                iResno, iGroup, selp)
            newres = prompt(ps, "")%9999%0
            if (isAmino and (newres.size==3)) {
                newres = g1from3[newres]
            }
            else if (newres.size==2) {
                newres = newres[2]
            }
            if ((newres != "") and (newres != "NULL")) {
                if (sels.find(newres[1]) > 0) {
                    if (isAmino) {
                        convert_aa(iResno, iChain, newres[1])
                    }
                    else {
                        convert_nt(iResno, iChain, newres[1])
                    }
                }
                else {
                    prompt("Invalid entry")
                }
            }
        }
        else {
            prompt("Not a polypeptide or polynucleotide")
        }
        select {(resno=iResno) and (chain=iChain) and (file=f) and (model=m)}
        halo off
    }
}

function convert_exit_mb() {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    unbind
    set echo TOP LEFT
    echo
    set allowRotateSelected gAllowRotateSelected
    set allowMoveAtoms gAllowMoveAtoms
    select ((file=f) and (model=m))
    color {selected} @gScheme
    select {gSelsave}
}

# Top level of Modify
function plico_convert() {
    gBusy = false
    gSelsave = {selected}
    gPlico = "CONVERT RESIDUE"

    # Load common functions if not already
    if (kCommon < 3) {
        script $SCRIPT_PATH$plicoCommon.spt
        if (kCommon < 3) {
            prompt ("A newer version of plicoCommon.SPT is required")
            quit
        }
    }
    if (kNTcommon < 4) {
        script $SCRIPT_PATH$plicoNTcommon.spt
        if (kNTcommon < 4) {
            prompt ("A newer version of plicoNTcommon.SPT is required")
            quit
        }
    }


    set echo TOP LEFT
    background ECHO yellow

    gEcho = ("____CONVERT_RESIDUE____|ALT-CLICK=select|DOUBLE-CLICK=exit")
    echo @gEcho
    gChain = ""
    unbind

    bind "ALT-LEFT-CLICK" "_pickAtom";
    bind "ALT-LEFT-CLICK" "+:convert_mb";
    bind "DOUBLE" "convert_exit_mb";

}

# End of CONVERT_RESIDUE.SPT

Contributors

Remig