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.

The script also allows the user to double-bond or single bond all planars (aromatics, amides, etc) in an amino-acid or nucletotide chain by a shift-click or alt-shift-click respectively. Double-bonding is useful to prevent certain distortions introduced by minimization and allows proper placement of hydrogens with the 'calculate hydrogens' command.

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
#   v1.5 beta    4/12/2016 -require latest common includes
#
# Converts a selected residue base from one form to another.
# Alt-Click to select a residue
# Then enter new residue type:
#   One of ACDEFGHIKLMNPQRSTUVWXY for polypeptide or
#   One of ACGUT for nucleotides
# Or add or remove double bonds from aromatics, amides, and carboxyls
# Click to select a chain (Shift-Click to add, Alt-Shift-Click to remove)
kConvert = 1
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 orientation
    var aO = get_atom_rcn(iResno, iChain, "O")
    var aC = get_atom_rcn(iResno, iChain, "C")
    var aCA = get_atom_rcn(iResno, iChain, "CA")
    var aN = get_atom_rcn(iResno, iChain, "N")
    var aNp = {connected(aC) and (atomname="N")}
    var aCAp = {connected(aNp) and (atomname="CA")}
    var aCxyz = aC.xyz + {0 0 0}
    var aOxyz = aO.xyz + {0 0 0}
    var angC = angle(aNp, aC, aCA)
    var dihedralC = angle(aCAp, aNp, aC, aCA)
    var psi = angle(aNp, aC, aCA, aN)
    gN = aN.atomno

    # Delete the original
    delete {(resno=iResno) and (chain=iChain) and thisModel}

    # Make a new AA    
    gA = "data \"append aa\"\n"
    
    # Call gen_aa in ribozyme.spt
    gA += gen_aa(iResno, newres);
    gA += "end \"append aa\""
    gAppendNew = appendNew
    set appendNew false
    script inline @{gA}
    appendNew = gAppendNew
    
    # Recollect data and move backbone to coords of old aa
    aO = get_atom_rcn(iResno, iChain, "O")
    aC = get_atom_rcn(iResno, iChain, "C")
    aCA = get_atom_rcn(iResno, iChain, "CA")
    aN = get_atom_rcn(iResno, iChain, "N")
    
    select {(chain=iChain) and (resno=iResno) and thisModel}
    var v = aCxyz - aC.xyz
    translate Selected @v
    var v1=aNp.xyz - aC.xyz
    var v2=aCA.xyz - aC.xyz
    var caxis = cross(v1, v2) + aC.xyz
    var curangle =  angle(aNp, aC, aCA)
    rotateselected @aC @caxis @{angC-curangle}
    curangle =  angle(aCAp, aNp, aC, aCA)
    rotateselected @aNp @aC @{dihedralC-curangle}
    curangle =  angle(aNp, aC, aCA, aN)
    rotateselected @aC @aCA @{psi-curangle}
    aO.xyz = aOxyz
    
    # Connect the new AA
    var aCm = get_atom_rcn(iResno-1, iChain, "C")
    connect @aN @aCm
    connect @aC @aNp

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

    set echo TOP LEFT
    background ECHO yellow
    refresh
    gBusy = false

}

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

function convert_nt(iResno, iChain, newres) {
    gChain1 = iChain

    # Collect data
    var topno = {(resno=iResno) and (chain=iChain)
        and thisModel}.atomno.max + 0
    var idmax = {thisModel}.atomIndex.max
    var aO4 = get_atom_rcn(iResno, iChain, "O4\'")
    if (newres = "") {
        newres = aO4.group
    }
    var aC1 = get_atom_rcn(iResno, iChain, "C1\'")
    var aC4 = get_atom_rcn(iResno, iChain, "C4\'")
    var aP = get_atom_rcn(iResno, iChain, "P")
    var aPxyz = aP.xyz + {0 0 0}
    var aOP1xyz = get_atom_rcn(iResno, iChain, "OP1").xyz + {0 0 0}
    var aOP2xyz = get_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 = get_atom_rcn(iResno, iChain, "O3\'").xyz + {0 0 0}
    var aC3xyz = get_atom_rcn(iResno, iChain, "C3\'").xyz + {0 0 0}
    var aC2xyz = get_atom_rcn(iResno, iChain, "C2\'").xyz + {0 0 0}
    var aO2xyz = get_atom_rcn(iResno, iChain, "O2\'").xyz + {0 0 0}
    var aC4xyz = aC4.xyz + {0 0 0}
    var aC5xyz = get_atom_rcn(iResno, iChain, "C5\'").xyz + {0 0 0}
    var aO5xyz = get_atom_rcn(iResno, iChain, "O5\'").xyz + {0 0 0}
    var isR  = (aC1 and {purine})
    var N1or9 = (isR ? "N9" : "N1")
    var C6or8 = (isR ? "C8" : "C6")
    if (aC1.group = "PSU") {
        N1or9 = "C5"
    }
    var aN = get_atom_rcn(iResno, iChain, N1or9)
    var aC = get_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 thisModel}
    
    # Gen NT ==================================================
    var isRna = (aO2xyz != -1)
    gA = "data \"append nt\"\n"
    gA += gen_nt(iResno, newres, isRna, false); # CALL
    gA += "end \"append nt\""
    gAppendNew = appendNew
    set appendNew false
    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")
    var N3or7 = (isR ? "N7" : "N3")
    aN = get_atom_rcn(iResno, iChain, N1or9)
    aC = get_atom_rcn(iResno, iChain, C6or8)
    var aN3or7 = get_atom_rcn(iResno, iChain, N3or7)
    var aC4 = get_atom_rcn(iResno, iChain, "C4\'")
    aO4 = get_atom_rcn(iResno, iChain, "O4\'")
    aC1 = get_atom_rcn(iResno, iChain, "C1\'")
    aP = get_atom_rcn(iResno, iChain, "P")
    var aO3 = get_atom_rcn(iResno, iChain, "O3\'")
    if (aPxyz != -1) {
        aP.xyz = aPxyz
        atom_rcn_xyz(iResno, iChain, "OP1", aOP1xyz)
        atom_rcn_xyz(iResno, iChain, "OP2", aOP2xyz)
    }
    else {
        delete aP
        aP = get_atom_rcn(iResno, iChain, "OP1")
        delete aP
        aP = get_atom_rcn(iResno, iChain, "OP2")
        delete aP
    }
    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 thisModel)
    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 = get_atom_rcn(iResno-1, iChain, "O3\'")
    var aPp = get_atom_rcn(iResno+1, iChain, "P")
    connect @aP @aO3m
    connect @aO3 @aPp
    refresh
    
    gBusy = false
}

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

        if (isAmino) {
            if (not kPHI) {
                script $SCRIPT_PATH$ribozome.spt
                if (not kPHI) {
                    prompt ("The Plico script ribozome.spt is required")
                    quit
                }
            }
            sels = "ABCDEFGHIKLMNOPQRSTUVWXYZ"
            var selp = "   (enter 1 or 3 characters)"
        }
        else if (isNT) {
            if (kPolymeraze < 1) {
                script $SCRIPT_PATH$polymeraze.spt
                if (kPolymeraze < 1) {
                    prompt ("The Plico script polymeraze.spt (1.14+) is required")
                    quit
                }
            }
            sels = "ACGTU"
            selp = "   (enter A, C, G, T, or U)"
        }
        if (sels) {
            var ps = format("Change residue %d from %s to ?\n%s",
                iResno, iGroup, selp)
            var 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) {
                    gBusy = true
                    background ECHO pink
                    refresh
                    if (isAmino) {
                        convert_aa(iResno, iChain, newres[1])
                    }
                    else {
                        convert_nt(iResno, iChain, newres[1])
                    }
                    update_atomnos(iChain)
                    set echo TOP LEFT
                    background ECHO yellow
                    refresh
                }
                else {
                    prompt("Invalid entry")
                }
            }
        }
        else {
            prompt("Not a polypeptide or polynucleotide")
        }
        select {(resno=iResno) and (chain=iChain) and thisModel}
        halo off
    }
}

function double_mb() {
    var idx = _atomPicked
    var iChain = {atomIndex=idx}.chain
    background ECHO pink
    refresh
    double_bond_planars(iChain, false)
    background ECHO yellow
    refresh
}

function undouble_mb() {
    var idx = _atomPicked
    var iChain = {atomIndex=idx}.chain
    background ECHO pink
    refresh
    double_bond_planars(iChain, true)
    background ECHO yellow
    refresh
}

function convert_exit_mb() {
    if (plico_exit()) {
        set allowRotateSelected gAllowRotateSelected
        set allowMoveAtoms gAllowMoveAtoms
    }
}

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

    # 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
        }
    }
    if (kNTcommon < 6) {
        script $SCRIPT_PATH$plicoNTcommon.spt
        if (kNTcommon < 6) {
            prompt ("A newer version of plicoNTcommon.SPT is required")
            quit
        }
    }


    set echo TOP LEFT
    background ECHO yellow

    gEcho = ("____CONVERT_RESIDUE____|ALT-CLICK=select residue"+
        "|SHIFT-CLICK=add double bonds to chain"+
        "|ALT-SHIFT-CLICK=remove double bonds|SHIFT-DOUBLE-CLICK=exit")
    echo @gEcho
    gChain = ""
    gMenuMin = false
    unbind

    bind "ALT-LEFT-CLICK" "_pickAtom";
    bind "ALT-LEFT-CLICK" "+:convert_mb";
    bind "SHIFT-LEFT-CLICK" "_pickAtom";
    bind "SHIFT-LEFT-CLICK" "+:double_mb";
    bind "ALT-SHIFT-LEFT-CLICK" "_pickAtom";
    bind "ALT-SHIFT-LEFT-CLICK" "+:undouble_mb";
    bind "ALT-CTRL-LEFT-CLICK" "align_trna";
    bind "SHIFT-DOUBLE" "convert_exit_mb";
    bind "LEFT-CLICK" "+:plico_menu_toggle";

}

function connect_res_nt( r5, r3, iChain, del) {
    var aO3 = get_atom_rcn(r5, iChain, "O3\'")
    var aP = get_atom_rcn(r3, iChain, "P")
    if (del) {
        connect @aO3 @aP DELETE
    }
    else {
        connect @aO3 @aP
        fix_p_res(r3, iChain, false)
    }
}
# End of CONVERT_RESIDUE.SPT

Contributors

Remig