User:Remig/plico/toab

ToAlphaBeta allows the user to mark a section of a polypeptide chain to fold towards an alpha helix configuration or towards a beta strand configuration as described here.

ToAlphaBeta 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 To Alpha/Beta
Script=script <path to your scripts directory>/toab.spt;plico_to_ab

saved as plicotoab.macro in your .jmol/macros directory as described in Macro.

A copy of the Plico scripts tug.spt and plicoCommon.spt must be in the same directory as this script.

Copy and paste the following into a text editor and save in your scripts directory as toab.spt.

#   toAlphaBeta - Jmol script by Ron Mignery
#   v1.7 beta    4/12/2016 -require latest common includes
#
#   Move a stretch of polypeptide from alpha to beta or vice versa
#   or change an amino acid to alpha, beta or L
#
gToab = false
gToabAlt = false
gBusy = false

# Bound to LEFT-UP by to_ab_enable_drag
function to_ab_drag_done_mb() {
    if (not gToabAlt) {
        if (gNanchorIdx >= 0) {
            tug_drag_done_mb()
        }
    }
    else {
        if (gCanchorIdx >= 0) {
            tug_drag_done_mb()
        }
    }
}

# Bound to ALT-SHIFT-LEFT-DRAG by to_ab_enable_drag
function to_ab_drag_2_mb() {
    gToabAlt = true
    to_ab_drag()
}

# Bound to ALT-LEFT-DRAG by to_ab_enable_drag
function to_ab_drag_mb() {
    gToabAlt = false
    to_ab_drag()
}

# Bound to ALT-LEFT-DOWN by tug_enable_drag
function tug_mark_mb() {
    gMouseX = _mouseX
    gMouseY = _mouseY
    gNewDrag = true
}

function to_ab_drag() {
    if (not gBusy) {
        gBusy = true
        var dx = (40.0 * (_mouseX - gMouseX))/_width
        var dy = (40.0 * (_mouseY - gMouseY))/_height
        var q = quaternion()
        var ptd = {@dx @dy 0}
        var pt = (!q)%ptd
        if (distance(pt,  {0 0 0}) > 0.004) {

            # If sidechain mode
            if (gSCidx >= 0) {
                if ({atomIndex=gSCidx}.atomName == "O") {
                    var dir = ((abs(dx) > abs(dy))
                        ? ((dx < 0) ? 2 : -2)
                        : ((dy < 0) ? 2 : -2))
                    counterRotate(gSCidx, dir, not gToabAlt)
                }
                else {
                    gSCcheck = not gToabAlt
                    tugSideChain(pt)
                }
            }

            # Else
            else {

                # If new drag
                if (gNewDrag) {
                    gNewDrag = false
                    save state gState
                }

                # Move the cargo
                select {gCargoSet}

                var phi = ((dx < 0) ? -57 : -90)
                var psi = ((dx < 0) ? -47 : 120)

                # Move between alpha and beta
                f = {atomIndex=_atomPicked}.file
                m = {atomIndex=_atomPicked}.model
                var nIdx = gNcargoIdx
                var cmin = {(chain=gChain) and thisModel}.atomno.min
                var cmax = {(chain=gChain) and thisModel}.atomno.max
                var maxIdx = {(atomno=cmax) and (chain=gchain) and thisModel}.atomIndex
                var minIdx = {(atomno=cmin) and (chain=gchain) and thisModel}.atomIndex
                while (true) {

                    # Adjust phi
                    var ncIdx = get_nward_bb_idx(nIdx, gChain)
                    var caIdx = get_cward_bb_idx(nIdx, gChain)
                    var cIdx = get_cward_bb_idx(caIdx, gChain)
                    if (ncIdx >= 0) {
                        var dh= angle({atomIndex=ncIdx}, {atomIndex=nIdx},
                            {atomIndex=caIdx}, {atomIndex=cIdx})
                        var dir = ((phi > dh) ? abs(8*dx) : -(abs(8*dx)))
                        if (not gToabAlt) {
                            select_nward_idx(nIdx, ((gNanchorIdx >= 0) ? gNcargoIdx : minIdx))
                        }
                        else {
                            select_cward_idx(caIdx, ((gCanchorIdx >= 0) ? gCcargoIdx : maxIdx))
                        }
                        if (abs(phi-dh) > 0.5) {
                            rotate_selected_record(caIdx, {atomIndex=nIdx}, dir)
                        }
                    }

                    # Adjust psi
                    var cnIdx = get_cward_bb_idx (cIdx, gChain)
                    dh= angle({atomIndex=nIdx}, {atomIndex=caIdx},
                        {atomIndex=cIdx}, {atomIndex=cnIdx})
                    dir = ((psi > dh) ? abs(8*dx) : -(abs(8*dx)))
                    if (not gToabAlt) {
                        select_nward_idx(caIdx, ((gNanchorIdx >= 0) ? gNcargoIdx : minIdx))
                    }
                    else {
                        select_cward_idx(cIdx, ((gCanchorIdx >= 0) ? gCcargoIdx : maxIdx))
                    }
                    if (abs(psi-dh) > 0.5) {
                        rotate_selected_record(cIdx, {atomIndex=caIdx}, dir)
                    }

                    if (gCcargoIdx== cIdx) {
                        break
                    }
                    nIdx = cnIdx
                } # endwhile

            }

            gMouseX = _mouseX
            gMouseY = _mouseY
        }

        select {gCargoSet}
        var lcset = (within(kCtolerance, false, {selected})
            and not {selected} and not connected({selected}))
        gOk2 = true
        if (lcset) {
            for (var i = 1; i <= lcset.size; i++) {
                to_handle_collisions(lcset[i].atomIndex)
            }
        }
        var bkc = (gOk2 ? "yellow" : "pink")
        background ECHO @bkc


        gBusy = false
    }
}

# Called by to_ab_cargo_mb when gToab is true
function to_ab_enable_drag() {
    gEcho = "____Alpha <==> Beta____|ALT-CLICK=mark block|SHIFT-CLICK=anchors" +
        "|ALT-DRAG=move|SHIFT-ALT-DRAG=alt move|DOUBLE-CLICK=exit"
    echo @gEcho

    # Allow atoms to be dragged
    bind "ALT-LEFT-DOWN" "tug_mark_mb";
    bind "ALT-LEFT-UP" "tug_drag_done_mb";
    bind "ALT-LEFT-DRAG" "to_ab_drag_mb";
    bind "ALT-SHIFT-LEFT-UP" "to_ab_drag_done_mb";
    bind "ALT-SHIFT-LEFT-DRAG" "to_ab_drag_2_mb";

    unbind "SHIFT-LEFT-CLICK"
    bind "SHIFT-LEFT-CLICK" "_pickAtom";
    bind "SHIFT-LEFT-CLICK" "+:tug_anchor_mb";

}

# Bound to ALT-LEFT-CLICK by plico_to_ab
function to_ab_cargo_mb() {
    gToab = true
    tug_cargo_mb()
}

function set_phi_psi( r, iChain, phi, psi) {
    var aCp = get_atom_rcn( r-1, iChain, "C")
    var aN = get_atom_rcn( r, iChain, "N")
    var aCA = get_atom_rcn( r, iChain, "CA")
    var aC = get_atom_rcn( r, iChain, "C")
    var aO = get_atom_rcn( r, iChain, "O")
    var aNn = get_atom_rcn( r+1, iChain, "N")
    if (aNn) {
        select {(resno <= r) and not aC and not aO and chain=iChain
            and thisModel}
        set_dihedral_atoms(aNn, aC, aCA, aN, psi)
    }
    if (aCp) {
        select {(resno < r) and chain=iChain and thisModel}
        set_dihedral_atoms(aC, aCA, aN, aCp, phi)
    }
    color {resno=r} @gAltScheme
    color {(resno=r) and oxygen} pink
}

# Bound to ALT-SHIFT-LEFT-CLICK by plico_to_ab
function to_alpha_mb() {
    var r = {atomIndex=_atomPicked}.resno
    var iChain = {atomIndex=_atomPicked}.chain
    print r+" to alpha"
    set_phi_psi( r, iChain, -50, -45)
}

# Bound to CTRL-SHIFT-LEFT-CLICK by plico_to_ab
function to_beta_mb() {
    var r = {atomIndex=_atomPicked}.resno
    var iChain = {atomIndex=_atomPicked}.chain
    print r+" to beta"
    set_phi_psi( r, iChain, -100, 135)
}

# Bound to ALT-CTRL-LEFT-CLICK by plico_to_ab
function to_L_mb() {
print "L"
    var r = {atomIndex=_atomPicked}.resno
    var iChain = {atomIndex=_atomPicked}.chain
    set_phi_psi( r, iChain, 50, 45)
}

function to_ab_menu_mb() {
    gEcho="______Menu_______|Twist|Bend|SuperCoil| BACK"
    set echo top left
    color echo black
    background echo lightgrey
    echo @gEcho

    bind "LEFT-CLICK" "+:to_ab_routines_mb";
}

function to_ab_routines_mb() {
    # If in menu zone
    if ((_mouseX < 100) and ((_height-_mouseY) < 343)) {
        var line = ((_mouseX < 125) ? ((_height-_mouseY)\26) : 0)
        switch (line) {
        case 1:
            print "twistTBD"
            break
        case 2:
            print "bendTBD"
            break
        case 3:
            print "supercoilTBD"
            break
        case 4:
            plico_to_ab()
            break
        }
    }
}

# Top level of ToAlphaBeta
function plico_to_ab() {

    # 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
        }
    }
    
    # Load tug functions if not already
    if (kTug < 3) {
        script $SCRIPT_PATH$tug.spt
        if (kTug < 3) {
            prompt ("A newer version of tug.SPT is required")
            quit
        }
    }

    gPlico = "TO ALPHA/BETA"
    plico_prelim(true, true)

    gEcho = ("______Alpha <==> Beta______|ALT-CLICK=mark block" +
    "|CTRL-SHIFT-CLICK=to beta|ALT-SHIFT-CLICK=to alpha" +
    "|ALT-CTRL-CLICK=to L|CTRL-CLICK=menu|SHIFT-DOUBLE-CLICK=exit")
    echo @gEcho

    bind "ALT-LEFT-CLICK" "_pickAtom";
    bind "ALT-LEFT-CLICK" "+:to_ab_cargo_mb";
    bind "ALT-SHIFT-LEFT-CLICK" "_pickAtom";
    bind "ALT-SHIFT-LEFT-CLICK" "+:to_alpha_mb";
    bind "CTRL-SHIFT-LEFT-CLICK" "_pickAtom";
    bind "CTRL-SHIFT-LEFT-CLICK" "+:to_beta_mb";
    bind "ALT-CTRL-LEFT-CLICK" "_pickAtom";
    bind "ALT-CTRL-LEFT-CLICK" "+:to_L_mb";
    bind "CTRL-LEFT-CLICK" "to_ab_menu_mb";
    unbind "CTRL-LEFT-DOWN"
    bind "SHIFT-DOUBLE" "plico_exit(true)";
    bind "LEFT-CLICK" "+:plico_menu_toggle";
}

# MENU functions
function toab_twist(iChain, rmin, rmax, phi, psi, omega) {
    if (rmin < 0) {
        rmin = get_resno_min(iChain)
    }
    if (rmax < 0) {
        rmax = get_resno_max(iChain)
    }
    for (var r = rmin; r <= rmax; r++) {
        var aCAp = get_atom_rcn(r-1, iChain, "CA")
        var aCp = get_atom_rcn(r-1, iChain, "C")
        var aN = get_atom_rcn(r, iChain, "N")
        var aCA = get_atom_rcn(r, iChain, "CA")
        var aC = get_atom_rcn(r, iChain, "C")
        var aO = get_atom_rcn(r, iChain, "O")
        var aNn = get_atom_rcn(r+1, iChain, "N")
        if (aNn) {
            select {(resno > r) or aO}
print "psi=t"
if (x1) throw context t            
            set_dihedral_atoms(aN, aCA, aC, aNn, psi)
        }
        if (aCp) {
            select {(resno >= r)}
print "phi=t"
if (x1) throw context t            
            set_dihedral_atoms(aCAp, aCp, aN, aCA, omega)
            set_dihedral_atoms(aCp, aN, aCA, aC, phi)
        }
    }
}

function toab_bend(iChain, rmin, rmax, cacn, cnca, ncac) {
    if (rmin < 0) {
        rmin = get_resno_min(iChain)
    }
    if (rmax < 0) {
        rmax = get_resno_max(iChain)
    }
    for (var r = rmin; r <= rmax; r++) {
        var aCAp = get_atom_rcn(r-1, iChain, "CA")
        var aCp = get_atom_rcn(r-1, iChain, "C")
        var aN = get_atom_rcn(r, iChain, "N")
        var aCA = get_atom_rcn(r, iChain, "CA")
        var aC = get_atom_rcn(r, iChain, "C")
        var aO = get_atom_rcn(r, iChain, "O")
        var aNn = get_atom_rcn(r+1, iChain, "N")
        if (aCp) {
            select {(resno >= r) or aOp}
print "phi=t"
if (x1) throw context t            
            set_angle_atoms(aCAp, aCp, aN, cacn)
            select remove aOp
            set_angle_atoms(aCp, aN, aCA, cnca)
        }
        select {(resno > r) or aO or aC}
print "psi=t"
if (x1) throw context t            
        set_angle_atoms(aN, aCA, aC, ncac)
    }
}

function toab_supercoil(iChain, rmin, rmax, n, f) {
    var delta = [-1, 0, 1, 2, 1, 0, -1]
    if (rmin < 0) {
        rmin = get_resno_min(iChain)
    }
    if (rmax < 0) {
        rmax = get_resno_max(iChain)
    }
    for (var r = rmin; r <= rmax; r++) {
    
        var aN = get_atom_rcn(r, iChain, "N")
        var aCA = get_atom_rcn(r, iChain, "CA")
        var aC = get_atom_rcn(r, iChain, "C")
        var aO = get_atom_rcn(r, iChain, "O")
        var aNn = get_atom_rcn(r+1, iChain, "N")
        if (aNn) {
            select {(resno > r) or aO}
            var ca = angle(aN, aCA, aC, aNn)
print ca            
            set_dihedral_atoms(aN, aCA, aC, aNn, ca+(f*delta[n]))
        }
        n = 1+((++n)%7)
    }
}

# End of TOAB.SPT

Contributors

Remig