User:Remig/plico/tug

Tug allows the user to pull or push by mouse actions to move or rotate one part of a polypeptide against the rest by rotation on its psi and phi bonds with collision detection and restriction. It also allows the user to move an entire chain to nest against another chain.

Tug is a member of the Plico suite of protein folding tools described in User:Remig/plico . It may be installed and accessed as a macro with the file:

Title=PLICO Tug
Script=script <path to your scripts directory>/tug.spt;plico_tug

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

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

#   tug - Jmol script by Ron Mignery
#   v1.13 beta    7/16/2014 -support multi-frame environment
#
#   Translate or rotate a stretch of a polypeptide against itself
#    or against other chains by mouse actions
#
kTug = 3
gCanchorIdx = -1
gCanchorNo = -1
gPlico = "TUG"
gNanchorIdx = -1
gNanchorNo = -1
gCcargoIdx = -1
gNcargoIdx = -1
gCcargoNo = -1
gNcargoNo = -1
gDestAtomIdx = -1
g1pivotIdx = -1
g2pivotIdx = -1
gSelSaves = ({})
gCrotors = array()
gNrotors = array()
gOkCollide = ({})
gChain = ""
gMinNo = 1
gMaxNo = 9999
gCargoSet = ({})
gMovingSet = ({})
gBusy = FALSE
gSCidx = -1
gSCcircle = -1
gSCpt = {0 0 0}
gTargetPt = {0 0 0}
gNewDrag = FALSE
gEcho = ""
gZoom = ""
gRotate = ""
gTow = FALSE
g1dynamicIdx = -1
g2dynamicIdx = -1
gSCcheck = TRUE
gBondPicking = FALSE
gFreeze = array()


function get_cp_idx (idx) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    var no = {atomIndex=idx}.atomno
    while ((no < gMaxNo) and ({(atomno=no) and (chain=gChain)
        and (file=f) and (model=m)}.atomName != "C")) {
        no++
    }
    return ({(atomno=no) and (chain=gChain) and (file=f) and (model=m)}.atomIndex)
}

function get_cm_no (iNo) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    while ((iNo > 0) and ({(atomno=iNo) and (chain=gChain)
        and (file=f) and (model=m)}.atomName != "C")) {
        iNo--
    }
    return iNo
}

function get_nm_idx (idx) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    var no = {atomIndex=idx}.atomno
    while ((no > 0) and ({(atomno=no) and (chain=gChain)
        and (file=f) and (model=m)}.atomName != "N")) {
        no--
    }
    return ({(atomno=no) and (chain=gChain) and (file=f) and (model=m)}.atomIndex)
}

function get_np_no (iNo) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    while ((iNo < gMaxNo) and ({(atomno=iNo) and (chain=gChain)
        and (file=f) and (model=m)}.atomName != "N")) {
        iNo++
    }
    return iNo
}

function get_cb_idx (BBidx) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    var no = {atomIndex=BBidx}.atomno
    var i = 1
    for (; i < 5; i++) {
        if ({(atomno=@{no+i}) and (chain=gChain)
            and (file=f) and (model=m)}.atomName == "CB") {
            break
        }
    }
    return {(atomno=@{no+i}) and (chain=gChain) and (file=f) and (model=m)}.atomIndex
}

function get_o_idx (BBidx) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    var no = {atomIndex=BBidx}.atomno
    var i = 1
    for (; i < 4; i++) {
        if ({(atomno=@{no+i}) and (chain=gChain)
            and (file=f) and (model=m)}.atomName == "O") {
            break
        }
    }
    return {(atomno=@{no+i}) and (chain=gChain) and (file=f) and (model=m)}.atomIndex
}

function get_nward_bb_idx (idx, iChain) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    var no = {atomIndex=idx}.atomno - 1
    for (; no >= 0; no--) {
        var atomName = {(atomno=no) and (chain=iChain)
            and (file=f) and (model=m)}.atomName
        if ((atomName = "N") or (atomName = "C") or (atomName = "CA")) {
            break
        }
    }
    return ((no >= 0) ? ({(atomno=no) and (chain=iChain)
        and (file=f) and (model=m)}.atomIndex) : -1)
}

function get_cward_bb_idx (idx, iChain) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    var no = {atomIndex=idx}.atomno + 1
    for (; no < gMaxNo; no++) {
        var atomName = {(atomno=no) and (chain=iChain)
            and (file=f) and (model=m)}.atomName
        if ((atomName = "N") or (atomName = "C") or (atomName = "CA")) {
            break
        }
    }
    return ((no >= 0) ? ({(atomno=no) and (chain=iChain)
        and (file=f) and (model=m)}.atomIndex) : -1)
}

function get_sc_set (scIdx, iChain) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    var scSet = ({})
    var idx = get_sc_bb_idx(scIdx, iChain)
    var iNo = {atomIndex=idx}.atomno + 3

    for (var i = 1; i < 20; i++) {
        idx = {(atomno=@{iNo+i}) and (chain=iChain)
            and (file=f) and (model=m)}.atomIndex
        if (is_bb_idx(idx)) {
            break
        }
        scSet = scSet or {atomIndex=idx}
    }
    return scSet
}

function get_sc_bb_idx (idx, iChain) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    var no = {atomIndex=idx}.atomno
    for (; no > 0; no--) {
        if ({(atomno=no) and (chain=iChain)
            and (file=f) and (model=m)}.atomName == "CA") {
            break
        }
        else if ({(atomno=no) and (chain=iChain)
            and (file=f) and (model=m)}.atomName == "C") {
            break
        }
        else if ({(atomno=no) and (chain=iChain)
            and (file=f) and (model=m)}.atomName == "N") {
            break
        }
        else if ({(atomno=no) and (chain=iChain)
            and (file=f) and (model=m)}.atomName == "CB") {
            no -= 3
            break
        }
    }
    return {(atomno=no) and (chain=iChain) and (file=f) and (model=m)}.atomIndex
}

function is_bb_idx(aIdx) {
    var ret = FALSE
    switch({atomIndex=aIdx}.atomName) {
    case "N":
    case "CA":
    case "C":
        ret = TRUE
        break
    }
    return ret
}

function is_sc_idx(aIdx) {

    var ret = FALSE
    if (not is_bb_idx(aIDx)) {

        ret = TRUE
        switch({atomIndex=aIdx}.atomName) {
        case "O":
        case "CB":
            ret = FALSE
            break
        }
    }
    return ret
}

function add_sc_to_select(CAno, isAdd, addOXT, iChain) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    var iNo = CAno+3
    var res = {(atomno=iNo) and (chain=iChain) and (file=f) and (model=m)}.resno
    var scset = {(resno=res) and (chain=iChain) and (file=f)
        and (model=m) and sidechain}
    if (addOXT) {
        scset = scset or atom_rcn(res, iChain, "OXT")
    }
    if (isAdd) {
        select add scset
    }
    else {
        select remove scset
    }
}

function select_add_sc(fromIdx) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    var iNo = {atomIndex=fromIdx}.atomno
    var iChain = {atomIndex=fromIdx}.chain
    select none
    while ({(atomno=iNo) and (chain=iChain)
        and (file=f) and (model=m) and sidechain}.size > 0) {
        var a = {(atomno=iNo) and (chain=iChain)and (file=f) and (model=m)}
        a.selected = TRUE
        iNo++
    }
}

# Resolve collisions
function handle_collisions( targetIdx) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)

    # For all selected atoms
    for (var iNo = {selected}.min.atomno; iNo <= {selected}.max.atomno; iNo++) {
        var idx = {(atomno=iNo) and (chain=gchain)
            and (file=f) and (model=m)}.atomIndex
        if ({atomindex=idx}.selected) {

            # Collect local colliders
            var lcAtoms = (within(kCtolerance, FALSE, {atomIndex=idx})
                and not {atomIndex=idx}
                and not {gOkCollide}
                and not connected({atomIndex=idx}))
            if (lcAtoms.size > 0) {

                # Ignore kinked BB
                if (is_bb_idx(idx) and angle({atomIndex=@{get_cward_bb_idx(idx, gChain)}},
                    {atomIndex=idx} , {atomIndex=@{get_nward_bb_idx(idx, gChain)}}) < 100) {
                    continue
                }

                # For all local colliders
                for (var c = 1; c <= lcAtoms.size; c++ ) {
                    var cidx = lcAtoms[c].atomIndex

                    # If it is with water, delete it
                    if (lcAtoms[c].group = "HOH") {
                        delete {atomIndex=cidx}
                    }

                    # else if it is with side chain not proline, fix it
                    else if (is_sc_idx(cidx) and ({atomIndex=cidx}.group != "PRO")) {
                        fix_sc_collision_2(cidx)
                        recollect = TRUE

                        # If not fixed, exit fail
                        if (not gOk2) {
                            return # early exit (break n jmol bug)
                        }
                    }

                    # else if it is itself a side chain not proline, fix it
                    else if (is_sc_idx(idx) and ({atomIndex=idx}.group != "PRO")) {
                        fix_sc_collision_2(idx)
                        recollect = TRUE

                        # If not fixed, exit fail
                        if (not gOk2) {
                            return # early exit (break n jmol bug)
                        }
                    }

                    # Else if it is with O, counter-rotate
                    else if (lcAtoms[c].atomName = "O") {
                        counter_rotate_2(lcAtoms[c].atomIndex,
                            {atomIndex=idx}.xyz, targetIdx, FALSE)

                        # If not fixed, exit fail
                        if (not gOk2) {
                            return # early exit (break n jmol bug)
                        }
                    }

                    # Else if it is itself O, counter-rotate
                    else if ({atomIndex=idx}.atomName = "O") {
                        counter_rotate_2(idx, lcAtoms[c].xyz, targetIdx, FALSE)

                        # If not fixed, exit fail
                        if (not gOk2) {
                            return # early exit (break n jmol bug)
                        }
                    }

                    else {    # Else not fixed, exit fail
                        gOk2 = FALSE
                        return # early exit (break n jmol bug)
                    }
                } # endfor
            }
        }
    } # endfor iNo
}

# Rotate rotor set to move target atom to its proper place
function tug_track_idx(targetIdx, targetPt, nWard, cDetect) {
    gOK = FALSE
    var pt = targetPt
    var dist = distance(pt, {atomIndex=targetIdx}.xyz)

    var rotors = (nWard ? gNrotors : gCrotors)

    # For a number of passes
    for (var pass1 = 0; pass1 < 20; pass1++) {
        var blocked = ({})
        for (var pass2 = 0; pass2 < (rotors.size/4); pass2++) {

            var v1 = {atomIndex=targetIdx}.xyz - pt

            # Find the most orthgonal unused rotor
            var imax = 0
            var smax = 0.5
            for (var i = 1; i < rotors.size; i += 4) {
                var i2 = rotors[i+1]
                var i3 = rotors[i+2]
                var i4 = rotors[i+3]
                if ((i2 != targetIdx) and (i3 != targetIdx) and (i4 != targetIdx)) {
                    if ({blocked and {atomIndex=i2}}.count == 0) {
                        var v2 = {atomIndex=i3}.xyz - {atomIndex=i2}.xyz

                        var s = sin(abs(angle(v1, {0 0 0}, v2)))
                        if (s > smax) {
                            smax = s
                            imax = i
                        }
                    }
                }
            }

            # If no more rotors, break to next full try
            if (imax == 0) {
               break
            }
            var i1 = rotors[imax+0]
            var i2 = rotors[imax+1]
            var i3 = rotors[imax+2]
            var i4 = rotors[imax+3]

            # Get dihedral of rotor with target point
            var dt = angle({atomIndex=targetIdx}, {atomIndex=i2}, {atomIndex=i3}, pt)
            var dh = angle({atomIndex=i1}, {atomIndex=i2}, {atomIndex=i3}, {atomIndex=i4})
            if (dh == "NaN") {
                dh = -50
            }
            var psi = dh + dt
            var phi = dh + dt

            # Compute resultant psi and phi
            #  and select from target atom to first half of rotor
            var movePt = FALSE
            if (nWard) {
                if ({atomIndex=i2}.atomName="CA") {
                    psi = angle({atomIndex=@{get_cward_bb_idx(i1, gChain)}}, {atomIndex=i1},
                        {atomIndex=i2}, {atomIndex=i3}) + dt
                }
                else {
                    phi = angle({atomIndex=i1}, {atomIndex=i2},
                        {atomIndex=i3}, {atomIndex=@{get_nward_bb_idx(i3, gChain)}}) + dt
                }

                if ({atomIndex=i2}.atomno > {atomIndex=targetIdx}.atomno) {
                    movePt = TRUE
                    select_nward_idx(i3, get_cward_bb_idx(targetIdx, gChain))
                    {atomIndex=targetIdx}.selected = TRUE
                }
                else {
                    select_cward_idx(i2, targetIdx)
                }
            }
            else {
                if (({atomIndex=i2}.atomName="CA")) {
                    phi = angle({atomIndex=@{get_nward_bb_idx(i1, gChain)}}, {atomIndex=i1},
                        {atomIndex=i2}, {atomIndex=i3}) + dt
                }
                else {
                    psi = angle({atomIndex=i2}, {atomIndex=i3},
                        {atomIndex=i4}, {atomIndex=@{get_cward_bb_idx(i4, gChain)}}) + dt
                }

                if ({atomIndex=i2}.atomno < {atomIndex=targetIdx}.atomno) {
                    movePt = TRUE
                    select_cward_idx(i3, get_nward_bb_idx(targetIdx, gChain))
                    {atomIndex=targetIdx}.selected = TRUE
                }
                else {
                    select_nward_idx(i2, targetIdx)
                }
            }

            # Relax rules if desperate
            if (pass1 > 10) {
                phi = -50
            }

            # If rotation within ramachandran limits
            if ((abs(dt) >= 0.1) and
                (({atomIndex=i2}.group=="GLY") or (phi < 0))) {

                # If moving target point, put the target atom there
                var cp = {atomIndex=targetIdx}.xyz
                if (movePt) {
                    dt = -dt
                    {atomIndex=targetIdx}.xyz = pt
                }

                # Rotate to minimize vector ====================
                rotateSelected {atomIndex=i2} {atomIndex=i3} @dt

                # If collision checking
                if (cDetect) {

                    # If collision, back off by eighths
                    var wasCollision = FALSE
                    for (var ci = 0; ci < 4; ci++) {
                        if (ci < 3) {
                            dt /= 2
                        }
                        handle_collisions( targetIdx)
                        if (not gOk2) {
                            wasCollision = TRUE
                            rotateSelected {atomIndex=i2} {atomIndex=i3} @{-dt}
                        }
                        else if (wasCollision) {
                            if (ci <3) {
                                rotateSelected {atomIndex=i2} {atomIndex=i3} @{dt}
                            }
                        }
                        else {
                            break
                        }

                        if (dt < 0.01) {
                            break
                        }
                    } # endfor
                }

                # If moving target point, put the target atom back
                if (movePt) {
                    pt = {atomIndex=targetIdx}.xyz
                    {atomIndex=targetIdx}.xyz = cp
                }

            }

            # If close enough, stop
            if (distance(pt, {atomIndex=targetIdx}) < kDtolerance) {
                gOK = TRUE
                gTargetPt = pt
                break
            }

            # Block rotor
            blocked |= {atomIndex=i2}

        }   # endfor num rotors passes

        if (gOK) {
            break
        }
    }   # endfor 20 passes
}

# Counter rotate bonds on either side of a BB O
function do_counter_rotate(caPhiIdx, nIdx, cIdx, oIdx, caPsiIdx, dir, nWard) {

    # Rotate psi
    {atomIndex=nIdx}.selected = nWard
    {atomIndex=cIdx}.selected = nWard
    {atomIndex=oIdx}.selected = nward
    rotateSelected {atomIndex=caPsiIdx} {atomIndex=cIdx} @{dir}

    # Counter-rotate phi
    {atomIndex=nIdx}.selected = not nWard
    {atomIndex=cIdx}.selected = not nWard
    {atomIndex=oIdx}.selected = not nward
    rotateSelected {atomIndex=nIdx} {atomIndex=caPhiIdx} @{-dir}
}

function counter_rotate(oIdx, dir, nWard) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)

    var iChain = {atomIndex=oIdx}.chain
    var selsave = {selected}
    var cIdx = get_sc_bb_idx(oIdx, iChain)
    var nIdx = get_cward_bb_idx(cIdx, iChain)
    var caPhiIdx = get_cward_bb_idx(nIdx, iChain)
    var caPsiIdx = get_nward_bb_idx(cIdx, iChain)

    if (nWard) {
        nNo = {(chain=iChain) and (file=f) and (model=m)}.atomno.min
        select_nward_idx(caPsiIdx, {(atomno=nNo) and (chain=iChain)
            and (file=f) and (model=m)}.atomIndex)
    }
    else {
        cNo = {(chain=iChain) and (file=f) and (model=m)}.atomno.max
        select_cward_idx(caPhiIdx, {(atomno=cNo) and (chain=iChain)
            and (file=f) and (model=m)}.atomIndex)
    }

    # Counter-rotate
    do_counter_rotate(caPhiIdx, nIdx, cIdx, oIdx, caPsiIdx, dir, not nWard)
    select selsave
}

function counter_rotate_2(oIdx, toPt, terminalIdx, oDrag) {

    var iChain = {atomIndex=oIdx}.chain
    var selsave = {selected}
    var gOk2 = TRUE
    var cIdx = get_sc_bb_idx(oIdx, iChain)
    var nIdx = get_cward_bb_idx(cIdx, iChain)
    var caPhiIdx = get_cward_bb_idx(nIdx, iChain)
    var caPsiIdx = get_nward_bb_idx(cIdx, iChain)

    var nTward = ({atomIndex=oIdx}.atomno < {atomIndex=terminalIdx}.atomno)
    if (nTward) {
        select_cward_idx(cIdx, terminalIdx)
    }
    else {
        select_nward_idx(nIdx, terminalIdx)
    }

    # Until all collisions cancelled
    var dir = 5
    var ang = angle(toPt, {atomIndex=oIdx}, {atomIndex=cIdx})
    var tcount = 0
    while (oDrag or (within(kCtolerance, FALSE, {atomIndex=oIdx})
            and not {atomIndex=oIdx} and not connected({atomIndex=oIdx})
            and not {gOkCollide} > 0)) {

        # Counter-rotate
        do_counter_rotate(caPhiIdx, nIdx, cIdx, oIdx, caPsiIdx, dir, nTward)
        var newang = angle(toPt, {atomIndex=oIdx}, {atomIndex=cIdx})

        # If wrong direction once, undo and reverse
        if (newang > ang) {
            do_counter_rotate(caPhiIDx, nIdx, cIdx, oIdx, caPsiIdx, -dir, nTward)

            # If first time, continue in opposite direction
            dir *= -1
            if (dir < 0) {
                continue
            }
        }

        if (oDrag) {
            break
        }

        # If no go, undo and exit
        tcount++
        if (tcount > (360/abs(dir))) {
            gOk2 = FALSE
            break
        }

    } # endwhile
    select selsave
}

# Repair proline
function repair_proline(BBidx) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    var cbidx = get_cb_idx(BBidx)
    var cbno = {atomIndex=cbidx}.atomno
    var cgidx = {(atomno=@{cbno+1}) and (chain=gChain)
        and (file=f) and (model=m)}.atomIndex
    var cdidx = {(atomno=@{cbno+2}) and (chain=gChain)
        and (file=f) and (model=m)}.atomIndex
    var caidx = {(atomno=@{cbno-3}) and (chain=gChain)
        and (file=f) and (model=m)}.atomIndex
    var nidx = {(atomno=@{cbno-4}) and (chain=gChain)
        and (file=f) and (model=m)}.atomIndex

    select {atomIndex=cbidx}
    set_angle_idx(nidx, caidx, cbidx, 109.5)

    select {atomIndex=cdidx}
    set_distance_idx(nidx, cdidx, 1.47)
    set_angle_idx(caidx, nidx, cdidx, 102.7)
    set_dihedral_idx(cbidx, caidx, nidx, cdidx, 16.2)

    select {atomIndex=cgidx}
    set_distance_idx(cdidx, cgidx, 1.51)
    set_angle_idx(nidx, cdidx, cgidx, 106.4)
    set_dihedral_idx(caidx, nidx, cdidx, cgidx, 16.2)
}

# Repair side chain
function repair_sc(targetIdx, nWard) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)

    var idx = (nWard ? get_cward_bb_idx(targetIdx, gChain) : get_nward_bb_idx(targetIdx, gChain))

    if (({atomIndex=targetIdx}.atomName == "CA")
        and ({atomIndex=targetIdx}.group != "GLY")) {
        var cbidx = get_cb_idx(targetIdx)
        select none
        select_add_sc(cbidx)
        set_angle_idx(idx, targetIdx, cbidx, 110.0)
        set_distance_idx(targetIdx, cbidx, 1.5)
        if ({atomIndex=targetIdx}.group != "PRO") {
            var colliders = (within(kCtolerance, FALSE, {selected})
                and not {atomIndex=targetIdx} and not {selected})
            if (colliders.size > 0) {
                if ({atomIndex=targetIdx}.group != "ALA") {
                    fix_sc_collision_2(cbidx)
                }
            }
        }
        else {
            if (nWard) {
            }
            else {
                set_dihedral_idx(get_nward_bb_idx(idx, gChain), idx, targetIdx, cbidx, 174.2)
            }
        }
    }

    else if ({atomIndex=targetIdx}.atomName == "C") {
        var oidx = get_o_idx(targetIdx)
        select {atomIndex=oidx}
        set_angle_idx(idx, targetIdx, oidx, 120.0)
        set_distance_idx(targetIdx, oidx, 1.21)
        if (nWard) {
            set_dihedral_idx(get_cward_bb_idx(idx, gChain), idx, targetIdx, oidx, 0.0)
        }
        if ({atomIndex=idx}.group == "PRO") {
            repair_proline(idx)
            var dNo = {atomIndex=targetIdx}.atomno + 4
            var dIdx = {(atomno=dNO) and (chain=gChain)
                and (file=f) and (model=m)}.atomIndex
            var colliders = (within(kCtolerance, FALSE, {atomIndex=dIdx})
                and not connected({atomIndex=dIdx})
                and not {atomIndex=dIdx})
            for (var i = 1; i <= colliders.size; i++) {
                if (colliders[i].atomName == "O") {
                    counter_rotate_2(colliders[i].atomIndex,
                        {atomIndex=dIdx}.xyz, targetIdx, FALSE)
                }
            }
        }
    }
}

# Rebuild Cward rotors set
function tug_track_c() {

    # For all bb atoms cWard of cargo
    var targetIdx = gCcargoIdx
    var okCount = 0

    # Allow collisions with cargo
    gOkCollide = gCargoSet
    var tcount = 0
    while (targetIdx != gCanchorIdx) {

        # Step to next atom
        targetIdx = get_cward_bb_idx(targetIdx, gChain)

        # No collision with cargo allowed after two atoms placed
        if (tcount == 2) {
           gOkCollide = ({})
        }
        tcount++

        # Compute targets desired coords
        var c1idx = get_cward_bb_idx(targetIdx, gChain)
        var n1idx = get_nward_bb_idx(targetIdx, gChain )
        var n2idx = get_nward_bb_idx(n1Idx, gChain)
        var n3idx = get_nward_bb_idx(n2Idx, gChain)
        var pt = {0 0 0}
        if ({atomIndex=targetIdx}.atomName == "N") {
            var oidx = get_o_idx(n1idx)
            select {atomIndex=oidx}

            # Desired target location is trigonal O
            set_distance_idx(n1idx, oidx, 1.5)
            pt = get_trigonal_idx(n2idx, n1idx, oidx, 1.37)
            set_distance_idx(n1idx, oidx, 1.21)
        }
        else if (({atomIndex=targetIdx}.atomName == "C")
            and ({atomIndex=targetIdx}.group != "GLY")) {

            # Desired target location is tetragonal CB
            var cbidx = get_cb_idx(n1idx)
            pt = get_tet_idx(n2idx, n1idx, cbidx, 1.5)
        }
        else { # CA (or GLY C)

            # Save current target coords
            var cp = {atomIndex=targetIdx}.xyz

            # Set target atom at desired distance and angle
            select {atomIndex=targetIdx}
            set_distance_idx(n1idx, targetIdx, 1.5)
            set_angle_idx(n2idx, n1idx, targetIdx, 120.0)
            if ({atomIndex=targetIdx}.atomName == "CA") {
                set_dihedral_idx(n3idx, n2idx, n1idx, targetIdx, 180)
            }

            # Record and restore target
            pt = {atomIndex=targetIdx}.xyz
            {atomIndex=targetIdx}.xyz = cp
        }

        # If target not at desired location
        if (distance(pt, {atomIndex=targetIdx}) > kDtolerance) {
            okCount = 0
            gTargetPt = pt
            var xcount = 0
            gOK = FALSE
            while ((xcount < 20) and (not gOK)) {

                # Rotate on cWard rotor set to move it there
                tug_track_idx(targetIdx, pt, FALSE, FALSE)
                xcount++
            }
        }
        else {
            gOK = TRUE
            okCount++
        }

        # If successful
        if (gOK == TRUE) {

            # Adust any side atoms
            repair_sc(targetIdx, FALSE)
        }

        # Else fail
        else {
            break
        }

        # If no movement in 4 tries, we are done
        if (okCount > 3) {
            break
        }
    } # endwhile (targetIdx != gCanchorIdx) {
}

# Rebuild Nward rotors set
function tug_track_n() {

    gOK = TRUE

    # For all bb atoms nWard of cargo
    var targetIdx = gNcargoIdx
    var okCount = 0

    # Allow collisions with cargo
    gOkCollide = gCargoSet
    var tcount = 0
    while (targetIdx != gNanchorIdx) {

        # Step to next atom
        targetIdx = get_nward_bb_idx(targetIdx, gChain)

        # No collision with cargo allowed after two atoms placed
        if (tcount == 2) {
           gOkCollide = ({})
        }
        tcount++

        # Compute targets desired coords
        var n1idx = get_nward_bb_idx(targetIdx, gChain)
        var c1idx = get_cward_bb_idx(targetIdx, gChain)
        var c2idx = get_cward_bb_idx(c1idx, gChain)
        var c3idx = get_cward_bb_idx(c2idx, gChain)
        var pt = {0 0 0}
        if ({atomIndex=targetIdx}.atomName == "CA") {

            # Desired target location is trigonal O
            var oidx = get_o_idx(c1idx)
            select {atomIndex=oidx}
            set_distance_idx(c1idx, oidx, 1.39)
            pt = get_trigonal_idx(c2idx, c1idx, oidx, 1.41)
            set_distance_idx(c1idx, oidx, 1.21)
        }
        else if (({atomIndex=targetIdx}.atomName == "N")
            and ({atomIndex=targetIdx}.group != "GLY")) {

            # Desired target location is r-tetragonal CB
            var cbidx = get_cb_idx(c1idx)
            pt = get_tet_idx(cbidx, c1idx, c2idx, 1.5)
        }
        else { # C

            # Save current target coords
            var cp = {atomIndex=targetIdx}.xyz

            # Set target atom at desired distance and angle
            select {atomIndex=targetIdx}
            set_distance_idx(c1idx, targetIdx, 1.37)
            set_angle_idx(c2idx, c1idx, targetIdx, 110.0)

            if ({atomIndex=targetIdx}.group == "PRO") {
                set_dihedral_idx(c3idx, c2idx, c1idx, targetIdx, -57.0)
            }

            # Record and restore target
            pt = {atomIndex=targetIdx}.xyz
            {atomIndex=targetIdx}.xyz = cp
        }

        # If target not at desired location
        if (distance(pt, {atomIndex=targetIdx}) > kDtolerance) {
            var okCount = 0
            gTargetPt = pt
            var xcount = 0
            gOK = FALSE
            while ((xcount < 20) and (not gOK)) {

                # Rotate on nWard rotor set to move it there
                tug_track_idx(targetIdx, pt, TRUE, FALSE)
                xcount++
            }
        }
        else {
            gOK = TRUE
            okCount++
        }

        # If sucessful
        if (gOK == TRUE) {

            # Adust any side atoms
            repair_sc(targetIdx, TRUE)
        }

        # Else fail
        else {
            break
        }

        # If no movement in 4 tries, we are done
        if (okCount > 3) {
            break
        }

    }   # endwhile (targetIdx != gNanchorIdx) {
}

# gPlicoRecord is maintained by the macro pilcoRecord
function translate_selected_record(pt) {
    if (gPlicoRecord != "") {
        plico_record(format("select %s;translateSelected %s;", {selected}, pt))
    }
    translateSelected @pt
}

# gPlicoRecord is maintained by the macro pilcoRecord
function rotate_selected_record(pivotIdx, axis, a) {
    if (gPlicoRecord != "") {
        plico_record(format("select %s;", {selected}))
        plico_record(format("rotateSelected {atomIndex=%d} @%s @%s;",
            pivotIdx, axis, a))
    }
    rotateSelected {atomIndex=pivotIdx} @axis @a
}

function collect_sc_rotors(no, iChain) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    var scBondIdxs = array()
    for (var iNo = no; iNo >= 0; iNo--) {
        var ile = 0
        switch ({(atomno=iNo) and (chain=iChain)
            and (file=f) and (model=m)}.atomName) {
        case "CA" :
            return scBondIdxs # Early exit since break 1 appears broken
        case "CZ" :
            if ({(atomno=iNo) and (chain=iChain)
                and (file=f) and (model=m)}.group == "TYR") {
                break
            }
        case "CE" :
            if ({(atomno=iNo) and (chain=iChain)
                and (file=f) and (model=m)}.group == "MET") {
                break
            }
        case "CG1" :
            if ({(atomno=iNo) and (chain=iChain)
                and (file=f) and (model=m)}.group == "VAL") {
                break
            }
            if ({(atomno=iNo) and (chain=iChain)
                and (file=f) and (model=m)}.group == "ILE") {
                ile = 1
            }
        case "NE" :
        case "CD" :
        case "SD" :
        case "CG" :
        case "CB" :
            scBondIdxs += {(atomno=@{iNo+1+ile}) and (chain=iChain)
                and (file=f) and (model=m)}.atomIndex
            scBondIdxs += {(atomno=@{iNo+0}) and (chain=iChain)
                and (file=f) and (model=m)}.atomIndex
            if ({(atomno=iNo) and (chain=iChain)
                and (file=f) and (model=m)}.atomName%2 == "CG") {
                scBondIdxs += {(atomno=@{iNo-1}) and (chain=iChain)
                    and (file=f) and (model=m)}.atomIndex
                scBondIdxs += {(atomno=@{iNo-4}) and (chain=iChain)
                    and (file=f) and (model=m)}.atomIndex
            }
            else if ({(atomno=iNo) and (chain=iChain)
                and (file=f) and (model=m)}.atomName == "CB") {
                scBondIdxs += {(atomno=@{iNo-3}) and (chain=iChain)
                    and (file=f) and (model=m)}.atomIndex
                scBondIdxs += {(atomno=@{iNo-4}) and (chain=iChain)
                    and (file=f) and (model=m)}.atomIndex
            }
            else {
                scBondIdxs += {(atomno=@{iNo-1}) and (chain=iChain)
                    and (file=f) and (model=m)}.atomIndex
                scBondIdxs += {(atomno=@{iNo-2}) and (chain=iChain)
                    and (file=f) and (model=m)}.atomIndex
            }
            break
        }

    }

    return scBondIdxs
}

# Drag Side Chain
function drag_sc() {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    var iNo = {atomIndex=gSCidx}.atomno
    var iChain  = {atomIndex=gSCidx}.chain
    if ({atomIndex=gSCidx}.group != "PRO") {

        var scBondIdxs = collect_sc_rotors( iNo, iChain)
        var numChi = scBondIdxs.size / 4
        var dist = distance({atomIndex=gSCidx}.xyz, gSCpt)

        var scSet = ({})
        if (gSCcheck) {
            scSet = get_sc_set(gSCidx, iChain)
        }

        # For all rotor combinations
        var dh = array()
        for (var i = 0; i < numChi; i++) {
            dh += angle({atomIndex=@{scBondIdxs[4+(4*i)]}},
                {atomIndex=@{scBondIdxs[3+(4*i)]}},
                {atomIndex=@{scBondIdxs[2+(4*i)]}},
                {atomIndex=@{scBondIdxs[1+(4*i)]}})
        }
        for (var i = 0; i < numChi; i++) {
            var rot = -120
            for (var j = 0; j < 6; j++) {
                rot += 60*j
                select_add_sc(scBondIdxs[1+(4*i)])
                set_dihedral_idx(scBondIdxs[4+(4*i)], scBondIdxs[3+(4*i)],
                    scBondIdxs[2+(4*i)], scBondIdxs[1+(4*i)], rot)
                var newDist = distance({atomIndex=gSCidx}.xyz, gSCpt)
                if (gSCcheck) {
                    var colliders = (within(kCtolerance, FALSE, scSet)
                        and not connected(scSet) and not {scSet})
                    if (colliders.size > 0) {
                        continue
                    }
                }

                # Find the best
                if (newDist < dist) {
                    dist = newDist
                    for (var k = 0; k < numChi; k++) {
                        dh[k+1] = angle({atomIndex=@{scBondIdxs[4+(4*k)]}},
                        {atomIndex=@{scBondIdxs[3+(4*k)]}},
                        {atomIndex=@{scBondIdxs[2+(4*k)]}},
                        {atomIndex=@{scBondIdxs[1+(4*k)]}})
                    }
                }
            }
        }

        # Now set the best
        for (var i = 0; i < numChi; i++) {
            select_add_sc(scBondIdxs[1+(4*i)])
            set_dihedral_idx(scBondIdxs[4+(4*i)], scBondIdxs[3+(4*i)],
                scBondIdxs[2+(4*i)], scBondIdxs[1+(4*i)], dh[i+1])
        }
    }
    else { # PRO - toggle between puckers up and down
        var icd = {(atomno=@{iNo+1}) and (chain=iChain)
            and (file=f) and (model=m)}.atomIndex
        var icb = {(atomno=@{iNo-1}) and (chain=iChain)
            and (file=f) and (model=m)}.atomIndex
        var ica = {(atomno=@{iNo-4}) and (chain=iChain)
            and (file=f) and (model=m)}.atomIndex
        var in = {(atomno=@{iNo-5}) and (chain=iChain)
            and (file=f) and (model=m)}.atomIndex
        select {atomIndex=gSCidx}

        if (angle({atomIndex=ica}, {atomIndex=in},
            {atomIndex=icd}, {atomIndex=gSCidx}) < -10.0) {
            set_dihedral_idx(ica, in, icd, gSCidx, 8.7)
            set_angle_idx(in, icd, gSCidx, 110.0)
            set_distance_idx(icd, gSCidx, 1.5)
        }
        else {
            set_dihedral_idx(ica, in, icd, gSCidx, -29.5)
            set_angle_idx(in, icd, gSCidx, 108.8)
            set_distance_idx(icd, gSCidx, 1.5)
        }
    }

    draw gSCcircle CIRCLE {atomIndex=gSCidx} MESH NOFILL
    gSCpt = {atomIndex=gSCidx}.xyz
}

# Fix side chain collisions
function fix_sc_collision_2(idx) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    gOk2 = FALSE
    var iNo = {atomIndex=idx}.atomno
    var iChain = {atomIndex=idx}.chain
    var resno = {(atomno=iNo) and (chain=iChain)
        and (file=f) and (model=m)}.resno

    # Get SC terminus
    while (resno == {(atomno=iNo) and (chain=iChain)
        and (file=f) and (model=m)}.resno) {
        iNo++
    }
    iNo--

    var sc = array()
    var iBno = iNo
    while ({(atomno=iBno) and (chain=iChain)
        and (file=f) and (model=m)}.atomName != "CB") {
        sc += {(atomno=iBno) and (chain=iChain)
            and (file=f) and (model=m)}
        iBno--
    }
    var cbidx = {(atomno=iBno) and (chain=iChain)
        and (file=f) and (model=m)}.atomIndex

    var scBondIdxs = collect_sc_rotors( iNo, iChain)
    var numChi = scBondIdxs.size / 4

    # For all rotor combinations
    for (var i = 0; i < numChi; i++) {
        var rot = -120
        for (var j = 0; j < 6; j++) {
            rot += 60
            select_add_sc(scBondIdxs[1+(4*i)])
            set_dihedral_idx(scBondIdxs[1+(4*i)], scBondIdxs[2+(4*i)],
                scBondIdxs[3+(4*i)], scBondIdxs[4+(4*i)], rot)

            # If no collision, exit
            colliders = (within(kCtolerance, FALSE, {sc})
                and not {atomIndex=cbidx} and not {sc})

            # If it is with water, delete the water
            for (var c = 1; c < colliders.size; c++ ) {
                if (colliders[c].group = "HOH") {
                    delete {atomIndex=@{colliders[c].atomIndex}}
                    colliders = {colliders and not @{colliders[c]}}
                }
            }

            if (colliders.size == 0) {
                gOk2 = TRUE
                return # Early exit since break 1 appears broken
            }

        }
    }
}

function is_moveable_sc(aIdx) {

    var ret = (({atomIndex=aIdx}.group != "PRO")
        or ({atomIndex=aIdx}.atomName == "CG"))
    switch({atomIndex=aIdx}.atomName) {
    case "N":
    case "CA":
    case "C":
    case "CB":
    case "O":
    case "O4\'":
        ret = FALSE
        break
    }
    return ret
}

function is_rotor_avail(i1idx, i2idx) {
    var ret = TRUE
    if (i1idx > i2idx) {
        var idx = @i1idx
        i1idx = @i2idx
        i2idx = @idx
    }

    for (var i = 1; i <= gFreeze.size; i += 2) {
        if ((gFreeze[i] == i1idx) and (gFreeze[i+1] == i2idx)) {
            ret = FALSE
            break
        }
    }

    return ret
}

function collect_bb_rotors(nWard) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    var anchorNo = (nWard
        ? ((gNanchorIdx >= 0) ? {atomIndex=gNanchorIdx}.atomno : gMinNo)
        : ((gCanchorIdx >= 0) ? {atomIndex=gCanchorIdx}.atomno : gMaxNo))
    var cargoNo = (nWard
        ? ((gNcargoIdx >= 0) ? {atomIndex=gNcargoIdx}.atomno
        : {atomIndex=gCcargoIdx}.atomno)
        : {atomIndex=gCcargoIdx}.atomno)
    var rotors = array()
    if (cargoNo < anchorNo) {

        for (var iNo = cargoNo; iNo <= anchorNo; iNo++) {
            if ({(atomno=iNo) and (chain=gChain)
                and (file=f) and (model=m)}.atomName == "CA") {
                if (is_rotor_avail(iNo)) {
                    if (({(atomno=iNo) and (chain=gChain)
                        and (file=f) and (model=m)}.group != "PRO") and (iNo > cargoNo)) { # phi
                        rotors += [{(atomno=@{get_cm_no(iNo-1)}) and (chain=gChain)
                            and (file=f) and (model=m)}.atomIndex,
                            {(atomno=@{iNo-1}) and (chain=gChain)
                                and (file=f) and (model=m)}.atomIndex]
                        rotors += [{(atomno=@{iNo}) and (chain=gChain)
                            and (file=f) and (model=m)}.atomIndex,
                            {(atomno=@{iNo+1}) and (chain=gChain)
                                and (file=f) and (model=m)}.atomIndex]
                    }
                    if (iNo != (anchorNo-1)) { # psi
                        rotors += [{(atomno=@{iNo-1}) and (chain=gChain)
                            and (file=f) and (model=m)}.atomIndex,
                            {(atomno=@{iNo}) and (chain=gChain)
                                and (file=f) and (model=m)}.atomIndex]
                        rotors += [{(atomno=@{iNo+1}) and (chain=gChain)
                            and (file=f) and (model=m)}.atomIndex,
                            {(atomno=@{get_np_no(iNo+2)}) and (chain=gChain)
                                and (file=f) and (model=m)}.atomIndex]
                    }
                }
            }
        }
    }
    else {

        for (var iNo = cargoNo; iNo >= anchorNo; iNo--) {
            if ({(atomno=iNo) and (chain=gChain)
                and (file=f) and (model=m)}.atomName == "CA") {
                if (is_rotor_avail(iNo)) {
                    if ((iNo != (anchorNo-1)) and (iNo < cargoNo)) { # psi
                        rotors += [{(atomno=@{get_np_no(iNo+2)}) and (chain=gChain)
                            and (file=f) and (model=m)}.atomIndex,
                            {(atomno=@{iNo+1}) and (chain=gChain)
                                and (file=f) and (model=m)}.atomIndex]
                        rotors += [{(atomno=@{iNo}) and (chain=gChain)
                            and (file=f) and (model=m)}.atomIndex,
                            {(atomno=@{iNo-1}) and (chain=gChain)
                                and (file=f) and (model=m)}.atomIndex]
                    }
                    if ({(atomno=iNo) and (chain=gChain)
                        and (file=f) and (model=m)}.group != "PRO") { # phi
                        rotors += [{(atomno=@{iNo+1}) and (chain=gChain)
                            and (file=f) and (model=m)}.atomIndex,
                            {(atomno=@{iNo}) and (chain=gChain)
                                and (file=f) and (model=m)}.atomIndex]
                        rotors += [{(atomno=@{iNo-1}) and (chain=gChain)
                            and (file=f) and (model=m)}.atomIndex,
                            {(atomno=@{get_cm_no(iNo-1)}) and (chain=gChain)
                                and (file=f) and (model=m)}.atomIndex]
                    }
                }
            }
        }
    }

    if (nWard) {
        gNrotors = rotors
    }
    else {
        gCrotors = rotors
    }
}

function collect_rotors() {
    collect_bb_rotors(FALSE)
    collect_bb_rotors(TRUE)
}

function tug_sc(pt) {

    # If destination atom defined
    if (gDestAtomIdx >= 0) {
        var v = {atomIndex=gDestAtomIdx}.xyz - {atomIndex=gSCidx}.xyz
        if (abs(angle({atomIndex=gDestAtomIdx}.xyz, {0 0 0}, pt)) < 90) {
            pt = -v/20.0
        }
        else {
            pt = v/20.0
        }
    }
    gSCpt += pt
    draw arrow {atomIndex=gSCidx} @gSCpt
}

function set_colors() {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    select ((file=f) and (model=m))
    color {selected} @gScheme
    color {atomIndex=g1pivotIdx} green
    color {atomIndex=g2pivotIdx} green
    color @gCargoSet @gAltScheme
    select {(atomIndex=gCcargoIdx) or (atomIndex=gNcargoIdx)
        or (atomIndex=gCanchorIdx) or (atomIndex=gNanchorIdx)}
    halo on
    select {atomIndex=gDestAtomIdx}
    star on
    select none
}

function clear_atom_idxs() {
    gCcargoIdx = -1
    gNcargoIdx = -1
    gCanchorIdx = -1
    gNanchorIdx = -1
    g1pivotIdx = -1
    g2pivotIdx = -1
    g1dynamicIdx = -1
    g2dynamicIdx = -1
    gDestAtomIdx = -1
    gSCidx = -1
}

function timed_out (s) {
    timeout ID"tug" OFF
    p = prompt(format("%s - Undo?", s), "Yes|No", TRUE)
    if (p == "Yes") {
        gBusy = FALSE
        background ECHO yellow
        restore state gState
        connect
        select gCargoSet
        refresh
        quit
    }
}

function record_drag() {
    var ls = format("select %s;", {selected})
    ls += format("gCanchorIdx = %d;", gCanchorIdx)
    ls += format("gCanchorNo = %d;", gCanchorNo)
    ls += format("gNanchorIdx = %d;", gNanchorIdx)
    ls += format("gNanchorNo = %d;", gNanchorNo)
    ls += format("gCcargoIdx = %d;", gCcargoIdx)
    ls += format("gNcargoIdx = %d;", gNcargoIdx)
    ls += format("gCcargoNo = %d;", gCcargoNo)
    ls += format("gNcargoNo = %d;", gNcargoNo)
    ls += format("gDestAtomIdx = %d;", gDestAtomIdx)
    ls += format("g1pivotIdx = %d;", g1pivotIdx)
    ls += format("g2pivotIdx = %d;", g2pivotIdx)
    ls += format("gOkCollide = %s;", gOkCollide)
    ls += format("gChain = \"%s\";", gChain)
    ls += format("gMinNo = %d;", gMinNo)
    ls += format("gMaxNo = %d;", gMaxNo)
    ls += format("gCargoSet = %s;", gCargoSet)
    ls += format("gSCidx = %d;", gSCidx)
    ls += format("gSCcircle = %d;", gSCcircle)
    ls += format("gSCpt = %s;", gSCpt)
    ls += "collect_rotors();"
    ls += "tug_drag_done_mb();"
    plico_record(ls)
}

# Pick call-back for freeze
function tug_pick_cb() {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    if (_pickInfo[3][6] == "bond") {
        var sel = {selected}
        var i = _pickInfo.find(":")
        var iChain = _pickInfo[i+1]
        i = _pickInfo.find("#")
        var a1no = 0 + _pickInfo[i+1][i+3]
        j = _pickInfo[i+1][9999].find("#")
        var a2no = 0 + _pickInfo[i+j+1][i+j+3]
        var i1idx = {(atomno=a1no) and (chain=iChain)
            and (file=f) and (model=m)}.atomIndex
        var i2idx = {(atomno=a2no) and (chain=iChain)
            and (file=f) and (model=m)}.atomIndex
        if (({atomIndex=i1idx}.atomName == "CA")
            or ({atomIndex=i2idx}.atomName == "CA")) {
            if (({atomIndex=i1idx}.atomName != "CB")
                and ({atomIndex=i2idx}.atomName != "CB")) {
                if (i1idx > i2idx) {
                    idx = 0 + i1idx
                    i1idx = 0 + i2idx
                    i2idx = 0 + idx
                }
                select {atomIndex=i1idx} or {atomIndex=i2idx}

                for (i = 1; i <= gFreeze.size; i += 2) {
                    if ((gFreeze[i] == i1idx) and (gFreeze[i+1] == i2idx)) {
                        gFreeze[i] == -1
                        color bonds NONE
                        break
                    }
                }
                if (i > gFreeze.size) {
                    gFreeze += i1idx
                    gFreeze += i2idx
                    color bonds lightblue
                }
            }
        }
        select {sel}
    }
}

# Bound to LEFT-UP by tug_enable_drag
function tug_drag_done_mb() {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    if (not gBusy) {
        if (gPlicoRecord != "") {
            record_drag()
        }

        # Move by rotation on rotor sets, smallest first
        gBusy = TRUE
        background ECHO pink
        refresh

        # If side chain mode
        if (gSCidx >= 0) {
            drag_sc()
        }

        # Else
        else if (not gTow) {
            gOK = TRUE
            timeout ID"tug" 20.0 "timed_out(\"Tug timed out\")"
            if ((gCrotors.size < gNrotors.size) or (gNanchorIdx < 0)) {
                if (gCrotors.size > 4) {
                    tug_track_c()
                }
                if (gOK and (gNrotors.size > 4)) {
                    tug_track_n()
                }
            }
            else {
                if (gNrotors.size > 4) {
                    tug_track_n()
                }
                if (gOK and (gCrotors.size > 4)) {
                    tug_track_c()
                }
            }
            timeout ID"tug" OFF

            # If anchor angles acute, fail
            if (gOK == TRUE) {
                if (gCanchorIdx >= 0) {
                    var ic = get_cward_bb_idx(gCanchorIdx, gChain)
                    var in = get_nward_bb_idx(gCanchorIdx, gChain)
                    if ((ic >= 0) and
                        angle({atomIndex=ic}, {atomIndex=gCanchorIdx}, {atomIndex=in})
                        < 100.0) {
                        gOK = FALSE
                    }
                }
                if (gNanchorIdx >= 0) {
                    var ic = get_cward_bb_idx(gNanchorIdx, gChain)
                    var in = get_nward_bb_idx(gNanchorIdx, gChain)
                    if ((in >= 0) and
                        angle({atomIndex=ic}, {atomIndex=gNanchorIdx}, {atomIndex=in})
                        < 100.0) {
                        gOK = FALSE
                    }
                }
            }

            # If too far
            if (not gOK) {
                timed_out("TUG TOO FAR!")
            }

            # Else OK
            else {

                select ((atomno >= gNanchorNo) and (atomno <= gCanchorNo)
                    and (chain = gChain) and (file=f) and (model=m))
                var idx = {
                    (atomno=@{{(chain=gChain) and (file=f) and (model=m)}.atomno.min})
                    and (chain=gChain) and (file=f) and (model=m)}.atomIndex


                var ihc = 0
                for (ihc = 0; ihc < 10; ihc++) {
                    handle_collisions( idx)
                    if (count_collisions(({})).size == 0) {
                        break
                    }
                }
                if (ihc == 10) {
                    timed_out("Unable to handle all collisions!")
                }
            }
        }
        select {gCargoSet}
        gBusy = FALSE
        background ECHO yellow
        refresh
    }
}

# Bound to ALT-SHIFT-LEFT-DRAG by tug_enable_drag
function tug_drag_2_mb() {
    tug_drag_mb(TRUE)
}

# Bound to ALT-LEFT-DRAG by tug_enable_drag
function tug_drag_mb(alt) {
    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
        var axis = {0 0 0}
        if (distance(pt,  {0 0 0}) > 0.004) {
            # If sidechain mode
            if (gSCidx >= 0) {
                if ({atomIndex=gSCidx}.atomName == "O") {
                    dir = ((abs(dx) > abs(dy))
                        ? ((dx < 0) ? 10 : -10)
                        : ((dy < 0) ? 1 : -1))
                    counter_rotate(gSCidx, dir, not alt)
                }
                else {
                    gSCcheck = not alt
                    tug_sc(pt)
                }
            }

            # Else
            else {

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

                # If destination atom defined
                if (gDestAtomIdx >= 0) {
                    var v = {atomIndex=gDestAtomIdx}.xyz - {selected}.xyz
                    if (abs(angle({atomIndex=gDestAtomIdx}.xyz, {0 0 0}, pt)) < 90) {
                        pt = -v/20.0
                    }
                    else {
                        pt = v/20.0
                    }
                }

                # Move the cargo
                select {gCargoSet}

                # If pivots defined, rotate it
                if (g1pivotIdx >= 0) {

                    # If two pivots
                    if (g2pivotIdx >= 0) {
                        axis = {atomIndex=g2pivotIdx}
                    }

                    # Else
                    else {
                        axis = cross(pt, {0 0 0}) + {atomIndex=g1pivotIdx}.xyz
                    }

                    dir = ((abs(dx) > abs(dy))
                        ? ((dx < 0) ? 2 : -2)
                        : ((dy < 0) ? 2 : -2))
                    rotate_selected_record(g1pivotIdx, axis, dir)

                }

                # Else translate it
                else {
                    translate_selected_record(pt)
                }

                # If collisions
                var cNotSels = (within(kCtolerance, FALSE, {selected})
                    and not {gMovingSet})
                if ((cNotSels.size > 0) and (not alt)) {
                    gOk2 = TRUE
                    for (var i = 1; i <= cNotSels.size;  i++) {

                        # If net collision vector same as move vector
                        cSels = (within(kCtolerance, FALSE, cNotSels[i]) and {selected})
                        for (var j = 1; j <= cSels.size;  j++) {
                            var v1 = cNotSels[i].xyz - cSels[j].xyz
                            if (abs(angle(v1, {0 0 0}, pt)) < 90) {

                                # If tow mode
                                if (gTow) {

                                    # Make a dynamic pivot
                                    if (g1pivotIdx < 0) {
                                        g1pivotIdx = cSels[j].atomIndex
                                        g1dynamicIdx = cNotSels[i].atomIndex
                                        color {atomIndex=g1pivotIdx} lightgreen
                                        set_distance_idx(cNotSels[i].atomIndex,
                                            cSels[j].atomIndex,
                                            kCtolerance + kDtolerance)
                                    }
                                    else if (g2pivotIdx < 0) {
                                        g2pivotIdx = cSels[j].atomIndex
                                        g2dynamicIdx = cNotSels[i].atomIndex
                                        color {atomIndex=g2pivotIdx} lightgreen
                                        set_distance_idx(cNotSels[i].atomIndex,
                                            cSels[j].atomIndex,
                                            kCtolerance + kDtolerance)
                                    }
                                    else {
                                        gOk2 = FALSE
                                    }
                                }
                                else {

                                    # Try to resolve
                                    select cSels[j]
                                    var idx = {(atomno=@{{(chain=gChain)
                                        and (file=f) and (model=m)}.atomno.min})
                                        and (chain=gChain) and (file=f)
                                        and (model=m)}.atomIndex
                                    handle_collisions( idx)
                                }
                            }
                        } # endfor
                        if (not gOk2) {
                            break
                        }
                    } # endfor

                    # If unable
                    if (not gOk2) {

                        # Back off
                        background ECHO pink
                        delay 1
                        if (g1pivotIdx >= 0) {
                            rotate_selected_record(g1pivotIdx, axis, -a)
                        }
                        else {
                            translate_selected_record(-pt)
                        }
                        background ECHO yellow
                    }
                }
            }

            # If dynamic pivots
            if (g1dynamicIdx >= 0) {
                var v1 = {atomIndex=g1dynamicIdx}.xyz - {atomIndex=g1pivotIdx}.xyz
                if (abs(angle(v1, {0 0 0}, pt)) > 90) {
                    color {atomIndex=g1pivotIdx} @gAltScheme
                    g1pivotIdx = -1
                    g1dynamicIdx = -1

                }
            }
            if (g2dynamicIdx >= 0) {
                var v1 = {atomIndex=g2dynamicIdx}.xyz - {atomIndex=g2pivotIdx}.xyz
                if (abs(angle(v1, {0 0 0}, pt)) > 90) {
                    color {atomIndex=g2pivotIdx} @gAltScheme
                    g2pivotIdx = -1
                    g2dynamicIdx = -1
                }
            }

            gMouseX = _mouseX
            gMouseY = _mouseY
        }
        select {gCargoSet}
        gBusy = FALSE
    }
}

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

# Called by tug_cargo_mb
function tug_enable_drag() {
    gEcho = "__________TUG__________|ALT-CLICK=mark block|SHIFT-CLICK=anchors" +
        "|ALT-CTRL-CLICK=pivots|ALT-SHIFT-CLICK=dest atom|ALT-DRAG=move" +
        "|SHIFT-ALT-DRAG=alt move|CLICK bond=freeze|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-SHIFT-LEFT-DOWN" "tug_mark_mb";
    bind "ALT-SHIFT-LEFT-UP" "tug_drag_done_mb";
    bind "ALT-LEFT-DRAG" "tug_drag_mb";
    bind "ALT-SHIFT-LEFT-DRAG" "tug_drag_2_mb";

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

    bind "ALT-CTRL-LEFT-CLICK" "_pickAtom";
    bind "ALT-CTRL-LEFT-CLICK" "+:tug_pivot_mb";

    bind "ALT-SHIFT-LEFT-CLICK" "_pickAtom";
    bind "ALT-SHIFT-LEFT-CLICK" "+:tug_dest_atom_mb";
}

# Bound to SHIFT-LEFT-CLICK by tug_cargo_mb
function tug_anchor_mb() {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    if ({atomIndex=_atomPicked}.chain == gChain) {
        var aPidx = get_sc_bb_idx( _atomPicked, gChain)

        var pno = {atomIndex=aPidx}.atomno
        if (pno > {atomIndex=gCcargoIdx}.atomno) {
            select {atomIndex=gCanchorIdx}
            halo off
            if (gCanchorIdx == aPidx) {
                gCanchorIdx = -1
                gCanchorNo = gMaxNo + 1
            }
            else {
                gCanchorIdx = aPidx
                gCanchorNo = {atomIndex=gCanchorIdx}.atomno
                select {atomIndex=gCanchorIdx}
                halo on
            }
            collect_bb_rotors(FALSE)
        }
        else if (pno < {atomIndex=gNcargoIdx}.atomno) {
            select {atomIndex=gNanchorIdx}
            halo off
            if (gNanchorIdx == aPidx) {
                gNanchorIdx = -1
                gNanchorNo = gMinNo - 1
            }
            else {
                gNanchorIdx = aPidx
                gNanchorNo = {atomIndex=gNanchorIdx}.atomno
                select {atomIndex=gNanchorIdx}
                halo on
            }
            collect_bb_rotors(TRUE)
        }
        else {
            tow_cargo_mb()
        }

        # Get moving atoms set
        gMovingSet = {((atomno < gCanchorNo) and (atomno > gNanchorNo)
            and (chain=gChain) and (file=f) and (model=m))}
    }
    select {gCargoSet}
}

# Bound to ALT-SHIFT-LEFT-CLICK by tug_cargo_mb
function tug_dest_atom_mb() {
    var aOk = TRUE
    if ({atomIndex=_atomPicked}.chain == gChain) {

        var pno = {atomIndex=_atomPicked}.atomno
        if ((pno <= {atomIndex=gCcargoIdx}.atomno)
            and (pno >= {atomIndex=gNcargoIdx}.atomno)) {
            aOk = FALSE
        }
    }
    if (aOk) {
        select {atomIndex=gDestAtomIdx}
        star off
        if (gDestAtomIdx == _atomPicked) {
            gDestAtomIdx = -1
        }
        else {
            gDestAtomIdx = _atomPicked
            select {atomIndex=gDestAtomIdx}
            star on
        }
        select {gCargoSet}
    }
}

# Bound to CTRL-LEFT-CLICK by tug_cargo_mb
function tug_pivot_mb() {
    if (g1pivotIdx == _atomPicked) {
        color {atomIndex=g1pivotIdx} @gScheme
        if (g2pivotIdx >= 0) {
            g1pivotIdx = g2pivotIdx
            g2pivotIdx = -1
            g2dynamicIdx = -1
        }
        else {
            g1pivotIdx = -1
            g1dynamicIdx = -1
        }
    }
    else if (g2pivotIdx == _atomPicked) {
        color {atomIndex=g2pivotIdx} @gScheme
        g2pivotIdx = -1
        g2dynamicIdx = -1
    }
    else if (g1pivotIdx >= 0) {
        if (g2pivotIdx >= 0) {
            color {atomIndex=g2pivotIdx} @gScheme
        }

        g2pivotIdx = _atomPicked
        g2dynamicIdx = -1
        color {atomIndex=g2pivotIdx} green
    }
    else {
        g1pivotIdx = _atomPicked
        g1dynamicIdx = -1
        color {atomIndex=g1pivotIdx} green
    }
    select {gCargoSet}
}

# Bound to SHIFT-LEFT-CLICK by plico_tug
function tow_cargo_mb() {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    gTow = TRUE
    gChain = {atomIndex=_atomPicked}.chain
    gMinNo = {(chain=gChain) and (file=f) and (model=m)}.atomno.min
    gMaxNo = {(chain=gChain) and (file=f) and (model=m)}.atomno.max
    gCcargoIdx = -1
    gNcargoIdx = -1
    gCanchorIdx = -1
    gCanchorNo = gMaxNo + 1
    gNanchorIdx = -1
    gNanchorNo = gMinNo - 1

    # Highlight cargo cluster
    select {(chain=gChain) and (file=f) and (model=m)}
    gCargoSet = {selected}
    gMovingSet = {selected}
    set_colors()

    # Enable dragging
    tug_enable_drag()
    select {gCargoSet}
    halo off
    var es = gEcho.replace("anchors","mark chain")
    echo @es
    unbind "SHIFT-LEFT-CLICK"
    bind "SHIFT-LEFT-CLICK" "_pickAtom";
    bind "SHIFT-LEFT-CLICK" "+:tow_cargo_mb";
}

# Bound to ALT-LEFT-CLICK by plico_tug or called by plicotoab.toabCargoMB
function tug_cargo_mb() {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)

    # If O or movable side chain atom picked
    if (({atomIndex=_atomPicked}.atomName = "O")
        or (is_moveable_sc( _atomPicked))) {
        if (gSCidx >= 0) {
            draw gSCcircle DELETE
        }
        if (gSCidx == _atomPicked) {
            gSCidx = -1
        }
        else {
            gSCidx = _atomPicked
            gSCpt = {atomIndex=gSCidx}.xyz
            draw gSCcircle CIRCLE {atomIndex=gSCidx} MESH NOFILL
        }
    }
    else {
        if ({atomIndex=_atomPicked}.chain != gChain) {
            if (gTow) {
                select {(chain=gChain) and (file=f) and (model=m)}
                color {selected} @gScheme
            }
            gChain = {atomIndex=_atomPicked}.chain
            select ({atomIndex=gCcargoIdx} or {atomIndex=gNcargoIdx}
                or {atomIndex=gCanchorIdx} or {atomIndex=gNanchorIdx})
            halo off
            gCcargoIdx = -1
            gNcargoIdx = -1
            gCanchorIdx = -1
            gNanchorIdx = -1
        }
        gTow = FALSE
        gMinNo = {(chain=gChain) and (file=f) and (model=m)}.atomno.min
        gMaxNo = {(chain=gChain) and (file=f) and (model=m)}.atomno.max
        if (gNanchorIdx < 0) {
            gNanchorNo = gMinNo - 1
        }
        if (gCanchorIdx < 0) {
            gCanchorNo = gMaxNo + 1
        }
        var aPidx = get_sc_bb_idx( _atomPicked, gChain)

        gSCidx = -1
        draw gSCcircle DELETE

        # If existing cWard cargo picked
        if (gCcargoIdx == aPidx) {

            # Clear the highlight
            select {atomIndex=gCcargoIdx}
            halo off

            # If nWard cargo exists, mark it as the cWard cargo
            if (gNcargoIdx != gCcargoIdx) {
                gCcargoIdx = get_cp_idx(gNcargoIdx)
                gCcargoNo = {atomIndex=gCcargoIdx}.atomno
            }
            else {
                gCcargoIdx = -1
                gNcargoIdx = -1
            }
        }
        else if (gNcargoIdx == aPidx) {
            select {atomIndex=gNcargoIdx}
            halo off
            gNcargoIdx = get_nm_idx(gCcargoIdx)
            gNcargoNo = {atomIndex=gNcargoIdx}.atomno
        }
        else if (gCcargoIdx >= 0) {

            var no = {atomIndex=aPidx}.atomno

            # If pick is nWard of it
            if (no < {atomIndex=gCcargoIdx}.atomno) {

                # If exists, clear its highlight
                if (gNcargoIdx != gCcargoIdx) {
                    select {atomIndex=gNcargoIdx}
                    halo off
                }

                # Set new nWard cargo and highlight it
                gNcargoIdx = get_nm_idx(aPidx)
                gNcargoNo = {atomIndex=gNcargoIdx}.atomno
            }

            # Else cWard
            else {

                # Clear its old highlight
                select {atomIndex=gCcargoIdx}
                if (gNcargoIdx != gCcargoIdx) {
                    halo off
                }

                # Set new cWard cargo and highlight
                gCcargoIdx = get_cp_idx(aPidx)
                gCcargoNo = {atomIndex=gCcargoIdx}.atomno
            }
        }

        # Else no cWard cargo
        else {

            # Set new cWard cargo and highlight
            gCcargoIdx = get_cp_idx(aPidx)
            gCcargoNo = {atomIndex=gCcargoIdx}.atomno
            gNcargoIdx = get_nm_idx(gCcargoIdx)
            gNcargoNo = {atomIndex=gNcargoIdx}.atomno

            # Set default cWard anchor at cWard N
            var iNo = gMaxNo
            for (; iNo > 0; iNo--) {
                if ({(atomno=iNo) and (chain=gChain)
                    and (file=f) and (model=m)}.atomName == "N") {
                    break;
                }
            }
            gCanchorIdx = {(atomno=iNo) and (chain=gChain)
                and (file=f) and (model=m)}.atomIndex
            gCanchorNo = {atomIndex=gCanchorIdx}.atomno
        }

        # If any anchor now inside cargo cluster, kill it
        if ({atomIndex=gCanchorIdx}.atomno <= {atomIndex=gCcargoIdx}.atomno) {
            gCanchorIdx = -1
            gCanchorNo = gMaxNo + 1
        }
        if ({atomIndex=gNanchorIdx}.atomno >= {atomIndex=gNcargoIdx}.atomno) {
            gNanchorIdx = -1
            gNanchorNo = gMinNo - 1
        }

        # Highlight cargo cluster
        select_nward_idx(gCcargoIdx, gNcargoIdx)
        gCargoSet = {selected}
        set_colors()

        # Collect the rotor sets
        collect_rotors()

        # Get moving atoms set
        gMovingSet = {((atomno < gCanchorNo) and (atomno > gNanchorNo)
            and (chain=gChain) and (file=f) and (model=m))}
    }

    # Enable dragging
    if (gToab) {
        toabEnableDrag()
    }
    else {
        tug_enable_drag()
    }

    select {gCargoSet}
}

# Top level of Tug
function plico_tug() {

    # 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
        }
    }

    gPlico = "TUG"
    plico_prelim(TRUE)
    gBondPicking = bondPicking
    set bondPicking TRUE
    set PickCallback "jmolscript:tug_pick_cb"

    gEcho = ("_________TUG_________|ALT-CLICK=mark block|SHIFT-CLICK=mark chain" +
        "|CLICK bond=freeze|DOUBLE-CLICK=exit")
    echo @gEcho
    gCrotors = array()
    gNrotors = array()
    clear_atom_idxs()

    bind "ALT-LEFT-CLICK" "_pickAtom";
    bind "ALT-LEFT-CLICK" "+:tug_cargo_mb";
    bind "SHIFT-LEFT-CLICK" "_pickAtom";
    bind "SHIFT-LEFT-CLICK" "+:tow_cargo_mb";
    bind "DOUBLE" "tug_exit";
}

# Bound to DOUBLE by plico_tug
function tug_exit() {
    if (plico_exit) {
        set bondPicking gBondPicking
        set PickCallback NONE
        select all
        color bonds none
    }
}

# End of TUG.SPT

Contributors

Remig