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

Latest revision as of 17:15, 12 April 2016

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. A full description of its capabilities can be found here.

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
#   v1.20 beta    4/12/2016 -axis is now a reserved word
#
#   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
gTow = false
g1dynamicIdx = -1
g2dynamicIdx = -1
gSCcheck = true
gBondPicking = false
gFreeze = array()
gToab = false


function get_cp_idx (idx) {
    var no = {atomIndex=idx}.atomno
    while ((no < gMaxNo) and ({(atomno=no) and (chain=gChain)
        and thisModel}.atomName != "C")) {
        no++
    }
    return ({(atomno=no) and (chain=gChain) and thisModel}.atomIndex)
}

function get_cm_no (iNo) {
    while ((iNo > 0) and ({(atomno=iNo) and (chain=gChain)
        and thisModel}.atomName != "C")) {
        iNo--
    }
    return iNo
}

function get_nm_idx (idx) {
    var no = {atomIndex=idx}.atomno
    while ((no > 0) and ({(atomno=no) and (chain=gChain)
        and thisModel}.atomName != "N")) {
        no--
    }
    return ({(atomno=no) and (chain=gChain) and thisModel}.atomIndex)
}

function get_np_no (iNo) {
    while ((iNo < gMaxNo) and ({(atomno=iNo) and (chain=gChain)
        and thisModel}.atomName != "N")) {
        iNo++
    }
    return iNo
}

function get_cb_idx (BBidx) {
    var no = {atomIndex=BBidx}.atomno
    var i = 1
    for (; i < 5; i++) {
        if ({(atomno=@{no+i}) and (chain=gChain)
            and thisModel}.atomName == "CB") {
            break
        }
    }
    return {(atomno=@{no+i}) and (chain=gChain) and thisModel}.atomIndex
}

function get_o_idx (BBidx) {
    var no = {atomIndex=BBidx}.atomno
    var i = 1
    for (; i < 4; i++) {
        if ({(atomno=@{no+i}) and (chain=gChain)
            and thisModel}.atomName == "O") {
            break
        }
    }
    return {(atomno=@{no+i}) and (chain=gChain) and thisModel}.atomIndex
}

function get_nward_bb_idx (idx, iChain) {
    var no = {atomIndex=idx}.atomno - 1
    for (; no >= 0; no--) {
        var atomName = {(atomno=no) and (chain=iChain)
            and thisModel}.atomName
        if ((atomName = "N") or (atomName = "C") or (atomName = "CA")) {
            break
        }
    }
    return ((no >= 0) ? ({(atomno=no) and (chain=iChain)
        and thisModel}.atomIndex) : -1)
}

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

function get_sc_set (scIdx, iChain) {
    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 thisModel}.atomIndex
        if (is_bb_idx(idx)) {
            break
        }
        scSet = scSet or {atomIndex=idx}
    }
    return scSet
}

function get_sc_bb_idx (idx, iChain) {
    var no = {atomIndex=idx}.atomno
    for (; no > 0; no--) {
        if ({(atomno=no) and (chain=iChain)
            and thisModel}.atomName == "CA") {
            break
        }
        else if ({(atomno=no) and (chain=iChain)
            and thisModel}.atomName == "C") {
            break
        }
        else if ({(atomno=no) and (chain=iChain)
            and thisModel}.atomName == "N") {
            break
        }
        else if ({(atomno=no) and (chain=iChain)
            and thisModel}.atomName == "CB") {
            no -= 3
            break
        }
    }
    return {(atomno=no) and (chain=iChain) and thisModel}.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 select_add_sc(fromIdx) {
    var iNo = {atomIndex=fromIdx}.atomno
    var iChain = {atomIndex=fromIdx}.chain
    select none
    while ({(atomno=iNo) and (chain=iChain)
        and thisModel and sidechain}) {
        var a = {(atomno=iNo) and (chain=iChain)and thisModel}
        a.selected = true
        iNo++
    }
}

# Resolve collisions on selection
function handle_collisions( targetIdx) {

    # For all selected atoms
    for (var iNo = {selected}.min.atomno; iNo <= {selected}.max.atomno; iNo++) {
        var idx = {(atomno=iNo) and (chain=gchain)
            and thisModel}.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) {
                # Ignore kinked BB
                try {
                    if (is_bb_idx(idx) and (angle(
                        {atomIndex=@{get_cward_bb_idx(idx, gChain)}}, {atomIndex=idx},
                        {atomIndex=@{get_nward_bb_idx(idx, gChain)}}) < 100.0)) {
                        continue
                    }
                }
                catch {
                }

                # 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)
                        
                        # 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)

                        # 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 (abs(dh).type == "string") {
                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 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) {
        var nNo = {(chain=iChain) and thisModel}.atomno.min
        select_nward_idx(caPsiIdx, {(atomno=nNo) and (chain=iChain)
            and thisModel}.atomIndex)
    }
    else {
        var cNo = {(chain=iChain) and thisModel}.atomno.max
        select_cward_idx(caPhiIdx, {(atomno=cNo) and (chain=iChain)
            and thisModel}.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 cbidx = get_cb_idx(BBidx)
    var cbno = {atomIndex=cbidx}.atomno
    var cgidx = {(atomno=@{cbno+1}) and (chain=gChain)
        and thisModel}.atomIndex
    var cdidx = {(atomno=@{cbno+2}) and (chain=gChain)
        and thisModel}.atomIndex
    var caidx = {(atomno=@{cbno-3}) and (chain=gChain)
        and thisModel}.atomIndex
    var nidx = {(atomno=@{cbno-4}) and (chain=gChain)
        and thisModel}.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 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) {
                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 thisModel}.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 != gNanchorIdx) {

        # Step to next atom
        targetIdx = get_cward_bb_idx(targetIdx, gChain)
        if (targetIdx < 0) {
            break
        }

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

        # Compute targets desired coords
        try {
            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++
            }
        }
        catch {
        }

        # 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)
        if (targetIdx < 0) {
            break
        }
        
        # 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, caxis, a) {
    if (gPlicoRecord != "") {
        plico_record(format("select %s;", {selected}))
        plico_record(format("rotateSelected {atomIndex=%d} @%s @%s;",
            pivotIdx, caxis, a))
    }
    rotateSelected {atomIndex=pivotIdx} @caxis @a
}

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

    }

    return scBondIdxs
}

# Drag Side Chain
function drag_sc() {
    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 = 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) {
                        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])
        }
        
        if (gSCcheck = false) {
            plico_minimize( scSet)
        }
    }
    else { # PRO - toggle between puckers up and down
        var icd = {(atomno=@{iNo+1}) and (chain=iChain)
            and thisModel}.atomIndex
        var icb = {(atomno=@{iNo-1}) and (chain=iChain)
            and thisModel}.atomIndex
        var ica = {(atomno=@{iNo-4}) and (chain=iChain)
            and thisModel}.atomIndex
        var in = {(atomno=@{iNo-5}) and (chain=iChain)
            and thisModel}.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) {
    gOk2 = false
    var iNo = {atomIndex=idx}.atomno
    var iChain = {atomIndex=idx}.chain
    var resno = {(atomno=iNo) and (chain=iChain)
        and thisModel}.resno

    # Get SC terminus
    while (resno == {(atomno=iNo) and (chain=iChain)
        and thisModel}.resno) {
        iNo++
    }
    iNo--

    var sc = array()
    var iBno = iNo
    while ({(atomno=iBno) and (chain=iChain)
        and thisModel}.atomName != "CB") {
        sc += {(atomno=iBno) and (chain=iChain)
            and thisModel}
        iBno--
    }
    var cbidx = {(atomno=iBno) and (chain=iChain)
        and thisModel}.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
            var 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) { # frozen bonds are kept as lo-hi
        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 xcollect_bb_rotors(nWard) {
    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 thisModel}.atomName == "CA") {
                if (is_rotor_avail(iNo)) {# xxx
                    if (({(atomno=iNo) and (chain=gChain)
                        and thisModel}.group != "PRO") and (iNo > cargoNo)) { # phi
                        rotors += [{(atomno=@{get_cm_no(iNo-1)}) and (chain=gChain)
                            and thisModel}.atomIndex,
                            {(atomno=@{iNo-1}) and (chain=gChain)
                                and thisModel}.atomIndex]
                        rotors += [{(atomno=@{iNo}) and (chain=gChain)
                            and thisModel}.atomIndex,
                            {(atomno=@{iNo+1}) and (chain=gChain)
                                and thisModel}.atomIndex]
                    }
                    if (iNo != (anchorNo-1)) { # psi
                        rotors += [{(atomno=@{iNo-1}) and (chain=gChain)
                            and thisModel}.atomIndex,
                            {(atomno=@{iNo}) and (chain=gChain)
                                and thisModel}.atomIndex]
                        rotors += [{(atomno=@{iNo+1}) and (chain=gChain)
                            and thisModel}.atomIndex,
                            {(atomno=@{get_np_no(iNo+2)}) and (chain=gChain)
                                and thisModel}.atomIndex]
                    }
                }
            }
        }
    }
    else {

        for (var iNo = cargoNo; iNo >= anchorNo; iNo--) {
            if ({(atomno=iNo) and (chain=gChain)
                and thisModel}.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 thisModel}.atomIndex,
                            {(atomno=@{iNo+1}) and (chain=gChain)
                                and thisModel}.atomIndex]
                        rotors += [{(atomno=@{iNo}) and (chain=gChain)
                            and thisModel}.atomIndex,
                            {(atomno=@{iNo-1}) and (chain=gChain)
                                and thisModel}.atomIndex]
                    }
                    if ({(atomno=iNo) and (chain=gChain)
                        and thisModel}.group != "PRO") { # phi
                        rotors += [{(atomno=@{iNo+1}) and (chain=gChain)
                            and thisModel}.atomIndex,
                            {(atomno=@{iNo}) and (chain=gChain)
                                and thisModel}.atomIndex]
                        rotors += [{(atomno=@{iNo-1}) and (chain=gChain)
                            and thisModel}.atomIndex,
                            {(atomno=@{get_cm_no(iNo-1)}) and (chain=gChain)
                                and thisModel}.atomIndex]
                    }
                }
            }
        }
    }

    if (nWard) {
        gNrotors = rotors
    }
    else {
        gCrotors = rotors
    }
}
function collect_bb_rotors(nWard) {
    if (nWard) {
        gNrotors = array()
        var nres = {atomIndex=gNcargoIdx}.resno
        var nname = {atomIndex=gNcargoIdx}.atomName
        var ares = get_resno_min(gChain)
        var aA = get_atom_rcn( ares, gChain, "N")
        if (gNanchorIdx >= 0) {
            aA = {atomIndex=gNanchorIdx}
        }
        var aname = aA.atomName
        for (var r = nres; r >= ares; r--) {
            var aCp = get_atom_rcn( r-1, gChain, "C")
            var aN = get_atom_rcn( r, gChain, "N")
            var aCa = get_atom_rcn( r, gChain, "CA")
            var aC = get_atom_rcn( r, gChain, "C")
            var aNn = get_atom_rcn( r+1, gChain, "N")
            if (aCp.size < 1) {
                aCp = aNn
            }
            # psi
            if (((r < nres) and (r > ares))
                or ((r == nres) and (nname == "C"))
                or ((r == ares) and (aname != "C"))) {
                if (is_rotor_avail(aCa.atomIndex, aC.atomIndex)) {
                    gNrotors += aNn.atomIndex
                    gNrotors += aC.atomIndex
                    gNrotors += aCa.atomIndex
                    gNrotors += aN.atomIndex
                }
            }
                        
            # phi
            if (aCa.group != "PRO") {
                if (((r <= nres) and (r > ares))
                    or ((r == ares) and (aname == "N"))) {
                    if (is_rotor_avail(aCa.atomIndex, aN.atomIndex)) {
                        gNrotors += aC.atomIndex
                        gNrotors += aCa.atomIndex
                        gNrotors += aN.atomIndex
                        gNrotors += aCp.atomIndex
                    }
                }
            }
        } # endfor
    }
    else {
        gCrotors = array()
        var cres = {atomIndex=gCcargoIdx}.resno
        var cname = {atomIndex=gCcargoIdx}.atomName
        var ares = get_resno_max(gChain)
        var aA = get_atom_rcn( ares, gChain, "C")
        if (gCanchorIdx >= 0) {
            aA = {atomIndex=gCanchorIdx}
        }
        var aname = aA.atomName
        for (var r = cres; r <= ares; r++) {
            var aCp = get_atom_rcn( r-1, gChain, "C")
            var aN = get_atom_rcn( r, gChain, "N")
            var aCa = get_atom_rcn( r, gChain, "CA")
            var aC = get_atom_rcn( r, gChain, "C")
            var aNn = get_atom_rcn( r+1, gChain, "N")
            if (aNn.size < 1) {
                aNn = aCp
            }
            
            # phi
            if (aCa.group != "PRO") {
                if (((r > cres) and (r < ares))
                    or ((r == cres) and (aname == "N"))
                    or ((r == ares) and (aname != "N"))) {
                    if (is_rotor_avail(aN.atomIndex, aCa.atomIndex)) {
                        gCrotors += aCp.atomIndex
                        gCrotors += aN.atomIndex
                        gCrotors += aCa.atomIndex
                        gCrotors += aC.atomIndex
                    }
                }
            }
            
            # psi
            if (((r >= cres) and (r < ares))
                or ((r == cres) and (aname != "C"))
                or ((r == ares) and (aname == "C"))) {
                if (is_rotor_avail(aCa.atomIndex, aC.atomIndex)) {
                    gCrotors += aN.atomIndex
                    gCrotors += aCa.atomIndex
                    gCrotors += aC.atomIndex
                    gCrotors += aNn.atomIndex
                }
            }
        } # endfor
    }
}

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() {
    select (thisModel)
    color {selected} @gScheme
    color {atomIndex=g1pivotIdx} green
    color {atomIndex=g2pivotIdx} green
    color @gCargoSet @gAltScheme
    color {gCargoSet and oxygen} pink
    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
    refresh
    if (prompt(format("%s - Undo?", s), "Yes|No", true) == "Yes") {
        gBusy = false
        restore state gState
        connect
        select gCargoSet
        set bondPicking true
        refresh
        for (var i = 1; i <= gFreeze.size; i+=2) {
            select {atomIndex=@{gFreeze[i]}} or {atomIndex=@{gFreeze[i+1]}}
            color bonds lightblue
        }
        background ECHO yellow
        echo @gEcho
        select all
        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() {
    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]
        var j = _pickInfo[i+1][9999].find("#")
        var a2no = 0 + _pickInfo[i+j+1][i+j+3]
        var i1idx = {(atomno=a1no) and (chain=iChain)
            and thisModel}.atomIndex
        var i2idx = {(atomno=a2no) and (chain=iChain)
            and thisModel}.atomIndex
        if (({atomIndex=i1idx}.atomName == "CA")
            or ({atomIndex=i2idx}.atomName == "CA")) {
            if (({atomIndex=i1idx}.atomName != "CB")
                and ({atomIndex=i2idx}.atomName != "CB")) {
                if (i1idx > i2idx) {
                    var 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)) {
                        if (i > 1) {
                            if (gFreeze.size = (i+1)) {
                                gFreeze = gFreeze[1][i-1]
                            }
                            else {
                                gFreeze = gFreeze[1][i-1] + gFreeze[i+2][0]
                            }
                        }
                        else {
                            gFreeze = gFreeze[i+2][0]
                        }
                        color bonds NONE
                        i = 0
                        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() {
    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 {

                var idx = {
                    (atomno=@{{(chain=gChain) and thisModel}.atomno.min})
                    and (chain=gChain) and thisModel}.atomIndex


                var ihc = 0
                for (ihc = 0; ihc < 10; ihc++) {
                    select ((atomno >= gNanchorNo) and (atomno <= gCanchorNo)
                        and (chain = gChain) and thisModel)
                    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
        set bondPicking true
        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 caxis = {0 0 0}
        if (distance(pt,  {0 0 0}) > 0.004) {
            # If sidechain mode
            if (gSCidx >= 0) {
                if ({atomIndex=gSCidx}.atomName == "O") {
                    if ({atomIndex=gSCidx}.group != "PRO") {
                        var 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) {
                        caxis = {atomIndex=g2pivotIdx}
                    }

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

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

                }

                # Else translate it
                else {
                    translate_selected_record(pt)
                }

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

                        # If net collision vector same as move vector
                        var 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 thisModel}.atomno.min})
                                        and (chain=gChain) and thisModel}.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, caxis, -a)
                        }
                        else {
                            translate_selected_record(-pt)
                        }
                        background ECHO yellow
                        set bondPicking true
                    }
                }
            }

            # 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" +
        "|ALT-SHIFT-DRAG=alt move|CLICK bond=freeze|ALT-DOUBLE-CLICK=undo" +
        "|SHIFT-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-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() {
    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 thisModel)}
    }
    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() {
    gTow = true
    gChain = {atomIndex=_atomPicked}.chain
    gMinNo = {(chain=gChain) and thisModel}.atomno.min
    gMaxNo = {(chain=gChain) and thisModel}.atomno.max
    gCcargoIdx = -1
    gNcargoIdx = -1
    gCanchorIdx = -1
    gCanchorNo = gMaxNo + 1
    gNanchorIdx = -1
    gNanchorNo = gMinNo - 1

    # Highlight cargo cluster
    select {(chain=gChain) and thisModel}
    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() {

    # If O or movable side chain atom picked
    if ((({atomIndex=_atomPicked}.atomName = "O")
        and ({atomIndex=_atomPicked}.group != "PRO"))
        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 thisModel}
                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 thisModel}.atomno.min
        gMaxNo = {(chain=gChain) and thisModel}.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
        }

        # 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 thisModel)}
    }

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

    select {gCargoSet}
}

function tug_undo_mb() {
    if (prompt("Undo", "Yes|No", true) == "Yes") {
        restore state gState
    }
}

# Top level of Tug
function plico_tug() {

    # 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
        }
    }

    gPlico = "TUG"
    plico_prelim(true, 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|ALT-DOUBLE-CLICK=undo|SHIFT-DOUBLE-CLICK=exit")
    echo @gEcho
    gCrotors = array()
    gNrotors = array()
    clear_atom_idxs()
    gToab = false

    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 "ALT-LEFT-DOUBLE" "tug_undo_mb";
    bind "SHIFT-DOUBLE" "tug_exit(true)";
    bind "LEFT-CLICK" "+:plico_menu_toggle";
}

# Bound to DOUBLE by plico_tug
function tug_exit() {
    if (plico_exit()) {
        set bondPicking gBondPicking
        set PickCallback NONE
        select all
        color bonds none
        
        reset kTug
        reset gCanchorIdx  
        reset gCanchorNo   
        reset gPlico       
        reset gNanchorIdx  
        reset gNanchorNo   
        reset gCcargoIdx   
        reset gNcargoIdx   
        reset gCcargoNo    
        reset gNcargoNo    
        reset gDestAtomIdx 
        reset g1pivotIdx   
        reset g2pivotIdx   
        reset gSelSaves    
        reset gCrotors     
        reset gNrotors     
        reset gOkCollide   
        reset gChain       
        reset gMinNo       
        reset gMaxNo       
        reset gCargoSet    
        reset gMovingSet   
        reset gSCidx       
        reset gSCcircle    
        reset gSCpt        
        reset gTargetPt    
        reset gNewDrag     
        reset gTow         
        reset g1dynamicIdx 
        reset g2dynamicIdx 
        reset gSCcheck     
        reset gBondPicking 
        reset gFreeze      
        reset gToab        
        reset function "get_cp_idx"
        reset function "get_cm_no"
        reset function "get_nm_idx"
        reset function "get_np_no"
        reset function "get_cb_idx"
        reset function "get_o_idx"
        reset function "get_nward_bb_idx"
        reset function "get_cward_bb_idx"
        reset function "get_sc_set"
        reset function "get_sc_bb_idx"
        reset function "is_bb_idx"
        reset function "is_sc_idx"
        reset function "select_add_sc"
        reset function "handle_collisions"
        reset function "tug_track_idx"
        reset function "do_counter_rotate"
        reset function "counter_rotate"
        reset function "counter_rotate_2"
        reset function "repair_proline"
        reset function "repair_sc"
        reset function "tug_track_c"
        reset function "tug_track_n"
        reset function "translate_selected_record"
        reset function "rotate_selected_record"
        reset function "collect_sc_rotors"
        reset function "drag_sc"
        reset function "fix_sc_collision_2"
        reset function "is_moveable_sc"
        reset function "is_rotor_avail"
        reset function "xcollect_bb_rotors"
        reset function "collect_bb_rotors"
        reset function "collect_rotors"
        reset function "tug_sc"
        reset function "set_colors"
        reset function "clear_atom_idxs"
        reset function "timed_out"
        reset function "record_drag"
        reset function "tug_pick_cb"
        reset function "tug_drag_done_mb"
        reset function "tug_drag_2_mb"
        reset function "tug_drag_mb"
        reset function "tug_mark_mb"
        reset function "tug_anchor_mb"
        reset function "tug_enable_drag"
        reset function "tug_dest_atom_mb"
        reset function "tug_pivot_mb"
        reset function "tow_cargo_mb"
        reset function "tug_cargo_mb"
        reset function "tug_undo_mb"
        reset function "plico_tug"


    }
}

# End of TUG.SPT

Contributors

Remig

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

Latest revision as of 17:15, 12 April 2016

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@@ Line 1: / Line 1: @@
-'''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.
+'''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. A full description of its capabilities can be found [[User:Remig/plico/tugManual|here]].
 '''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:
 <pre>Title=PLICO Tug
-Script=script <path to your scripts folder>/tug.spt;plicotug</pre>
+Script=script <path to your scripts directory>/tug.spt;plico_tug</pre>
-saved as plicotug.macro in your .jmol/macros folder as described in [[Macro]].
+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 folder as tug.spt.
+Copy and paste the following into a text editor and save in your scripts directory as tug.spt.
 <pre>#   tug - Jmol script by Ron Mignery
-#   v1.0 beta    2/4/2014 for Jmol 13.4
+#   v1.20 beta    4/12/2016 -axis is now a reserved word
 #
-#   These functions support protein manipulation in Jmol
+#   Translate or rotate a stretch of a polypeptide against itself
-var kTug = 1
+#    or against other chains by mouse actions
-var kDtolerance = 0.2
+#
-var kAtolerance = 5.0
+kTug = 3
-var kCtolerance = 1.85
+gCanchorIdx = -1
-var kMtolerance = 0.8
+gCanchorNo = -1
-var kMinRama = 2
+gPlico = "TUG"
-var kCollisionLimit = 200
+gNanchorIdx = -1
-var gCanchorIdx = -1
+gNanchorNo = -1
-var gCanchorNo = -1
+gCcargoIdx = -1
-var gNanchorIdx = -1
+gNcargoIdx = -1
-var gNanchorNo = -1
+gCcargoNo = -1
-var gNanchorPidx = -1
+gNcargoNo = -1
-var gCanchorXyz = {0 0 0}
+gDestAtomIdx = -1
-var gNanchorXyz = {0 0 0}
+g1pivotIdx = -1
-var gNanchorPxyz = {0 0 0}
+g2pivotIdx = -1
-var gCcargoIdx = -1
+gSelSaves = ({})
-var gNcargoIdx = -1
+gCrotors = array()
-var gCcargoXyz = {0 0 0}
+gNrotors = array()
-var gNcargoXyz = {0 0 0}
+gOkCollide = ({})
-var gCcargoNo = -1
+gChain = ""
-var gNcargoNo = -1
+gMinNo = 1
-var gDestAtomIdx = -1
+gMaxNo = 9999
-var g1pivotIdx = -1
+gCargoSet = ({})
-var g2pivotIdx = -1
+gMovingSet = ({})
-var gSelSaves = ({})
+gBusy = false
-var gCrotors = array()
+gSCidx = -1
-var gNrotors = array()
+gSCcircle = -1
-var gMouseX = 0
+gSCpt = {0 0 0}
-var gMouseY = 0
+gTargetPt = {0 0 0}
-var gAc = ({})
+gNewDrag = false
-var gChain = ""
+gTow = false
-var gMinNo = 1
+g1dynamicIdx = -1
-var gMaxNo = 9999
+g2dynamicIdx = -1
-var gScheme = "Jmol"
+gSCcheck = true
-var gAltScheme = "Rasmol"
+gBondPicking = false
-var gCargoAtoms = ({})
+gFreeze = array()
-var gSeed = 23423.52
+gToab = false
-var gBusy = FALSE
-var gSCidx = -1
-var gSCcircle = -1
-var gSCpt = {0 0 0}
-var gOK = TRUE # global return value to work around jmol *feature*
-var gOk2 = TRUE # "    "
-var gTargetPt = {0 0 0}
-var gNewDrag = FALSE
-var gEcho = ""
-var gCountdown = 0
-var gZoom = ""
-var gRotate = ""
-# Return L tetrahedron point if i1<i2<i3, else R point
-function getTet(i1, i2, i3, dist) {
-    var v1 = {atomIndex=i3}.xyz - {atomIndex=i2}.xyz
-    var v2 = {atomIndex=i1}.xyz - {atomIndex=i2}.xyz
-    var axis = cross(v1, v2)
-    var pma = ({atomIndex=i1}.xyz + {atomIndex=i3}.xyz)/2
-    var pmo = {atomIndex=i2}.xyz + {atomIndex=i2}.xyz - pma
-    var pt = pmo + (axis/axis)
-    var v = pt - {atomIndex=i2}.xyz
+function get_cp_idx (idx) {
-    var cdist = distance(pt, {atomIndex=i2})
+     var no = {atomIndex=idx}.atomno
-    var factor = (dist/cdist)
+     while ((no < gMaxNo) and ({(atomno=no) and (chain=gChain)
-    var lpt = v * factor
+        and thisModel}.atomName != "C")) {
+         no++
-    return lpt + {atomIndex=i2}.xyz
-}
-function getTrigonal(i1, i2, i3, dist) {
-     var v1 = {atomIndex=i1}.xyz - {atomIndex=i2}.xyz
-     var v2 = {atomIndex=i3}.xyz - {atomIndex=i2}.xyz
-    var pt = {atomIndex=i2}.xyz - (v1 + v2)
-    var v = pt - {atomIndex=i2}.xyz
-    var cdist = distance(pt, {atomIndex=i2})
-    var factor = (dist/cdist)
-    var lpt = (v * factor)
-    return lpt + {atomIndex=i2}.xyz
-}
-function abs( x) {
-    if (x < 0) {
-         x = -x
      }
-     return x
+     return ({(atomno=no) and (chain=gChain) and thisModel}.atomIndex)
 }
-function getCAmNo (iNo) {
+function get_cm_no (iNo) {
-     while ((iNo > 0) and ({(atomno=iNo) and (chain=gChain)}.atomName != "CA")) {
+     while ((iNo > 0) and ({(atomno=iNo) and (chain=gChain)
+        and thisModel}.atomName != "C")) {
          iNo--
      }
@@ Line 105: / Line 67: @@
 }
-function getCAmIdx (idx) {
+function get_nm_idx (idx) {
-     var no = {atomIndex=idx and (chain=gChain)}.atomno
+     var no = {atomIndex=idx}.atomno
-     no = getCAmNo( no)
+     while ((no > 0) and ({(atomno=no) and (chain=gChain)
-    return ({(atomno=no) and (chain=gChain)}.atomIndex)
+         and thisModel}.atomName != "N")) {
-}
+         no--
-function getCApNo (iNo) {
-    while ((iNo < gMaxNo) and ({(atomno=iNo) and (chain=gChain)}.atomName != "CA")) {
-         iNo++
-    }
-    return iNo
-}
-function getCpIdx (idx) {
-    var no = {atomIndex=idx and (chain=gChain)}.atomno
-    no = getCpNo( no)
-    return ({(atomno=no) and (chain=gChain)}.atomIndex)
-}
-function getCpNo (iNo) {
-    while ((iNo < gMaxNo) and ({(atomno=iNo) and (chain=gChain)}.atomName != "C")) {
-         iNo++
-    }
-    return iNo
-}
-function getCApIdx (idx) {
-    var no = {atomIndex=idx and (chain=gChain)}.atomno
-    no = getCApNo( no)
-    return ({(atomno=no) and (chain=gChain)}.atomIndex)
-}
-function getCmNo (iNo) {
-    while ((iNo > 0) and ({(atomno=iNo) and (chain=gChain)}.atomName != "C")) {
-        iNo--
      }
-     return iNo
+     return ({(atomno=no) and (chain=gChain) and thisModel}.atomIndex)
-}
-function getCmIdx (idx) {
-    var no = {atomIndex=idx and (chain=gChain)}.atomno
-    no = getCmNo( no)
-    return ({(atomno=no) and (chain=gChain)}.atomIndex)
-}
-function getNmNo (iNo) {
-    while ((iNo > 0) and ({(atomno=iNo) and (chain=gChain)}.atomName != "N")) {
-        iNo--
-    }
-    return iNo
-}
-function getNmIdx (idx) {
-    var no = {atomIndex=idx and (chain=gChain)}.atomno
-    no = getNmNo( no)
-    return ({(atomno=no) and (chain=gChain)}.atomIndex)
 }
-function getNpNo (iNo) {
+function get_np_no (iNo) {
-     while ((iNo < gMaxNo) and ({(atomno=iNo) and (chain=gChain)}.atomName != "N")) {
+     while ((iNo < gMaxNo) and ({(atomno=iNo) and (chain=gChain)
+        and thisModel}.atomName != "N")) {
          iNo++
      }
@@ Line 170: / Line 84: @@
 }
-function getNpIdx (idx) {
+function get_cb_idx (BBidx) {
-    var no = {atomIndex=idx}.atomno
-    no = getNpNo( no)
-    return ({(atomno=no) and (chain=gChain)}.atomIndex)
-}
-function getCBidx (BBidx) {
      var no = {atomIndex=BBidx}.atomno
      var i = 1
      for (; i < 5; i++) {
-         if ({(atomno=@{no+i}) and (chain=gChain)}.atomName == "CB") {
+         if ({(atomno=@{no+i}) and (chain=gChain)
+            and thisModel}.atomName == "CB") {
              break
          }
      }
-     return {(atomno=@{no+i}) and (chain=gChain)}.atomIndex
+     return {(atomno=@{no+i}) and (chain=gChain) and thisModel}.atomIndex
 }
-function getOidx (BBidx) {
+function get_o_idx (BBidx) {
      var no = {atomIndex=BBidx}.atomno
      var i = 1
      for (; i < 4; i++) {
-         if ({(atomno=@{no+i}) and (chain=gChain)}.atomName == "O") {
+         if ({(atomno=@{no+i}) and (chain=gChain)
+            and thisModel}.atomName == "O") {
              break
          }
      }
-     return {(atomno=@{no+i}) and (chain=gChain)}.atomIndex
+     return {(atomno=@{no+i}) and (chain=gChain) and thisModel}.atomIndex
 }
-function getNwardBBno (iNo) {
+function get_nward_bb_idx (idx, iChain) {
-     while ((iNo >= 0) and (
+     var no = {atomIndex=idx}.atomno - 1
-         ({(atomno=iNo) and (chain=gChain)}.atomName != "N")
+    for (; no >= 0; no--) {
-         and ({(atomno=iNo) and (chain=gChain)}.atomName != "C")
+         var atomName = {(atomno=no) and (chain=iChain)
-        and ({(atomno=iNo) and (chain=gChain)}.atomName != "CA"))) {
+            and thisModel}.atomName
-         iNo--
+         if ((atomName = "N") or (atomName = "C") or (atomName = "CA")) {
+            break
+         }
      }
-     return iNo
+     return ((no >= 0) ? ({(atomno=no) and (chain=iChain)
+        and thisModel}.atomIndex) : -1)
 }
-function getNwardBBidx (idx) {
+function get_cward_bb_idx (idx, iChain) {
-     var no = {atomIndex=idx}.atomno - 1
+     var no = {atomIndex=idx}.atomno + 1
-     no = getNwardBBno( no)
+     for (; no < gMaxNo; no++) {
-     return ((no >= 0) ? ({(atomno=no) and (chain=gChain)}.atomIndex) : -1)
+        var atomName = {(atomno=no) and (chain=iChain)
+            and thisModel}.atomName
+        if ((atomName = "N") or (atomName = "C") or (atomName = "CA")) {
+            break
+        }
+    }
+     return ((no >= 0) ? ({(atomno=no) and (chain=iChain)
+        and thisModel}.atomIndex) : -1)
 }
-function getCwardBBno (iNo) {
+function get_sc_set (scIdx, iChain) {
-     while ((iNo < gMaxNo) and (
+     var scSet = ({})
-        ({(atomno=iNo) and (chain=gChain)}.atomName != "N")
+    var idx = get_sc_bb_idx(scIdx, iChain)
-         and ({(atomno=iNo) and (chain=gChain)}.atomName != "C")
+    var iNo = {atomIndex=idx}.atomno + 3
-         and ({(atomno=iNo) and (chain=gChain)}.atomName != "CA"))) {
-         iNo++
+    for (var i = 1; i < 20; i++) {
+         idx = {(atomno=@{iNo+i}) and (chain=iChain)
+            and thisModel}.atomIndex
+         if (is_bb_idx(idx)) {
+            break
+        }
+         scSet = scSet or {atomIndex=idx}
      }
-     return iNo
+     return scSet
 }
-function getCwardBBidx (idx) {
+function get_sc_bb_idx (idx, iChain) {
-    var no = {atomIndex=idx}.atomno + 1
-    no = getCwardBBno( no)
-    return ((no >= 0) ? ({(atomno=no) and (chain=gChain)}.atomIndex) : -1)
-}
-function getScBBidx (idx) {
      var no = {atomIndex=idx}.atomno
      for (; no > 0; no--) {
-         if ({(atomno=no) and (chain=gChain)}.atomName == "CA") {
+         if ({(atomno=no) and (chain=iChain)
+            and thisModel}.atomName == "CA") {
              break
          }
-         else if ({(atomno=no) and (chain=gChain)}.atomName == "C") {
+         else if ({(atomno=no) and (chain=iChain)
+            and thisModel}.atomName == "C") {
              break
          }
-         else if ({(atomno=no) and (chain=gChain)}.atomName == "N") {
+         else if ({(atomno=no) and (chain=iChain)
+            and thisModel}.atomName == "N") {
              break
          }
-         else if ({(atomno=no) and (chain=gChain)}.atomName == "CB") {
+         else if ({(atomno=no) and (chain=iChain)
+            and thisModel}.atomName == "CB") {
              no -= 3
              break
          }
      }
-     return {(atomno=no) and (chain=gChain)}.atomIndex
+     return {(atomno=no) and (chain=iChain) and thisModel}.atomIndex
 }
-function isBBidx(aIdx) {
+function is_bb_idx(aIdx) {
-     var ret = FALSE
+     var ret = false
      switch({atomIndex=aIdx}.atomName) {
      case "N":
      case "CA":
      case "C":
-         ret = TRUE
+         ret = true
          break
      }
@@ Line 262: / Line 186: @@
 }
-function isSCidx(aIdx) {
+function is_sc_idx(aIdx) {
-     var ret = FALSE
+     var ret = false
-     if (isBBidx(aIDx) == FALSE) {
+     if (not is_bb_idx(aIDx)) {
-         ret = TRUE
+         ret = true
          switch({atomIndex=aIdx}.atomName) {
          case "O":
          case "CB":
-             ret = FALSE
+             ret = false
              break
          }
@@ Line 278: / Line 202: @@
 }
-function addSideChainToSelection(CAno, isAdd, addOXT) {
+function select_add_sc(fromIdx) {
-    var iNo = CAno+3
-    while ({(atomno=iNo) and (chain=gChain)}.resno == {(atomno=CAno) and (chain=gChain)}.resno) {
-        {(atomno=iNo) and (chain=gChain)}.selected = isAdd
-        if ({(atomno=iNo) and (chain=gChain)}.atomName == "OXT") {
-            {(atomno=iNo) and (chain=gChain)}.selected = addOXT
-        }
-        iNo++
-    }
-}
-function selectAddSideChain(fromIdx) {
      var iNo = {atomIndex=fromIdx}.atomno
+    var iChain = {atomIndex=fromIdx}.chain
      select none
-     while ({(atomno=iNo) and (chain=gChain)}.atomName != "N") {
+     while ({(atomno=iNo) and (chain=iChain)
-         {(atomno=iNo) and (chain=gChain)}.selected = TRUE
+        and thisModel and sidechain}) {
-         iNo++
+         var a = {(atomno=iNo) and (chain=iChain)and thisModel}
-        if (iNo > gMaxNo) {
+        a.selected = true
-            break
+         iNo++
-        }
      }
 }
-# First and last are BB atoms
+# Resolve collisions on selection
-# Any side atoms in the range are also selected
+function handle_collisions( targetIdx) {
-function selectNward (firstIdx, lastIdx) {
-    var firstno = ((firstIdx < 0) ? {atomIndex=lastIdx}.atomno : {atomIndex=firstIdx}.atomno)
-    var lastno = ((lastIdx < 0) ? firstno : {atomIndex=lastIdx}.atomno)
-    select (atomno <= firstno) and (atomno >= lastno)
-    if ({(atomno=firstno) and (chain=gChain)}.atomName == "C") { # if psi
-        addSideChainToSelection(firstno-1, TRUE, TRUE)
-        {(atomno=@{firstno+1}) and (chain=gChain)}.selected = TRUE # add O
-    }
-    if ({(atomno=firstno) and (chain=gChain)}.atomName == "CA") {
-        addSideChainToSelection(firstno, TRUE, FALSE)
-    }
-    if ({(atomno=lastno) and (chain=gChain)}.atomName == "C") { # if psi
-        addSideChainToSelection(lastno-1, FALSE, FALSE)
-    }
-}
-# First and last are BB atoms
-# Any side atoms in the range are also selected
-function selectCward (firstIdx, lastIdx) {
-    var firstno = ((firstIdx < 0) ? gMaxNo : {atomIndex=firstIdx}.atomno)
-    var lastno = ((lastIdx < 0) ? 1 : {atomIndex=lastIdx}.atomno)
-    # If nWard anchor in range, begin selection with it
-    if (gNanchorIdx >= 0) {
-        var aNo = {atomIndex=gNanchorIdx}.atomno
-        if (aNo > firstNo) {
-            firstno = aNo
-        }
-    }
-    # If cWard anchor in range, end selection with it
-    if (gCanchorIdx >= 0) {
-        var aNo = {atomIndex=gCanchorIdx}.atomno
-        if (aNo < lastNo) {
-            lastno = aNo
-        }
-    }
-    select (atomno >= firstno) and (atomno <= lastno)
-    if ({(atomno=firstno) and (chain=gChain)}.atomName == "C") { # if psi
-        addSideChainToSelection(firstno-1, FALSE, FALSE)
-    }
-    if ({(atomno=lastno) and (chain=gChain)}.atomName == "CA") {
-        addSideChainToSelection(lastno, TRUE, FALSE)
-    }
-    if ({(atomno=lastno) and (chain=gChain)}.atomName == "C") { # if psi
-        addSideChainToSelection(lastno-1, TRUE, TRUE)
-        {(atomno=@{lastno+1}) and (chain=gChain)}.selected = TRUE # add O
-    }
-}
-# Selected must include second parameter but not the first
-function setDistanceIdx (staticIdx, mobileIdx, desired) {
-    try {
-        var v = {atomIndex=mobileIdx}.xyz - {atomIndex=staticIdx}.xyz
-        var dist = distance({atomIndex=staticIdx}, {atomIndex=mobileIdx})
-        translateSelected @{((v * (desired/dist)) - v)}
-    }
-    catch {
-    }
-}
-# Selected must include third parameter but not the first
-function setAngleIdx (statorIdx, pivotIdx, rotorIdx, toangle) {
-    try {
-        var v1={atomIndex=statorIdx}.xyz - {atomIndex=pivotIdx}.xyz
-        var v2={atomIndex=rotorIdx}.xyz - {atomIndex=pivotIdx}.xyz
-        var axis = cross(v1, v2) + {atomIndex=pivotIdx}.xyz
-        var curangle =  angle({atomIndex=statorIdx},
-            {atomIndex=pivotIdx}, {atomIndex=rotorIdx})
-        rotateselected @axis {atomIndex = pivotIdx} @{curangle-toangle}
-    }
-    catch {
-    }
-}
-# Selected must include fourth parameter but not the first
-function setDihedralIdx (stator1idx, stator2idx, rotor1idx, rotor2idx, toangle) {
-    try {
-        var a1={atomIndex = stator1idx}.xyz
-        var a2={atomIndex = stator2idx}.xyz
-        var a3={atomIndex = rotor1idx}.xyz
-        var a4={atomIndex = rotor2idx}.xyz
-        var curangle =  angle(a1, a2, a3, a4)
-        rotateselected {a3} {a2} @{curangle-toangle}
-    }
-    catch {
-    }
-}
-function countCollisions(rc) {
-    var lcAtoms = ({})
-    for (var idx = {*}.min.atomIndex; idx <= {*}.max.atomIndex; idx++) {
-        lcAtoms = lcAtoms or (within(kCtolerance, FALSE, {atomIndex=idx})
-            and {atomIndex > idx}
-            and not {rc}
-            and not connected({atomIndex=idx}))
-    }
-    return lcAtoms.size
-}
-# Resolve collisions
-function handleCollisions( nWard, targetIdx) {
      # For all selected atoms
      for (var iNo = {selected}.min.atomno; iNo <= {selected}.max.atomno; iNo++) {
-         var idx = {(atomno=iNo) and (chain=gchain)}.atomIndex
+         var idx = {(atomno=iNo) and (chain=gchain)
+            and thisModel}.atomIndex
          if ({atomindex=idx}.selected) {
              # Collect local colliders
-             var lcAtoms = (within(kCtolerance, FALSE, {atomIndex=idx})
+             var lcAtoms = (within(kCtolerance, false, {atomIndex=idx})
                  and not {atomIndex=idx}
                  and not {gOkCollide}
                  and not connected({atomIndex=idx}))
+             if (lcAtoms) {
-             if (lcAtoms.size > 0) {
                  # Ignore kinked BB
-                 if (isBBidx(idx) and angle({atomIndex=@{getCwardBBidx(idx)}},
+                 try {
-                    {atomIndex=idx} , {atomIndex=@{getNwardBBidx(idx)}}) < 100) {
+                    if (is_bb_idx(idx) and (angle(
-                    continue
+                        {atomIndex=@{get_cward_bb_idx(idx, gChain)}}, {atomIndex=idx},
-                }
+                        {atomIndex=@{get_nward_bb_idx(idx, gChain)}}) < 100.0)) {
+                         continue
-                #gCountdown--
-                if (gCountdown < 0) {
-                    timedOut("Too many collsions")
-                }
-                # For all local water colliders, delete
-                var recollect = FALSE
-                for (var c = 1; c <= lcAtoms.size; c++ ) {
-                    if (lcAtoms[c].group = "HOH") {
-                         delete {atomIndex=@{lcAtoms[c].atomIndex}}
-                        recollect = TRUE
                      }
                  }
+                 catch {
-                # Recollect local colliders if needed
-                if (recollect) {
-                    lcAtoms = (within(kCtolerance, FALSE, {atomIndex=idx})
-                        and not {atomIndex=idx}
-                        and not {gOkCollide}
-                        and not connected({atomIndex=idx}))
-                    recollect = FALSE
                  }
                  # For all local colliders
                  for (var c = 1; c <= lcAtoms.size; c++ ) {
-                    # If it is with side chain not proline, fix it
                      var cidx = lcAtoms[c].atomIndex
-                     if (isSCidx(cidx) and ({atomIndex=cidx}.group != "PRO")) {
-                         fixSCcollision2(cidx)
+                    # If it is with water, delete it
-                        recollect = TRUE
+                     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)
                          # If not fixed, exit fail
-                         if (gOk2 == FALSE) {
+                         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)
+                        # If not fixed, exit fail
+                        if (not gOk2) {
                              return # early exit (break n jmol bug)
                          }
                      }
-                }
+                    # Else if it is with O, counter-rotate
-                # Recollect local colliders if needed
+                    else if (lcAtoms[c].atomName = "O") {
-                if (recollect) {
+                        counter_rotate_2(lcAtoms[c].atomIndex,
-                    lcAtoms = (within(kCtolerance, FALSE, {atomIndex=idx})
+                            {atomIndex=idx}.xyz, targetIdx, false)
-                         and not {atomIndex=idx}
-                         and not {gOkCollide}
+                         # If not fixed, exit fail
-                        and not connected({atomIndex=idx}))
+                         if (not gOk2) {
-                }
+                            return # early exit (break n jmol bug)
+                        }
-                # For all local colliders
+                     }
-                for (var c = 1; c <= lcAtoms.size; c++ ) {
+                     # Else if it is itself O, counter-rotate
-                     # If it is with O, counter-rotate
+                     else if ({atomIndex=idx}.atomName = "O") {
-                     if ({atomIndex=@{lcAtoms[c].atomIndex}}.atomName = "O") {
+                         counter_rotate_2(idx, lcAtoms[c].xyz, targetIdx, false)
-                         counterRotate2(idx, lcAtoms[c].atomIndex, targetIdx)
                          # If not fixed, exit fail
-                         if (gOk2 == FALSE) {
+                         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
              }
          }
@@ Line 496: / Line 301: @@
 # Rotate rotor set to move target atom to its proper place
-function tugTrackIdx(targetIdx, targetPt, nWard, cDetect) {
+function tug_track_idx(targetIdx, targetPt, nWard, cDetect) {
-     gOK = FALSE
+     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
@@ Line 519: / Line 325: @@
                      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) {
@@ Line 528: / Line 334: @@
                  }
              }
              # If no more rotors, break to next full try
              if (imax == 0) {
@@ Line 537: / Line 343: @@
              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") {
+             if (abs(dh).type == "string") {
                  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
+             var movePt = false
              if (nWard) {
                  if ({atomIndex=i2}.atomName="CA") {
-                     psi = angle({atomIndex=@{getCwardBBidx(i1)}}, {atomIndex=i1},
+                     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=@{getNwardBBidx(i3)}}) + dt
+                         {atomIndex=i3}, {atomIndex=@{get_nward_bb_idx(i3, gChain)}}) + dt
                  }
                  if ({atomIndex=i2}.atomno > {atomIndex=targetIdx}.atomno) {
-                     movePt = TRUE
+                     movePt = true
-                     selectNward(i3, getCwardBBidx(targetIdx))
+                     select_nward_idx(i3, get_cward_bb_idx(targetIdx, gChain))
-                     {atomIndex=targetIdx}.selected = TRUE
+                     {atomIndex=targetIdx}.selected = true
                  }
                  else {
-                     selectCward(i2, targetIdx)
+                     select_cward_idx(i2, targetIdx)
                  }
              }
              else {
                  if (({atomIndex=i2}.atomName="CA")) {
-                     phi = angle({atomIndex=@{getNwardBBidx(i1)}}, {atomIndex=i1},
+                     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=@{getCwardBBidx(i4)}}) + dt
+                         {atomIndex=i4}, {atomIndex=@{get_cward_bb_idx(i4, gChain)}}) + dt
                  }
                  if ({atomIndex=i2}.atomno < {atomIndex=targetIdx}.atomno) {
-                     movePt = TRUE
+                     movePt = true
-                     selectCward(i3, getNwardBBidx(targetIdx))
+                     select_cward_idx(i3, get_nward_bb_idx(targetIdx, gChain))
-                     {atomIndex=targetIdx}.selected = TRUE
+                     {atomIndex=targetIdx}.selected = true
                  }
                  else {
-                     selectNward(i2, targetIdx)
+                     select_nward_idx(i2, targetIdx)
                  }
              }
+             # Relax rules if desperate
+            if (pass1 > 10) {
+                phi = -50
+            }
              # If rotation within ramachandran limits
-            #var ridx = 1 + (36*(((-psi\10)%180)+18)+(((phi\10)%180)+18))
+             if ((abs(dt) >= 0.1) and
-             if ((abs(dt) >= 0.1) and
+                 (({atomIndex=i2}.group=="GLY") or (phi < 0))) {
-                 (({atomIndex=i2}.group=="GLY") or (phi < 0))) {#kRama[ridx] >= kMinRama))) {
                  # If moving target point, put the target atom there
@@ Line 600: / Line 410: @@
                      {atomIndex=targetIdx}.xyz = pt
                  }
                  # Rotate to minimize vector ====================
                  rotateSelected {atomIndex=i2} {atomIndex=i3} @dt
@@ Line 606: / Line 416: @@
                  # If collision checking
                  if (cDetect) {
                      # If collision, back off by eighths
-                     var wasCollision = FALSE
+                     var wasCollision = false
                      for (var ci = 0; ci < 4; ci++) {
                          if (ci < 3) {
                              dt /= 2
                          }
-                         handleCollisions( nWard, targetIdx)
+                         handle_collisions( targetIdx)
-                         if (gOk2==FALSE) {
+                         if (not gOk2) {
-                             wasCollision = TRUE
+                             wasCollision = true
                              rotateSelected {atomIndex=i2} {atomIndex=i3} @{-dt}
                          }
@@ Line 626: / Line 436: @@
                              break
                          }
                          if (dt < 0.01) {
                              break
@@ Line 632: / Line 442: @@
                      } # endfor
                  }
                  # If moving target point, put the target atom back
                  if (movePt) {
@@ Line 638: / Line 448: @@
                      {atomIndex=targetIdx}.xyz = cp
                  }
              }
              # If close enough, stop
              if (distance(pt, {atomIndex=targetIdx}) < kDtolerance) {
-                 gOK = TRUE
+                 gOK = true
                  gTargetPt = pt
                  break
              }
              # Block rotor
              blocked |= {atomIndex=i2}
          }   # endfor num rotors passes
          if (gOK) {
              break
          }
-     }   # endfor 10 passes
+     }   # endfor 20 passes
 }
 # Counter rotate bonds on either side of a BB O
-function docounterRotate2(caPhiIDx, nIdx, cIdx, oIdx, caPsiIdx, dir, nWard) {
+function do_counter_rotate(caPhiIdx, nIdx, cIdx, oIdx, caPsiIdx, dir, nWard) {
-     # Rotate phi
+     # Rotate psi
      {atomIndex=nIdx}.selected = nWard
      {atomIndex=cIdx}.selected = nWard
-     {atomIndex=oIdx}.selected = nWard
+     {atomIndex=oIdx}.selected = nward
      rotateSelected {atomIndex=caPsiIdx} {atomIndex=cIdx} @{dir}
-     # Counter-rotate psi
+     # Counter-rotate phi
      {atomIndex=nIdx}.selected = not nWard
      {atomIndex=cIdx}.selected = not nWard
-     {atomIndex=oIdx}.selected = not nWard
+     {atomIndex=oIdx}.selected = not nward
      rotateSelected {atomIndex=nIdx} {atomIndex=caPhiIdx} @{-dir}
 }
-function counterRotate2(aIdx, bIdx, targetIdx) {
+function counter_rotate(oIdx, dir, nWard) {
+    var iChain = {atomIndex=oIdx}.chain
      var selsave = {selected}
-     gOk2 = TRUE
+     var cIdx = get_sc_bb_idx(oIdx, iChain)
-     var oIdx = aIdx
+     var nIdx = get_cward_bb_idx(cIdx, iChain)
-     var xIdx = bIdx
+    var caPhiIdx = get_cward_bb_idx(nIdx, iChain)
-     if ({atomIndex=bIdx}.atomName=="O") {
+     var caPsiIdx = get_nward_bb_idx(cIdx, iChain)
-        oIdx = bIdx
-        xIdx = aIdx
+     if (nWard) {
+        var nNo = {(chain=iChain) and thisModel}.atomno.min
+        select_nward_idx(caPsiIdx, {(atomno=nNo) and (chain=iChain)
+            and thisModel}.atomIndex)
      }
-     var cIdx = getScBBidx(oIdx)
+    else {
-     var nIdx = getCwardBBidx(cIdx)
+        var cNo = {(chain=iChain) and thisModel}.atomno.max
-     var caPhiIdx = getCwardBBidx(nIdx)
+        select_cward_idx(caPhiIdx, {(atomno=cNo) and (chain=iChain)
-     var caPsiIdx = getNwardBBidx(cIdx)
+            and thisModel}.atomIndex)
+    }
-     var nWard = ({atomIndex=oIdx}.atomno < {atomIndex=targetIdx}.atomno)
-     if (nWard) {
+    # Counter-rotate
-         selectCward(cIdx, targetIdx)
+    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 {
-         selectNward(nIdx, targetIdx)
+         select_nward_idx(nIdx, terminalIdx)
      }
      # Until all collisions cancelled
      var dir = 5
-     var ang = angle({atomIndex=xIdx}, {atomIndex=oIdx}, {atomIndex=cIdx})
+     var ang = angle(toPt, {atomIndex=oIdx}, {atomIndex=cIdx})
      var tcount = 0
-     while (within(kCtolerance, FALSE, {atomIndex=oIdx})
+     while (oDrag or (within(kCtolerance, false, {atomIndex=oIdx})
              and not {atomIndex=oIdx} and not connected({atomIndex=oIdx})
-             and not {gOkCollide} > 0) {
+             and not {gOkCollide} > 0)) {
          # Counter-rotate
-         docounterRotate2(caPhiIDx, nIdx, cIdx, oIdx, caPsiIdx, dir, nWard)
+         do_counter_rotate(caPhiIdx, nIdx, cIdx, oIdx, caPsiIdx, dir, nTward)
-         var newang = angle({atomIndex=xIdx}, {atomIndex=oIdx}, {atomIndex=cIdx})
+         var newang = angle(toPt, {atomIndex=oIdx}, {atomIndex=cIdx})
          # If wrong direction once, undo and reverse
          if (newang > ang) {
-             docounterRotate2(caPhiIDx, nIdx, cIdx, oIdx, caPsiIdx, -dir, nWard)
+             do_counter_rotate(caPhiIDx, nIdx, cIdx, oIdx, caPsiIdx, -dir, nTward)
              # If first time, continue in opposite direction
              dir *= -1
@@ Line 718: / Line 549: @@
                  continue
              }
+        }
+        if (oDrag) {
+            break
          }
@@ Line 723: / Line 558: @@
          tcount++
          if (tcount > (360/abs(dir))) {
-             gOk2 = FALSE
+             gOk2 = false
              break
          }
      } # endwhile
      select selsave
 }
 # Repair proline
-function repairProline(idx) {
+function repair_proline(BBidx) {
-     var cbidx = getCBidx(idx)
+     var cbidx = get_cb_idx(BBidx)
      var cbno = {atomIndex=cbidx}.atomno
-     var cgidx = {(atomno=@{cbno+1}) and (chain=gChain)}.atomIndex
+     var cgidx = {(atomno=@{cbno+1}) and (chain=gChain)
-     var cdidx = {(atomno=@{cbno+2}) and (chain=gChain)}.atomIndex
+        and thisModel}.atomIndex
-     var caidx = {(atomno=@{cbno-3}) and (chain=gChain)}.atomIndex
+     var cdidx = {(atomno=@{cbno+2}) and (chain=gChain)
-     var nidx = {(atomno=@{cbno-4}) and (chain=gChain)}.atomIndex
+        and thisModel}.atomIndex
+     var caidx = {(atomno=@{cbno-3}) and (chain=gChain)
+        and thisModel}.atomIndex
+     var nidx = {(atomno=@{cbno-4}) and (chain=gChain)
+        and thisModel}.atomIndex
      select {atomIndex=cbidx}
-     setAngleIdx(nidx, caidx, cbidx, 109.5)
+     set_angle_idx(nidx, caidx, cbidx, 109.5)
      select {atomIndex=cdidx}
-     setDistanceIdx(nidx, cdidx, 1.47)
+     set_distance_idx(nidx, cdidx, 1.47)
-     setAngleIdx(caidx, nidx, cdidx, 102.7)
+     set_angle_idx(caidx, nidx, cdidx, 102.7)
-     setDihedralIdx(cbidx, caidx, nidx, cdidx, 16.2)
+     set_dihedral_idx(cbidx, caidx, nidx, cdidx, 16.2)
      select {atomIndex=cgidx}
-     setDistanceIdx(cdidx, cgidx, 1.51)
+     set_distance_idx(cdidx, cgidx, 1.51)
-     setAngleIdx(nidx, cdidx, cgidx, 106.4)
+     set_angle_idx(nidx, cdidx, cgidx, 106.4)
-     setDihedralIdx(caidx, nidx, cdidx, cgidx, 16.2)
+     set_dihedral_idx(caidx, nidx, cdidx, cgidx, 16.2)
 }
 # Repair side chain
-function plicoRepairSideChain(targetIdx, nWard) {
+function repair_sc(targetIdx, nWard) {
-     var idx = (nWard ? getCwardBBidx(targetIdx) : getNwardBBidx(targetIdx))
+     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 = getCBidx(targetIdx)
+         var cbidx = get_cb_idx(targetIdx)
          select none
-         selectAddSideChain(cbidx)
+         select_add_sc(cbidx)
-         setAngleIdx(idx, targetIdx, cbidx, 110.0)
+         set_angle_idx(idx, targetIdx, cbidx, 110.0)
-         setDistanceIdx(targetIdx, cbidx, 1.5)
+         set_distance_idx(targetIdx, cbidx, 1.5)
          if ({atomIndex=targetIdx}.group != "PRO") {
-             var colliders = (within(kCtolerance, FALSE, {selected})
+             var colliders = (within(kCtolerance, false, {selected})
                  and not {atomIndex=targetIdx} and not {selected})
-             if (colliders.size > 0) {
+             if (colliders) {
                  if ({atomIndex=targetIdx}.group != "ALA") {
-                     fixSCcollision2(cbidx)
+                     fix_sc_collision_2(cbidx)
                  }
              }
@@ Line 779: / Line 618: @@
              }
              else {
-                 setDihedralIdx(getNwardBBidx(idx), idx, targetIdx, cbidx, 174.2)
+                 set_dihedral_idx(get_nward_bb_idx(idx, gChain), idx, targetIdx, cbidx, 174.2)
              }
          }
      }
      else if ({atomIndex=targetIdx}.atomName == "C") {
-         var oidx = getOidx(targetIdx)
+         var oidx = get_o_idx(targetIdx)
          select {atomIndex=oidx}
-         setAngleIdx(idx, targetIdx, oidx, 120.0)
+         set_angle_idx(idx, targetIdx, oidx, 120.0)
-         setDistanceIdx(targetIdx, oidx, 1.21)
+         set_distance_idx(targetIdx, oidx, 1.21)
          if (nWard) {
-             setDihedralIdx(getCwardBBidx(idx), idx, targetIdx, oidx, 0.0)
+             set_dihedral_idx(get_cward_bb_idx(idx, gChain), idx, targetIdx, oidx, 0.0)
          }
          if ({atomIndex=idx}.group == "PRO") {
-             repairProline(idx)
+             repair_proline(idx)
              var dNo = {atomIndex=targetIdx}.atomno + 4
-             var dIdx = {(atomno=dNO) and (chain=gChain)}.atomIndex
+             var dIdx = {(atomno=dNO) and (chain=gChain)
-             var colliders = (within(kCtolerance, FALSE, {atomIndex=dIdx})
+                and thisModel}.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") {
-                     counterRotate2(dIdx, colliders[i].atomIndex, targetIdx)
+                     counter_rotate_2(colliders[i].atomIndex,
+                        {atomIndex=dIdx}.xyz, targetIdx, false)
                  }
              }
@@ Line 809: / Line 650: @@
 # Rebuild Cward rotors set
-function tugTrackC() {
+function tug_track_c() {
      # For all bb atoms cWard of cargo
      var targetIdx = gCcargoIdx
      var okCount = 0
      # Allow collisions with cargo
-     gOkCollide = gCargoAtoms
+     gOkCollide = gCargoSet
      var tcount = 0
-     while (targetIdx != gCanchorIdx) {
+     while (targetIdx != gNanchorIdx) {
          # Step to next atom
-         targetIdx = getCwardBBidx(targetIdx)
+         targetIdx = get_cward_bb_idx(targetIdx, gChain)
+         if (targetIdx < 0) {
+            break
+        }
          # No collision with cargo allowed after two atoms placed
          if (tcount == 2) {
@@ Line 828: / Line 672: @@
          }
          tcount++
          # Compute targets desired coords
-         var c1idx = getCwardBBidx(targetIdx)
+         try {
-        var n1idx = getNwardBBidx(targetIdx)
+            var c1idx = get_cward_bb_idx(targetIdx, gChain)
-        var n2idx = getNwardBBidx(n1Idx)
+            var n1idx = get_nward_bb_idx(targetIdx, gChain )
-        var n3idx = getNwardBBidx(n2Idx)
+            var n2idx = get_nward_bb_idx(n1Idx, gChain)
-        var pt = {0 0 0}
+            var n3idx = get_nward_bb_idx(n2Idx, gChain)
-        if ({atomIndex=targetIdx}.atomName == "N") {
+            var pt = {0 0 0}
-            var oidx = getOidx(n1idx)
+            if ({atomIndex=targetIdx}.atomName == "N") {
-            select {atomIndex=oidx}
+                var oidx = get_o_idx(n1idx)
+                select {atomIndex=oidx}
-            # Desired target location is trigonal O
-            setDistanceIdx(n1idx, oidx, 1.5)
+                # Desired target location is trigonal O
-            pt = getTrigonal(n2idx, n1idx, oidx, 1.37)
+                set_distance_idx(n1idx, oidx, 1.5)
-            setDistanceIdx(n1idx, oidx, 1.21)
+                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")) {
+            else if (({atomIndex=targetIdx}.atomName == "C")
+                and ({atomIndex=targetIdx}.group != "GLY")) {
-            # Desired target location is tetragonal CB
-            var cbidx = getCBidx(n1idx)
+                # Desired target location is tetragonal CB
-            pt = getTet(n2idx, n1idx, cbidx, 1.5)
+                var cbidx = get_cb_idx(n1idx)
-        }
+                pt = get_tet_idx(n2idx, n1idx, cbidx, 1.5)
-        else { # CA (or GLY C)
+            }
+            else { # CA (or GLY C)
-            # Save current target coords
-            var cp = {atomIndex=targetIdx}.xyz
+                # 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)) {
-            # Set target atom at desired distance and angle
+                    # Rotate on cWard rotor set to move it there
-            select {atomIndex=targetIdx}
+                    tug_track_idx(targetIdx, pt, false, false)
-            setDistanceIdx(n1idx, targetIdx, 1.5)
+                    xcount++
-             setAngleIdx(n2idx, n1idx, targetIdx, 110.0)
+                }
-             if ({atomIndex=targetIdx}.atomName == "CA") {
+             }
-                 setDihedralIdx(n3idx, n2idx, n1idx, targetIdx, 180)
+             else {
+                gOK = true
+                 okCount++
              }
+        }
-            # Record and restore target
+        catch {
-            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 (gOK == FALSE)) {
-                # Rotate on cWard rotor set to move it there
-                tugTrackIdx(targetIdx, pt, FALSE, FALSE)
-                    #(distance(pt, {atomIndex=targetIdx}) > kMtolerance))
-                xcount++
-            }
-        }
-        else {
-            gOK = TRUE
-            okCount++
-        }
          # If successful
-         if (gOK == TRUE) {
+         if (gOK == true) {
              # Adust any side atoms
-             plicoRepairSideChain(targetIdx, FALSE)
+             repair_sc(targetIdx, false)
          }
          # Else fail
          else {
              break
          }
          # If no movement in 4 tries, we are done
          if (okCount > 3) {
@@ Line 908: / Line 755: @@
 # Rebuild Nward rotors set
-function tugTrackN() {
+function tug_track_n() {
+    gOK = true
-    gOK = TRUE
      # For all bb atoms nWard of cargo
      var targetIdx = gNcargoIdx
      var okCount = 0
      # Allow collisions with cargo
-     gOkCollide = gCargoAtoms
+     gOkCollide = gCargoSet
      var tcount = 0
      while (targetIdx != gNanchorIdx) {
          # Step to next atom
-         targetIdx = getNwardBBidx(targetIdx)
+         targetIdx = get_nward_bb_idx(targetIdx, gChain)
+        if (targetIdx < 0) {
+            break
+        }
          # No collision with cargo allowed after two atoms placed
@@ Line 929: / Line 779: @@
          }
          tcount++
          # Compute targets desired coords
-         var n1idx = getNwardBBidx(targetIdx)
+         var n1idx = get_nward_bb_idx(targetIdx, gChain)
-         var c1idx = getCwardBBidx(targetIdx)
+         var c1idx = get_cward_bb_idx(targetIdx, gChain)
-         var c2idx = getCwardBBidx(c1idx)
+         var c2idx = get_cward_bb_idx(c1idx, gChain)
-         var c3idx = getCwardBBidx(c2idx)
+         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 = getOidx(c1idx)
+             var oidx = get_o_idx(c1idx)
              select {atomIndex=oidx}
-             setDistanceIdx(c1idx, oidx, 1.39)
+             set_distance_idx(c1idx, oidx, 1.39)
-             pt = getTrigonal(c2idx, c1idx, oidx, 1.41)
+             pt = get_trigonal_idx(c2idx, c1idx, oidx, 1.41)
-             setDistanceIdx(c1idx, oidx, 1.21)
+             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 = getCBidx(c1idx)
+             var cbidx = get_cb_idx(c1idx)
-             pt = getTet(cbidx, c1idx, c2idx, 1.5)
+             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}
-             setDistanceIdx(c1idx, targetIdx, 1.37)
+             set_distance_idx(c1idx, targetIdx, 1.37)
-             setAngleIdx(c2idx, c1idx, targetIdx, 110.0)
+             set_angle_idx(c2idx, c1idx, targetIdx, 110.0)
              if ({atomIndex=targetIdx}.group == "PRO") {
-                 setDihedralIdx(c3idx, c2idx, c1idx, targetIdx, -57.0)
+                 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
+             gOK = false
-             while ((xcount < 20) and (gOK == FALSE)) {
+             while ((xcount < 20) and (not gOK)) {
-                 # Rotate on cWard rotor set to move it there
+                 # Rotate on nWard rotor set to move it there
-                 tugTrackIdx(targetIdx, pt, TRUE, FALSE)
+                 tug_track_idx(targetIdx, pt, true, false)
-                    #(distance(pt, {atomIndex=targetIdx}) > kMtolerance))
                  xcount++
              }
          }
          else {
-             gOK = TRUE
+             gOK = true
              okCount++
          }
          # If sucessful
-         if (gOK == TRUE) {
+         if (gOK == true) {
              # Adust any side atoms
-             plicoRepairSideChain(targetIdx, TRUE)
+             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 plicoRecord(s) {
+function translate_selected_record(pt) {
-    var g = format("show file \"%s\"", gPlicoRecord)
-    var ls = script(g)
-    if (ls.find("FileNotFoundException")) {
-        ls = ""
-    }
-    ls += s
-    write var ls @gPlicoRecord
-}
-# gPlicoRecord is maintained by the macro pilcoRecord
-function translateSelectedRecord(pt) {
      if (gPlicoRecord != "") {
-         plicoRecord(format("select %s;translateSelected %s;", {selected}, pt))
+         plico_record(format("select %s;translateSelected %s;", {selected}, pt))
      }
      translateSelected @pt
@@ Line 1,031: / Line 868: @@
 # gPlicoRecord is maintained by the macro pilcoRecord
-function rotateSelectedRecord(g1pivotIdx, axis, a) {
+function rotate_selected_record(pivotIdx, caxis, a) {
      if (gPlicoRecord != "") {
-         plicoRecord(format("select %s;", {selected}))
+         plico_record(format("select %s;", {selected}))
-         plicoRecord(format("rotateSelected {atomIndex=%d} @%s @%s;",
+         plico_record(format("rotateSelected {atomIndex=%d} @%s @%s;",
-             g1pivotIdx, axis, a))
+             pivotIdx, caxis, a))
      }
-     rotateSelected {atomIndex=g1pivotIdx} @axis @a
+     rotateSelected {atomIndex=pivotIdx} @caxis @a
 }
-function collectSCrotors(no) {
+function collect_sc_rotors(no, iChain) {
      var scBondIdxs = array()
      for (var iNo = no; iNo >= 0; iNo--) {
          var ile = 0
-         switch ({(atomno=iNo) and (chain=gChain)}.atomName) {
+         switch ({(atomno=iNo) and (chain=iChain)
+            and thisModel}.atomName) {
          case "CA" :
              return scBondIdxs # Early exit since break 1 appears broken
-            #break 1
          case "CZ" :
-             if ({(atomno=iNo) and (chain=gChain)}.group == "TYR") {
+             if ({(atomno=iNo) and (chain=iChain)
+                and thisModel}.group == "TYR") {
                  break
              }
          case "CE" :
-             if ({(atomno=iNo) and (chain=gChain)}.group == "MET") {
+             if ({(atomno=iNo) and (chain=iChain)
+                and thisModel}.group == "MET") {
                  break
              }
          case "CG1" :
-             if ({(atomno=iNo) and (chain=gChain)}.group == "VAL") {
+             if ({(atomno=iNo) and (chain=iChain)
+                and thisModel}.group == "VAL") {
                  break
              }
-             if ({(atomno=iNo) and (chain=gChain)}.group == "ILE") {
+             if ({(atomno=iNo) and (chain=iChain)
+                and thisModel}.group == "ILE") {
                  ile = 1
              }
@@ Line 1,068: / Line 909: @@
          case "CG" :
          case "CB" :
-             scBondIdxs += {(atomno=@{iNo+1+ile}) and (chain=gChain)}.atomIndex
+             scBondIdxs += {(atomno=@{iNo+1+ile}) and (chain=iChain)
-             scBondIdxs += {(atomno=@{iNo+0}) and (chain=gChain)}.atomIndex
+                and thisModel}.atomIndex
-             if ({(atomno=iNo) and (chain=gChain)}.atomName%2 == "CG") {
+             scBondIdxs += {(atomno=@{iNo+0}) and (chain=iChain)
-                 scBondIdxs += {(atomno=@{iNo-1}) and (chain=gChain)}.atomIndex
+                and thisModel}.atomIndex
-                 scBondIdxs += {(atomno=@{iNo-4}) and (chain=gChain)}.atomIndex
+             if ({(atomno=iNo) and (chain=iChain)
+                and thisModel}.atomName%2 == "CG") {
+                 scBondIdxs += {(atomno=@{iNo-1}) and (chain=iChain)
+                    and thisModel}.atomIndex
+                 scBondIdxs += {(atomno=@{iNo-4}) and (chain=iChain)
+                    and thisModel}.atomIndex
              }
-             else if ({(atomno=iNo) and (chain=gChain)}.atomName == "CB") {
+             else if ({(atomno=iNo) and (chain=iChain)
-                 scBondIdxs += {(atomno=@{iNo-3}) and (chain=gChain)}.atomIndex
+                and thisModel}.atomName == "CB") {
-                 scBondIdxs += {(atomno=@{iNo-4}) and (chain=gChain)}.atomIndex
+                 scBondIdxs += {(atomno=@{iNo-3}) and (chain=iChain)
+                    and thisModel}.atomIndex
+                 scBondIdxs += {(atomno=@{iNo-4}) and (chain=iChain)
+                    and thisModel}.atomIndex
              }
              else {
-                 scBondIdxs += {(atomno=@{iNo-1}) and (chain=gChain)}.atomIndex
+                 scBondIdxs += {(atomno=@{iNo-1}) and (chain=iChain)
-                 scBondIdxs += {(atomno=@{iNo-2}) and (chain=gChain)}.atomIndex
+                    and thisModel}.atomIndex
+                 scBondIdxs += {(atomno=@{iNo-2}) and (chain=iChain)
+                    and thisModel}.atomIndex
              }
              break
          }
      }
      return scBondIdxs
 }
 # Drag Side Chain
-function dragSC() {
+function drag_sc() {
      var iNo = {atomIndex=gSCidx}.atomno
+     var iChain  = {atomIndex=gSCidx}.chain
      if ({atomIndex=gSCidx}.group != "PRO") {
-         var scBondIdxs = collectSCrotors( iNo)
+         var scBondIdxs = collect_sc_rotors( iNo, iChain)
          var numChi = scBondIdxs.size / 4
          var dist = distance({atomIndex=gSCidx}.xyz, gSCpt)
+        var scSet = get_sc_set(gSCidx, iChain)
          # For all rotor combinations
          var dh = array()
@@ Line 1,112: / Line 964: @@
              for (var j = 0; j < 6; j++) {
                  rot += 60*j
-                 selectAddSideChain(scBondIdxs[1+(4*i)])
+                 select_add_sc(scBondIdxs[1+(4*i)])
-                 setDihedralIdx(scBondIdxs[4+(4*i)], scBondIdxs[3+(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) {
+                        continue
+                    }
+                }
                  # Find the best
                  if (newDist < dist) {
@@ Line 1,129: / Line 988: @@
              }
          }
          # Now set the best
          for (var i = 0; i < numChi; i++) {
-             selectAddSideChain(scBondIdxs[1+(4*i)])
+             select_add_sc(scBondIdxs[1+(4*i)])
-             setDihedralIdx(scBondIdxs[4+(4*i)], scBondIdxs[3+(4*i)],
+             set_dihedral_idx(scBondIdxs[4+(4*i)], scBondIdxs[3+(4*i)],
                  scBondIdxs[2+(4*i)], scBondIdxs[1+(4*i)], dh[i+1])
+        }
+        if (gSCcheck = false) {
+            plico_minimize( scSet)
          }
      }
      else { # PRO - toggle between puckers up and down
-         var icd = {(atomno=@{iNo+1}) and (chain=gChain)}.atomIndex
+         var icd = {(atomno=@{iNo+1}) and (chain=iChain)
-         var icb = {(atomno=@{iNo-1}) and (chain=gChain)}.atomIndex
+            and thisModel}.atomIndex
-         var ica = {(atomno=@{iNo-4}) and (chain=gChain)}.atomIndex
+         var icb = {(atomno=@{iNo-1}) and (chain=iChain)
-         var in = {(atomno=@{iNo-5}) and (chain=gChain)}.atomIndex
+            and thisModel}.atomIndex
+         var ica = {(atomno=@{iNo-4}) and (chain=iChain)
+            and thisModel}.atomIndex
+         var in = {(atomno=@{iNo-5}) and (chain=iChain)
+            and thisModel}.atomIndex
          select {atomIndex=gSCidx}
          if (angle({atomIndex=ica}, {atomIndex=in},
              {atomIndex=icd}, {atomIndex=gSCidx}) < -10.0) {
-             setDihedralIdx(ica, in, icd, gSCidx, 8.7)
+             set_dihedral_idx(ica, in, icd, gSCidx, 8.7)
-             setAngleIdx(in, icd, gSCidx, 110.0)
+             set_angle_idx(in, icd, gSCidx, 110.0)
-             setDistanceIdx(icd, gSCidx, 1.5)
+             set_distance_idx(icd, gSCidx, 1.5)
          }
          else {
-             setDihedralIdx(ica, in, icd, gSCidx, -29.5)
+             set_dihedral_idx(ica, in, icd, gSCidx, -29.5)
-             setAngleIdx(in, icd, gSCidx, 108.8)
+             set_angle_idx(in, icd, gSCidx, 108.8)
-             setDistanceIdx(icd, gSCidx, 1.5)
+             set_distance_idx(icd, gSCidx, 1.5)
          }
      }
      draw gSCcircle CIRCLE {atomIndex=gSCidx} MESH NOFILL
      gSCpt = {atomIndex=gSCidx}.xyz
 }
 # Fix side chain collisions
-function fixSCcollision2(idx) {
+function fix_sc_collision_2(idx) {
-     gOk2 = FALSE
+     gOk2 = false
      var iNo = {atomIndex=idx}.atomno
-     var resno = {(atomno=iNo) and (chain=gChain)}.resno
+    var iChain = {atomIndex=idx}.chain
+     var resno = {(atomno=iNo) and (chain=iChain)
+        and thisModel}.resno
      # Get SC terminus
-     while (resno == {(atomno=iNo) and (chain=gChain)}.resno) {
+     while (resno == {(atomno=iNo) and (chain=iChain)
+        and thisModel}.resno) {
          iNo++
      }
      iNo--
      var sc = array()
      var iBno = iNo
-     while ({(atomno=iBno) and (chain=gChain)}.atomName != "CB") {
+     while ({(atomno=iBno) and (chain=iChain)
-         sc += {(atomno=iBno) and (chain=gChain)}
+        and thisModel}.atomName != "CB") {
+         sc += {(atomno=iBno) and (chain=iChain)
+            and thisModel}
          iBno--
      }
-     var cbidx = {(atomno=iBno) and (chain=gChain)}.atomIndex
+     var cbidx = {(atomno=iBno) and (chain=iChain)
+        and thisModel}.atomIndex
-     var scBondIdxs = collectSCrotors( iNo)
+     var scBondIdxs = collect_sc_rotors( iNo, iChain)
      var numChi = scBondIdxs.size / 4
      # For all rotor combinations
      for (var i = 0; i < numChi; i++) {
@@ Line 1,188: / Line 1,062: @@
          for (var j = 0; j < 6; j++) {
              rot += 60
-             selectAddSideChain(scBondIdxs[1+(4*i)])
+             select_add_sc(scBondIdxs[1+(4*i)])
-             #setDihedralIdx(scBondIdxs[4+(4*i)], scBondIdxs[3+(4*i)],
+             set_dihedral_idx(scBondIdxs[1+(4*i)], scBondIdxs[2+(4*i)],
-            #    scBondIdxs[2+(4*i)], scBondIdxs[1+(4*i)], rot)
-            setDihedralIdx(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})
+             var 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++ ) {
@@ Line 1,204: / Line 1,077: @@
                  }
              }
              if (colliders.size == 0) {
-                 gOk2 = TRUE
+                 gOk2 = true
                  return # Early exit since break 1 appears broken
-                #break 1
              }
          }
      }
 }
-function isMovableSideChain(aIdx) {
+function is_moveable_sc(aIdx) {
      var ret = (({atomIndex=aIdx}.group != "PRO")
@@ Line 1,226: / Line 1,098: @@
      case "O":
      case "O4\'":
-         ret = FALSE
+         ret = false
          break
      }
@@ Line 1,232: / Line 1,104: @@
 }
-# gFreeze is maintained by the script plicoFreeze that allows the user
+function is_rotor_avail(i1idx, i2idx) {
-# to inhibit rotation on selected rotors
+    var ret = true
-function isRotorAvailable(idx) {
+    if (i1idx > i2idx) { # frozen bonds are kept as lo-hi
-     return (gFreeze.find(idx) == 0)
+        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 collectBBrotors(nWard) {
+function xcollect_bb_rotors(nWard) {
      var anchorNo = (nWard
          ? ((gNanchorIdx >= 0) ? {atomIndex=gNanchorIdx}.atomno : gMinNo)
@@ Line 1,248: / Line 1,132: @@
      var rotors = array()
      if (cargoNo < anchorNo) {
-        # If cWard cargo is C, include its psi
-        if ({(atomno=cargoNo) and (chain=gChain)}.atomName == "C") {
-            #cargoNo--
-        }
          for (var iNo = cargoNo; iNo <= anchorNo; iNo++) {
-             if ({(atomno=iNo) and (chain=gChain)}.atomName == "CA") {
+             if ({(atomno=iNo) and (chain=gChain)
-                 if (isRotorAvailable(iNo)) {
+                and thisModel}.atomName == "CA") {
-                     if (({(atomno=iNo) and (chain=gChain)}.group != "PRO") and (iNo > cargoNo)) { # phi
+                 if (is_rotor_avail(iNo)) {# xxx
-                         rotors += [{(atomno=@{getCmNo(iNo-1)}) and (chain=gChain)}.atomIndex,
+                     if (({(atomno=iNo) and (chain=gChain)
-                             {(atomno=@{iNo-1}) and (chain=gChain)}.atomIndex]
+                        and thisModel}.group != "PRO") and (iNo > cargoNo)) { # phi
-                         rotors += [{(atomno=@{iNo}) and (chain=gChain)}.atomIndex,
+                         rotors += [{(atomno=@{get_cm_no(iNo-1)}) and (chain=gChain)
-                             {(atomno=@{iNo+1}) and (chain=gChain)}.atomIndex]
+                            and thisModel}.atomIndex,
+                             {(atomno=@{iNo-1}) and (chain=gChain)
+                                and thisModel}.atomIndex]
+                         rotors += [{(atomno=@{iNo}) and (chain=gChain)
+                            and thisModel}.atomIndex,
+                             {(atomno=@{iNo+1}) and (chain=gChain)
+                                and thisModel}.atomIndex]
                      }
                      if (iNo != (anchorNo-1)) { # psi
-                         rotors += [{(atomno=@{iNo-1}) and (chain=gChain)}.atomIndex,
+                         rotors += [{(atomno=@{iNo-1}) and (chain=gChain)
-                             {(atomno=@{iNo}) and (chain=gChain)}.atomIndex]
+                            and thisModel}.atomIndex,
-                         rotors += [{(atomno=@{iNo+1}) and (chain=gChain)}.atomIndex,
+                             {(atomno=@{iNo}) and (chain=gChain)
-                             {(atomno=@{getNpNo(iNo+2)}) and (chain=gChain)}.atomIndex]
+                                and thisModel}.atomIndex]
+                         rotors += [{(atomno=@{iNo+1}) and (chain=gChain)
+                            and thisModel}.atomIndex,
+                             {(atomno=@{get_np_no(iNo+2)}) and (chain=gChain)
+                                and thisModel}.atomIndex]
                      }
                  }
@@ Line 1,274: / Line 1,163: @@
      }
      else {
-        # If nWard cargo is C, include its phi
-        if ({(atomno=cargoNo) and (chain=gChain)}.atomName == "N") {
-            #cargoNo++
-        }
          for (var iNo = cargoNo; iNo >= anchorNo; iNo--) {
-             if ({(atomno=iNo) and (chain=gChain)}.atomName == "CA") {
+             if ({(atomno=iNo) and (chain=gChain)
-                 if (isRotorAvailable(iNo)) {
+                and thisModel}.atomName == "CA") {
+                 if (is_rotor_avail(iNo)) {
                      if ((iNo != (anchorNo-1)) and (iNo < cargoNo)) { # psi
-                         rotors += [{(atomno=@{getNpNo(iNo+2)}) and (chain=gChain)}.atomIndex,
+                         rotors += [{(atomno=@{get_np_no(iNo+2)}) and (chain=gChain)
-                             {(atomno=@{iNo+1}) and (chain=gChain)}.atomIndex]
+                            and thisModel}.atomIndex,
-                         rotors += [{(atomno=@{iNo}) and (chain=gChain)}.atomIndex,
+                             {(atomno=@{iNo+1}) and (chain=gChain)
-                             {(atomno=@{iNo-1}) and (chain=gChain)}.atomIndex]
+                                and thisModel}.atomIndex]
+                         rotors += [{(atomno=@{iNo}) and (chain=gChain)
+                            and thisModel}.atomIndex,
+                             {(atomno=@{iNo-1}) and (chain=gChain)
+                                and thisModel}.atomIndex]
                      }
-                     if ({(atomno=iNo) and (chain=gChain)}.group != "PRO") { # phi
+                     if ({(atomno=iNo) and (chain=gChain)
-                         rotors += [{(atomno=@{iNo+1}) and (chain=gChain)}.atomIndex,
+                        and thisModel}.group != "PRO") { # phi
-                             {(atomno=@{iNo}) and (chain=gChain)}.atomIndex]
+                         rotors += [{(atomno=@{iNo+1}) and (chain=gChain)
-                         rotors += [{(atomno=@{iNo-1}) and (chain=gChain)}.atomIndex,
+                            and thisModel}.atomIndex,
-                             {(atomno=@{getCmNo(iNo-1)}) and (chain=gChain)}.atomIndex]
+                             {(atomno=@{iNo}) and (chain=gChain)
+                                and thisModel}.atomIndex]
+                         rotors += [{(atomno=@{iNo-1}) and (chain=gChain)
+                            and thisModel}.atomIndex,
+                             {(atomno=@{get_cm_no(iNo-1)}) and (chain=gChain)
+                                and thisModel}.atomIndex]
                      }
                  }
@@ Line 1,299: / Line 1,193: @@
          }
      }
      if (nWard) {
          gNrotors = rotors
-         if (FALSE) {#DEBUG
+    }
-            print ("gNrotors atomnos")#DEBUG
+    else {
-            for (var i = 1; i < gNrotors.size; i += 4) {#DEBUG
+         gCrotors = rotors
-                print format("%d %d %s", {atomIndex=@{gNrotors[i]}}.atomno,
+    }
-                    {atomIndex=@{gNrotors[i+1]}}.atomno, format("%d %d",
+}
-                    {atomIndex=@{gNrotors[i+2]}}.atomno,
+function collect_bb_rotors(nWard) {
-                    {atomIndex=@{gNrotors[i+3]}}.atomno))
+    if (nWard) {
+        gNrotors = array()
+        var nres = {atomIndex=gNcargoIdx}.resno
+        var nname = {atomIndex=gNcargoIdx}.atomName
+        var ares = get_resno_min(gChain)
+        var aA = get_atom_rcn( ares, gChain, "N")
+        if (gNanchorIdx >= 0) {
+            aA = {atomIndex=gNanchorIdx}
+        }
+        var aname = aA.atomName
+        for (var r = nres; r >= ares; r--) {
+            var aCp = get_atom_rcn( r-1, gChain, "C")
+            var aN = get_atom_rcn( r, gChain, "N")
+            var aCa = get_atom_rcn( r, gChain, "CA")
+            var aC = get_atom_rcn( r, gChain, "C")
+            var aNn = get_atom_rcn( r+1, gChain, "N")
+            if (aCp.size < 1) {
+                aCp = aNn
              }
-         }#DEBUG
+            # psi
+            if (((r < nres) and (r > ares))
+                or ((r == nres) and (nname == "C"))
+                or ((r == ares) and (aname != "C"))) {
+                if (is_rotor_avail(aCa.atomIndex, aC.atomIndex)) {
+                    gNrotors += aNn.atomIndex
+                    gNrotors += aC.atomIndex
+                    gNrotors += aCa.atomIndex
+                    gNrotors += aN.atomIndex
+                }
+            }
+            # phi
+            if (aCa.group != "PRO") {
+                if (((r <= nres) and (r > ares))
+                    or ((r == ares) and (aname == "N"))) {
+                    if (is_rotor_avail(aCa.atomIndex, aN.atomIndex)) {
+                        gNrotors += aC.atomIndex
+                        gNrotors += aCa.atomIndex
+                        gNrotors += aN.atomIndex
+                        gNrotors += aCp.atomIndex
+                    }
+                }
+            }
+         } # endfor
      }
      else {
-         gCrotors = rotors
+         gCrotors = array()
-         if (FALSE) {#DEBUG
+        var cres = {atomIndex=gCcargoIdx}.resno
-             print ("gCrotors atomnos")#DEBUG
+        var cname = {atomIndex=gCcargoIdx}.atomName
-             for (var i = 1; i < gCrotors.size; i += 4) {#DEBUG
+        var ares = get_resno_max(gChain)
-                 print format("%d %d %s", {atomIndex=@{gCrotors[i]}}.atomno,
+        var aA = get_atom_rcn( ares, gChain, "C")
-                    {atomIndex=@{gCrotors[i+1]}}.atomno, format("%d %d",
+         if (gCanchorIdx >= 0) {
-                    {atomIndex=@{gCrotors[i+2]}}.atomno,
+             aA = {atomIndex=gCanchorIdx}
-                     {atomIndex=@{gCrotors[i+3]}}.atomno))
+        }
+        var aname = aA.atomName
+        for (var r = cres; r <= ares; r++) {
+            var aCp = get_atom_rcn( r-1, gChain, "C")
+            var aN = get_atom_rcn( r, gChain, "N")
+             var aCa = get_atom_rcn( r, gChain, "CA")
+            var aC = get_atom_rcn( r, gChain, "C")
+            var aNn = get_atom_rcn( r+1, gChain, "N")
+            if (aNn.size < 1) {
+                aNn = aCp
+            }
+            # phi
+            if (aCa.group != "PRO") {
+                 if (((r > cres) and (r < ares))
+                    or ((r == cres) and (aname == "N"))
+                    or ((r == ares) and (aname != "N"))) {
+                    if (is_rotor_avail(aN.atomIndex, aCa.atomIndex)) {
+                        gCrotors += aCp.atomIndex
+                        gCrotors += aN.atomIndex
+                        gCrotors += aCa.atomIndex
+                        gCrotors += aC.atomIndex
+                    }
+                }
+            }
+            # psi
+            if (((r >= cres) and (r < ares))
+                or ((r == cres) and (aname != "C"))
+                or ((r == ares) and (aname == "C"))) {
+                if (is_rotor_avail(aCa.atomIndex, aC.atomIndex)) {
+                    gCrotors += aN.atomIndex
+                     gCrotors += aCa.atomIndex
+                    gCrotors += aC.atomIndex
+                    gCrotors += aNn.atomIndex
+                }
              }
-         }#DEBUG
+         } # endfor
      }
 }
-function collectRotors() {
+function collect_rotors() {
-     collectBBrotors(FALSE)
+     collect_bb_rotors(false)
-     collectBBrotors(TRUE)
+     collect_bb_rotors(true)
 }
-function tugSideChain(pt) {
+function tug_sc(pt) {
      # If destination atom defined
      if (gDestAtomIdx >= 0) {
-         v = {atomIndex=gDestAtomIdx}.xyz - {atomIndex=gSCidx}.xyz
+         var v = {atomIndex=gDestAtomIdx}.xyz - {atomIndex=gSCidx}.xyz
          if (abs(angle({atomIndex=gDestAtomIdx}.xyz, {0 0 0}, pt)) < 90) {
              pt = -v/20.0
@@ Line 1,344: / Line 1,314: @@
      }
      gSCpt += pt
      draw arrow {atomIndex=gSCidx} @gSCpt
 }
-function setColors() {
+function set_colors() {
-     select all
+     select (thisModel)
      color {selected} @gScheme
-    color {atomIndex=gCanchorIdx} @gAltScheme
-    color {atomIndex=gNanchorIdx} @gAltScheme
      color {atomIndex=g1pivotIdx} green
      color {atomIndex=g2pivotIdx} green
-     color @gCargoAtoms @gAltScheme
+     color @gCargoSet @gAltScheme
-     select {(atomIndex=gCcargoIdx) or (atomIndex=gNcargoIdx)}
+    color {gCargoSet and oxygen} pink
+     select {(atomIndex=gCcargoIdx) or (atomIndex=gNcargoIdx)
+        or (atomIndex=gCanchorIdx) or (atomIndex=gNanchorIdx)}
      halo on
      select {atomIndex=gDestAtomIdx}
@@ Line 1,362: / Line 1,332: @@
 }
-function clearAtomIdxs() {
+function clear_atom_idxs() {
      gCcargoIdx = -1
      gNcargoIdx = -1
@@ Line 1,369: / Line 1,339: @@
      g1pivotIdx = -1
      g2pivotIdx = -1
+    g1dynamicIdx = -1
+    g2dynamicIdx = -1
      gDestAtomIdx = -1
      gSCidx = -1
 }
-function timedOut (s) {
+function timed_out (s) {
      timeout ID"tug" OFF
-    prompt(s)
-    gBusy = FALSE
-    background ECHO yellow
-    restore state gState
-    select gCargoAtoms
      refresh
-     quit
+     if (prompt(format("%s - Undo?", s), "Yes|No", true) == "Yes") {
+        gBusy = false
+        restore state gState
+        connect
+        select gCargoSet
+        set bondPicking true
+        refresh
+        for (var i = 1; i <= gFreeze.size; i+=2) {
+            select {atomIndex=@{gFreeze[i]}} or {atomIndex=@{gFreeze[i+1]}}
+            color bonds lightblue
+        }
+        background ECHO yellow
+        echo @gEcho
+        select all
+        quit
+    }
 }
-function recordDrag() {
+function record_drag() {
      var ls = format("select %s;", {selected})
      ls += format("gCanchorIdx = %d;", gCanchorIdx)
@@ Line 1,390: / Line 1,372: @@
      ls += format("gNanchorIdx = %d;", gNanchorIdx)
      ls += format("gNanchorNo = %d;", gNanchorNo)
-    ls += format("gNanchorPidx = %d;", gNanchorPidx)
-    ls += format("gCanchorXyz = %s;", gCanchorXyz)
-    ls += format("gNanchorXyz = %s;", gNanchorXyz)
-    ls += format("gNanchorPxyz = %s;", gNanchorPxyz)
      ls += format("gCcargoIdx = %d;", gCcargoIdx)
      ls += format("gNcargoIdx = %d;", gNcargoIdx)
-    ls += format("gCcargoXyz = %s;", gCcargoXyz)
-    ls += format("gNcargoXyz = %s;", gNcargoXyz)
      ls += format("gCcargoNo = %d;", gCcargoNo)
      ls += format("gNcargoNo = %d;", gNcargoNo)
@@ Line 1,403: / Line 1,379: @@
      ls += format("g1pivotIdx = %d;", g1pivotIdx)
      ls += format("g2pivotIdx = %d;", g2pivotIdx)
-     ls += format("gAc = %s;", gAc)
+     ls += format("gOkCollide = %s;", gOkCollide)
      ls += format("gChain = \"%s\";", gChain)
      ls += format("gMinNo = %d;", gMinNo)
      ls += format("gMaxNo = %d;", gMaxNo)
-     ls += format("gCargoAtoms = %s;", gCargoAtoms)
+     ls += format("gCargoSet = %s;", gCargoSet)
      ls += format("gSCidx = %d;", gSCidx)
      ls += format("gSCcircle = %d;", gSCcircle)
      ls += format("gSCpt = %s;", gSCpt)
-     ls += "collectRotors();"
+     ls += "collect_rotors();"
-     ls += "tugDragDoneMB();"
+     ls += "tug_drag_done_mb();"
-     plicoRecord(ls)
+     plico_record(ls)
 }
-# Bound to LEFT-UP by tugEnableDrag
+# Pick call-back for freeze
-function tugDragDoneMB() {
+function tug_pick_cb() {
-     if (gPlicoRecord != "") {
+     if (_pickInfo[3][6] == "bond") {
-        recordDrag()
+        var sel = {selected}
+        var i = _pickInfo.find(":")
+        var iChain = _pickInfo[i+1]
+        i = _pickInfo.find("#")
+        var a1no = 0 + _pickInfo[i+1][i+3]
+        var j = _pickInfo[i+1][9999].find("#")
+        var a2no = 0 + _pickInfo[i+j+1][i+j+3]
+        var i1idx = {(atomno=a1no) and (chain=iChain)
+            and thisModel}.atomIndex
+        var i2idx = {(atomno=a2no) and (chain=iChain)
+            and thisModel}.atomIndex
+        if (({atomIndex=i1idx}.atomName == "CA")
+            or ({atomIndex=i2idx}.atomName == "CA")) {
+            if (({atomIndex=i1idx}.atomName != "CB")
+                and ({atomIndex=i2idx}.atomName != "CB")) {
+                if (i1idx > i2idx) {
+                    var 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)) {
+                        if (i > 1) {
+                            if (gFreeze.size = (i+1)) {
+                                gFreeze = gFreeze[1][i-1]
+                            }
+                            else {
+                                gFreeze = gFreeze[1][i-1] + gFreeze[i+2][0]
+                            }
+                        }
+                        else {
+                            gFreeze = gFreeze[i+2][0]
+                        }
+                        color bonds NONE
+                        i = 0
+                        break
+                    }
+                }
+                if (i > gFreeze.size) {
+                    gFreeze += i1idx
+                    gFreeze += i2idx
+                    color bonds lightblue
+                }
+            }
+        }
+        select {sel}
      }
+}
-     # Move by rotation on rotor sets, smallest first
-    gBusy = TRUE
+# Bound to LEFT-UP by tug_enable_drag
-    background ECHO pink
+function tug_drag_done_mb() {
-    refresh
+     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 side chain mode
-    if (gSCidx >= 0) {
+        if (gSCidx >= 0) {
-        dragSC()
+             drag_sc()
-    }
-    # Else
-    else {
-        gOK = TRUE
-        timeout ID"tug" 20.0 "timedOut(\"Tug timed out\")"
-        gCountdown = kCollisionLimit
-        if ((gCrotors.size < gNrotors.size) or (gNanchorIdx < 0)) {
-             if (gCrotors.size > 4) {
-                tugTrackC()  # PULLSTRING MODEL
-            }
-            if (gOK and (gNrotors.size > 4)) {
-                tugTrackN()  # PULLSTRING MODEL
-            }
          }
-         else {
-             if (gNrotors.size > 4) {
+        # Else
-                 tugTrackN()  # PULLSTRING MODEL
+         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()
+                }
              }
-             if (gOK and (gCrotors.size > 4)) {
+             else {
-                tugTrackC()  # PULLSTRING MODEL
+                if (gNrotors.size > 4) {
+                    tug_track_n()
+                }
+                if (gOK and (gCrotors.size > 4)) {
+                    tug_track_c()
+                }
              }
-        }
+            timeout ID"tug" OFF
-        timeout ID"tug" OFF
+            # If anchor angles acute, fail
-        # If anchor angles acute, fail
+            if (gOK == true) {
-        if (gOK == TRUE) {
+                if (gCanchorIdx >= 0) {
-            if (gCanchorIdx >= 0) {
+                    var ic = get_cward_bb_idx(gCanchorIdx, gChain)
-                var ic = getCwardBBidx(gCanchorIdx)
+                    var in = get_nward_bb_idx(gCanchorIdx, gChain)
-                var in = getNwardBBidx(gCanchorIdx)
+                    if ((ic >= 0) and
-                if ((ic >= 0) and
+                        angle({atomIndex=ic}, {atomIndex=gCanchorIdx}, {atomIndex=in})
-                    angle({atomIndex=ic}, {atomIndex=gCanchorIdx}, {atomIndex=in})
+                        < 100.0) {
-                     < 100.0) {
+                        gOK = false
-                    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 (gNanchorIdx >= 0) {
-                 var ic = getCwardBBidx(gNanchorIdx)
+            # If too far
-                var in = getNwardBBidx(gNanchorIdx)
+             if (not gOK) {
-                if ((in >= 0) and
+                 timed_out("TUG TOO FAR!")
-                    angle({atomIndex=ic}, {atomIndex=gNanchorIdx}, {atomIndex=in})
-                    < 100.0) {
-                    gOK = FALSE
-                }
              }
-        }
-        # If too far
-        if (gOK == FALSE) {
-            timedOut("TUG TOO FAR!")
-        }
-        # Else OK
-        else {
-             select ((atomno >= gNanchorNo) and (atomno <= gCanchorNo)
+             # Else OK
-                 and (chain = gChain))
+            else {
-            var idx = {atomno=@{{chain=gChain}.min.atomno}}.atomIndex
+                 var idx = {
+                    (atomno=@{{(chain=gChain) and thisModel}.atomno.min})
+                    and (chain=gChain) and thisModel}.atomIndex
+                var ihc = 0
-            var i = 0
+                for (ihc = 0; ihc < 10; ihc++) {
-            for (; i < 3; i++) {
+                    select ((atomno >= gNanchorNo) and (atomno <= gCanchorNo)
-                handleCollisions(FALSE, idx)
+                        and (chain = gChain) and thisModel)
-                if (countCollisions() == 0) {
+                    handle_collisions( idx)
-                     break
+                    if (count_collisions(({})).size == 0) {
+                        break
+                    }
+                }
+                if (ihc == 10) {
+                     timed_out("Unable to handle all collisions!")
                  }
              }
-            if (i == 3) {
-                var p = prompt("Unable to handle all collisions!")
-                restore state gState
-            }
          }
+        select {gCargoSet}
+        gBusy = false
+        background ECHO yellow
+        set bondPicking true
+        refresh
      }
-    select {gCargoAtoms}
-    gBusy = FALSE
-    background ECHO yellow
-    refresh
 }
-# Bound to ALT-LEFT-DRAG by tugEnableDrag
+# Bound to ALT-SHIFT-LEFT-DRAG by tug_enable_drag
-function tugDragMB() {
+function tug_drag_2_mb() {
-     if (gBusy == FALSE) {
+    tug_drag_mb(true)
-         var dx = (20.0 * (_mouseX - gMouseX))/_width
+}
-         var dy = (20.0 * (_mouseY - gMouseY))/_height
-         var q = quaternion(script("show rotation"))
+# 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 caxis = {0 0 0}
          if (distance(pt,  {0 0 0}) > 0.004) {
              # If sidechain mode
              if (gSCidx >= 0) {
-                 tugSideChain(pt)
+                 if ({atomIndex=gSCidx}.atomName == "O") {
+                    if ({atomIndex=gSCidx}.group != "PRO") {
+                        var 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
+                     gNewDrag = false
                      save state gState
                  }
-                #mp = ({atomIndex=gNcargoIdx}.xyz + {atomIndex=gCcargoIdx}.xyz )/2.0
                  # If destination atom defined
                  if (gDestAtomIdx >= 0) {
@@ Line 1,546: / Line 1,593: @@
                      }
                  }
                  # Move the cargo
-                 select {gCargoAtoms}
+                 select {gCargoSet}
                  # If pivots defined, rotate it
                  if (g1pivotIdx >= 0) {
                      # If two pivots
-                    var axis = {0 0 0}
                      if (g2pivotIdx >= 0) {
-                         axis = {atomIndex=g2pivotIdx}
+                         caxis = {atomIndex=g2pivotIdx}
                      }
                      # Else
                      else {
-                         axis = cross(pt, {0 0 0}) + {atomIndex=g1pivotIdx}.xyz
+                         caxis = cross(pt, {0 0 0}) + {atomIndex=g1pivotIdx}.xyz
                      }
-                     var a = ((abs(angle(pt + {atomIndex=g1pivotIdx}.xyz,
+                     var dir = ((abs(dx) > abs(dy))
-                         {atomIndex=g1pivotIdx}.xyz, axis)) < 90) ? -2 : 2)
+                         ? ((dx < 0) ? 2 : -2)
-                     #rotateSelected {atomIndex=g1pivotIdx} @axis @a
+                        : ((dy < 0) ? 2 : -2))
-                    rotateSelectedRecord(g1pivotIdx, axis, a)
+                     rotate_selected_record(g1pivotIdx, caxis, dir)
                  }
                  # Else translate it
                  else {
-                     #translateSelected @pt
+                     translate_selected_record(pt)
-                    translateSelectedRecord(pt)
                  }
                  # If collisions
-                 var aset = {((atomno < gCanchorNo) and (atomno > gNanchorNo)
+                 var cNotSels = (within(kCtolerance, false, {selected})
-                     and (chain=gChain))}
+                    and not {gMovingSet})
-                var ac = (within(kCtolerance, FALSE, {aset}) and not {aset}
+                if ((cNotSels) and (not alt)) {
-                    and not connected(aset))
+                    gOk2 = true
-                if (ac.size > 0) {
+                     for (var i = 1; i <= cNotSels.size;  i++) {
-                    # Resolve them
-                    for (var i = 1; i <= ac.size;  i++) {
+                        # If net collision vector same as move vector
-                        select ac[i]
+                        var cSels = (within(kCtolerance, false, cNotSels[i]) and {selected})
-                         handleCollisions()
+                        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 thisModel}.atomno.min})
+                                        and (chain=gChain) and thisModel}.atomIndex
+                                    handle_collisions( idx)
+                                }
+                            }
+                        } # endfor
+                         if (not gOk2) {
+                            break
+                        }
+                     } # endfor
                      # If unable
-                     if (gOk2 == FALSE) {
+                     if (not gOk2) {
                          # Back off
                          background ECHO pink
                          delay 1
                          if (g1pivotIdx >= 0) {
-                             rotateSelectedRecord(g1pivotIdx, axis, -a)
+                             rotate_selected_record(g1pivotIdx, caxis, -a)
                          }
                          else {
-                             translateSelectedRecord(-pt)
+                             translate_selected_record(-pt)
                          }
                          background ECHO yellow
+                        set bondPicking true
                      }
                  }
-                #tugDragDoneMB()
              }
+             # 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 {gCargoAtoms}
+         select {gCargoSet}
+        gBusy = false
      }
 }
-# Bound to ALT-LEFT-DOWN by tugEnableDrag
+# Bound to ALT-LEFT-DOWN by tug_enable_drag
-function tugMarkMB() {
+function tug_mark_mb() {
      gMouseX = _mouseX
      gMouseY = _mouseY
-    gNcargoXyz = {atomIndex=gNcargoIdx}.xyz
+     gNewDrag = true
-    gCcargoXyz = {atomIndex=gCcargoIdx}.xyz
-     gNewDrag = TRUE
 }
-# Called by tugCargoMB and by tugAnchorMB or tugPivotMB when cargo exists
+# Called by tug_cargo_mb
-function tugEnableDrag() {
+function tug_enable_drag() {
-     gEcho = "ALT-CLICK=set cargo range|ALT-DRAG=move|SHIFT=set anchors|ALT-CTRL=set pivots|ALT-SHIFT=set dest atom |DOUBLE-CLICK=exit"
+     gEcho = "__________TUG__________|ALT-CLICK=mark block|SHIFT-CLICK=anchors" +
+        "|ALT-CTRL-CLICK=pivots|ALT-SHIFT-CLICK=dest atom|ALT-DRAG=move" +
+        "|ALT-SHIFT-DRAG=alt move|CLICK bond=freeze|ALT-DOUBLE-CLICK=undo" +
+        "|SHIFT-DOUBLE-CLICK=exit"
      echo @gEcho
      # Allow atoms to be dragged
-     bind "ALT-LEFT-DOWN" "tugMarkMB";
+     bind "ALT-LEFT-DOWN" "tug_mark_mb";
-     bind "ALT-LEFT-UP" "tugDragDoneMB";#ONCEMODE
+     bind "ALT-LEFT-UP" "tug_drag_done_mb";
-     bind "ALT-LEFT-DRAG" "tugDragMB";
+     bind "ALT-SHIFT-LEFT-DOWN" "tug_mark_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 tugCargoMB
+# Bound to SHIFT-LEFT-CLICK by tug_cargo_mb
-function tugAnchorMB() {
+function tug_anchor_mb() {
      if ({atomIndex=_atomPicked}.chain == gChain) {
-         var aPidx = getScBBidx( _atomPicked)
+         var aPidx = get_sc_bb_idx( _atomPicked, gChain)
          var pno = {atomIndex=aPidx}.atomno
          if (pno > {atomIndex=gCcargoIdx}.atomno) {
-             color {atomIndex=gCanchorIdx} @gScheme
+             select {atomIndex=gCanchorIdx}
+            halo off
              if (gCanchorIdx == aPidx) {
                  gCanchorIdx = -1
@@ Line 1,649: / Line 1,769: @@
                  gCanchorIdx = aPidx
                  gCanchorNo = {atomIndex=gCanchorIdx}.atomno
-                 gCanchorXyz = {atomIndex=gCanchorIdx}.xyz
+                 select {atomIndex=gCanchorIdx}
-                 color {atomIndex=gCanchorIdx} @gAltScheme
+                 halo on
              }
-             collectBBrotors(FALSE)
+             collect_bb_rotors(false)
          }
-         if (pno < {atomIndex=gNcargoIdx}.atomno) {
+         else if (pno < {atomIndex=gNcargoIdx}.atomno) {
-             color {atomIndex=gNanchorIdx} @gScheme
+             select {atomIndex=gNanchorIdx}
+            halo off
              if (gNanchorIdx == aPidx) {
                  gNanchorIdx = -1
@@ Line 1,663: / Line 1,784: @@
                  gNanchorIdx = aPidx
                  gNanchorNo = {atomIndex=gNanchorIdx}.atomno
-                 gNanchorPidx = getCwardBBidx( aPidx)
+                 select {atomIndex=gNanchorIdx}
-                gNanchorXyz = {atomIndex=gNanchorIdx}.xyz
+                 halo on
-                gNanchorPxyz = {atomIndex=gNanchorPidx}.xyz
-                 color {atomIndex=gNanchorIdx} @gAltScheme
              }
-             collectBBrotors(TRUE)
+             collect_bb_rotors(true)
+        }
+        else {
+            tow_cargo_mb()
          }
+        # Get moving atoms set
+        gMovingSet = {((atomno < gCanchorNo) and (atomno > gNanchorNo)
+            and (chain=gChain) and thisModel)}
      }
+     select {gCargoSet}
-    # Get connectors between fixed and moving part
-    var aset = {((atomno < gCanchorNo) and (atomno > gNanchorNo)
-        and (chain=gChain))}
-    gAc = (within(kCtolerance, FALSE, {aset}) and not {aset})
-     select {gCargoAtoms}
 }
-# Bound to ALT-SHIFT-LEFT-CLICK by tugCargoMB
+# Bound to ALT-SHIFT-LEFT-CLICK by tug_cargo_mb
-function tugDestAtomMB() {
+function tug_dest_atom_mb() {
-     var aOk = TRUE
+     var aOk = true
      if ({atomIndex=_atomPicked}.chain == gChain) {
          var pno = {atomIndex=_atomPicked}.atomno
-         if ((pno <= {atomIndex=gCcargoIdx}.atomno) and (pno >= {atomIndex=gNcargoIdx}.atomno)) {
+         if ((pno <= {atomIndex=gCcargoIdx}.atomno)
-             aOk = FALSE
+            and (pno >= {atomIndex=gNcargoIdx}.atomno)) {
+             aOk = false
          }
      }
@@ Line 1,700: / Line 1,822: @@
              star on
          }
-         select {gCargoAtoms}
+         select {gCargoSet}
      }
 }
-# Bound to CTRL-LEFT-CLICK by tugCargoMB
+# Bound to CTRL-LEFT-CLICK by tug_cargo_mb
-function tugPivotMB() {
+function tug_pivot_mb() {
      if (g1pivotIdx == _atomPicked) {
          color {atomIndex=g1pivotIdx} @gScheme
@@ Line 1,711: / Line 1,833: @@
              g1pivotIdx = g2pivotIdx
              g2pivotIdx = -1
+            g2dynamicIdx = -1
          }
          else {
              g1pivotIdx = -1
+            g1dynamicIdx = -1
          }
      }
@@ Line 1,719: / Line 1,843: @@
          color {atomIndex=g2pivotIdx} @gScheme
          g2pivotIdx = -1
+        g2dynamicIdx = -1
      }
      else if (g1pivotIdx >= 0) {
@@ Line 1,724: / Line 1,849: @@
              color {atomIndex=g2pivotIdx} @gScheme
          }
          g2pivotIdx = _atomPicked
+        g2dynamicIdx = -1
          color {atomIndex=g2pivotIdx} green
      }
      else {
          g1pivotIdx = _atomPicked
+        g1dynamicIdx = -1
          color {atomIndex=g1pivotIdx} green
      }
-     select {gCargoAtoms}
+     select {gCargoSet}
 }
-# Bound to ALT-LEFT-CLICK by plicoTug
+# Bound to SHIFT-LEFT-CLICK by plico_tug
-function tugCargoMB() {
+function tow_cargo_mb() {
+     gTow = true
-     if (gChain != {atomIndex=_atomPicked}.chain) {
+     gChain = {atomIndex=_atomPicked}.chain
-        clearAtomIdxs()
+    gMinNo = {(chain=gChain) and thisModel}.atomno.min
-        setColors()
+    gMaxNo = {(chain=gChain) and thisModel}.atomno.max
-        gChain = {atomIndex=_atomPicked}.chain
+    gCcargoIdx = -1
-     }
+    gNcargoIdx = -1
+    gCanchorIdx = -1
-     # If movable side chain atom picked
+    gCanchorNo = gMaxNo + 1
-     if (isMovableSideChain( _atomPicked)) {
+    gNanchorIdx = -1
+    gNanchorNo = gMinNo - 1
+    # Highlight cargo cluster
+    select {(chain=gChain) and thisModel}
+    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() {
+     # If O or movable side chain atom picked
+     if ((({atomIndex=_atomPicked}.atomName = "O")
+        and ({atomIndex=_atomPicked}.group != "PRO"))
+        or (is_moveable_sc( _atomPicked))) {
          if (gSCidx >= 0) {
              draw gSCcircle DELETE
@@ Line 1,751: / Line 1,904: @@
          if (gSCidx == _atomPicked) {
              gSCidx = -1
          }
          else {
              gSCidx = _atomPicked
@@ Line 1,758: / Line 1,911: @@
          }
      }
-     else if ((gChain == "") or ({atomIndex=_atomPicked}.chain == gChain)) {
+     else {
-         gMinNo = {chain=gChain}.atomno.min
+        if ({atomIndex=_atomPicked}.chain != gChain) {
-         gMaxNo = {chain=gChain}.atomno.max
+            if (gTow) {
+                select {(chain=gChain) and thisModel}
+                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 thisModel}.atomno.min
+         gMaxNo = {(chain=gChain) and thisModel}.atomno.max
          if (gNanchorIdx < 0) {
              gNanchorNo = gMinNo - 1
          }
          if (gCanchorIdx < 0) {
              gCanchorNo = gMaxNo + 1
          }
-         var aPidx = getScBBidx( _atomPicked)
+         var aPidx = get_sc_bb_idx( _atomPicked, gChain)
          gSCidx = -1
          draw gSCcircle DELETE
@@ Line 1,774: / Line 1,942: @@
          # 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 = getCpIdx(gNcargoIdx)
+                 gCcargoIdx = get_cp_idx(gNcargoIdx)
                  gCcargoNo = {atomIndex=gCcargoIdx}.atomno
              }
@@ Line 1,792: / Line 1,960: @@
              select {atomIndex=gNcargoIdx}
              halo off
-             gNcargoIdx = getNmIdx(gCcargoIdx)
+             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) {
@@ Line 1,806: / Line 1,975: @@
                      halo off
                  }
                  # Set new nWard cargo and highlight it
-                 gNcargoIdx = getNmIdx(aPidx)
+                 gNcargoIdx = get_nm_idx(aPidx)
                  gNcargoNo = {atomIndex=gNcargoIdx}.atomno
              }
              # Else cWard
              else {
                  # Clear its old highlight
                  select {atomIndex=gCcargoIdx}
@@ Line 1,820: / Line 1,989: @@
                      halo off
                  }
                  # Set new cWard cargo and highlight
-                 gCcargoIdx = getCpIdx(aPidx)
+                 gCcargoIdx = get_cp_idx(aPidx)
                  gCcargoNo = {atomIndex=gCcargoIdx}.atomno
              }
          }
          # Else no cWard cargo
          else {
              # Set new cWard cargo and highlight
-             gCcargoIdx = getCpIdx(aPidx)
+             gCcargoIdx = get_cp_idx(aPidx)
              gCcargoNo = {atomIndex=gCcargoIdx}.atomno
-             gNcargoIdx = getNmIdx(gCcargoIdx)
+             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)}.atomName == "N") {
-                    break;
-                }
-            }
-            gCanchorIdx = {(atomno=iNo) and (chain=gChain)}.atomIndex
-            gCanchorNo = {atomIndex=gCanchorIdx}.atomno
-            gCanchorXyz = {atomIndex=gCanchorIdx}.xyz
          }
          # If any anchor now inside cargo cluster, kill it
          if ({atomIndex=gCanchorIdx}.atomno <= {atomIndex=gCcargoIdx}.atomno) {
@@ Line 1,857: / Line 2,015: @@
              gNanchorNo = gMinNo - 1
          }
          # Highlight cargo cluster
-         selectNward(gCcargoIdx, gNcargoIdx)
+         select_nward_idx(gCcargoIdx, gNcargoIdx)
-         gCargoAtoms = {selected}
+         gCargoSet = {selected}
-         setColors()
+         set_colors()
          # Collect the rotor sets
-         collectRotors()
+         collect_rotors()
-         # Get connectors between fixed and moving part
+         # Get moving atoms set
-         var aset = {((atomno < gCanchorNo) and (atomno > gNanchorNo)
+         gMovingSet = {((atomno < gCanchorNo) and (atomno > gNanchorNo)
-             and (chain=gChain))}
+             and (chain=gChain) and thisModel)}
-        gAc = (within(kCtolerance, FALSE, {aset}) and not {aset})
      }
      # Enable dragging
-     tugEnableDrag()
+     if (gToab) {
+        to_ab_enable_drag()
+    }
+    else {
+        tug_enable_drag()
+    }
+    select {gCargoSet}
+}
-    # Bind other keys
+function tug_undo_mb() {
-     bind "SHIFT-LEFT-CLICK" "_pickAtom";
+     if (prompt("Undo", "Yes|No", true) == "Yes") {
-    bind "SHIFT-LEFT-CLICK" "+:tugAnchorMB";
+        restore state gState
+     }
-     bind "ALT-CTRL-LEFT-CLICK" "_pickAtom";
-    bind "ALT-CTRL-LEFT-CLICK" "+:tugPivotMB";
-    bind "ALT-SHIFT-LEFT-CLICK" "_pickAtom";
-    bind "ALT-SHIFT-LEFT-CLICK" "+:tugDestAtomMB";
-    select {gCargoAtoms}
 }
 # Top level of Tug
-function plicoTug() {
+function plico_tug() {
-     set allowModelKit TRUE
-     set allowRotateSelected TRUE
+     # Load common functions if not already
-     set allowMoveAtoms TRUE
+     if (kCommon < 7) {
+        script $SCRIPT_PATH$plicoCommon.spt
+        if (kCommon < 7) {
+            prompt ("A newer version of plicoCommon.SPT is required")
+            quit
+        }
+    }
+     gPlico = "TUG"
+    plico_prelim(true, true)
-     # Push selected
+     gBondPicking = bondPicking
-    gSelSaves = {selected}
+     set bondPicking true
-     select all
+     set PickCallback "jmolscript:tug_pick_cb"
-     gZoom = script("show zoom")
-     gRotate = script("show rotation")
+     gEcho = ("_________TUG_________|ALT-CLICK=mark block|SHIFT-CLICK=mark chain" +
-    write tugsave.pdb
+        "|CLICK bond=freeze|ALT-DOUBLE-CLICK=undo|SHIFT-DOUBLE-CLICK=exit")
-    select none
-    gScheme = defaultColorScheme
-    gAltScheme = ((gScheme == "Jmol") ? "Rasmol" : "Jmol")
-    set echo TOP LEFT
-    background ECHO yellow
-    gEcho = "ALT-CLICK=set cargo range"
      echo @gEcho
      gCrotors = array()
      gNrotors = array()
-     clearAtomIdxs()
+     clear_atom_idxs()
-     gChain = ""
+     gToab = false
-    unbind
-    set picking ON
      bind "ALT-LEFT-CLICK" "_pickAtom";
-     bind "ALT-LEFT-CLICK" "+:tugCargoMB";
+     bind "ALT-LEFT-CLICK" "+:tug_cargo_mb";
-     bind "DOUBLE" "tugExit";
+     bind "SHIFT-LEFT-CLICK" "_pickAtom";
+    bind "SHIFT-LEFT-CLICK" "+:tow_cargo_mb";
+    bind "ALT-LEFT-DOUBLE" "tug_undo_mb";
+    bind "SHIFT-DOUBLE" "tug_exit(true)";
+    bind "LEFT-CLICK" "+:plico_menu_toggle";
 }
-# Bound to DOUBLE by plicoTug
+# Bound to DOUBLE by plico_tug
-function tugExit() {
+function tug_exit() {
-     var p = prompt("Exit tug?", "Yes|No|Undo", TRUE)
+     if (plico_exit()) {
-    if (p == "Undo") {
+         set bondPicking gBondPicking
-        load tugsave.pdb
+         set PickCallback NONE
-        script inline gZoom
-        rotate @gRotate
-        echo Tug session undone
-        if (gPlicoRecord != "") {
-            plicoRecord("load tugsave.pdb;")
-        }
-    }
-    if (p != "No") {
-         unbind
-        halo off
-         set allowMoveAtoms FALSE
-        echo
          select all
-        halo off
+         color bonds none
-        star off
-         color {selected} @gScheme
-        draw gSCcircle DELETE
-        gBusy = FALSE
-        background ECHO yellow
-         # Pop selected
+         reset kTug
-         select gSelSaves
+         reset gCanchorIdx
+        reset gCanchorNo
+        reset gPlico
+        reset gNanchorIdx
+        reset gNanchorNo
+        reset gCcargoIdx
+        reset gNcargoIdx
+        reset gCcargoNo
+        reset gNcargoNo
+        reset gDestAtomIdx
+        reset g1pivotIdx
+        reset g2pivotIdx
+        reset gSelSaves
+        reset gCrotors
+        reset gNrotors
+        reset gOkCollide
+        reset gChain
+        reset gMinNo
+        reset gMaxNo
+        reset gCargoSet
+        reset gMovingSet
+        reset gSCidx
+        reset gSCcircle
+        reset gSCpt
+        reset gTargetPt
+        reset gNewDrag
+        reset gTow
+        reset g1dynamicIdx
+        reset g2dynamicIdx
+        reset gSCcheck
+        reset gBondPicking
+        reset gFreeze
+        reset gToab
+        reset function "get_cp_idx"
+        reset function "get_cm_no"
+        reset function "get_nm_idx"
+        reset function "get_np_no"
+        reset function "get_cb_idx"
+        reset function "get_o_idx"
+        reset function "get_nward_bb_idx"
+        reset function "get_cward_bb_idx"
+        reset function "get_sc_set"
+        reset function "get_sc_bb_idx"
+        reset function "is_bb_idx"
+        reset function "is_sc_idx"
+        reset function "select_add_sc"
+        reset function "handle_collisions"
+        reset function "tug_track_idx"
+        reset function "do_counter_rotate"
+        reset function "counter_rotate"
+        reset function "counter_rotate_2"
+        reset function "repair_proline"
+        reset function "repair_sc"
+        reset function "tug_track_c"
+        reset function "tug_track_n"
+        reset function "translate_selected_record"
+        reset function "rotate_selected_record"
+        reset function "collect_sc_rotors"
+        reset function "drag_sc"
+        reset function "fix_sc_collision_2"
+        reset function "is_moveable_sc"
+        reset function "is_rotor_avail"
+        reset function "xcollect_bb_rotors"
+        reset function "collect_bb_rotors"
+        reset function "collect_rotors"
+        reset function "tug_sc"
+        reset function "set_colors"
+        reset function "clear_atom_idxs"
+        reset function "timed_out"
+        reset function "record_drag"
+        reset function "tug_pick_cb"
+        reset function "tug_drag_done_mb"
+        reset function "tug_drag_2_mb"
+        reset function "tug_drag_mb"
+        reset function "tug_mark_mb"
+        reset function "tug_anchor_mb"
+        reset function "tug_enable_drag"
+        reset function "tug_dest_atom_mb"
+        reset function "tug_pivot_mb"
+        reset function "tow_cargo_mb"
+        reset function "tug_cargo_mb"
+        reset function "tug_undo_mb"
+        reset function "plico_tug"
      }
 }
-# End of TUG.SPT</pre>
+# End of TUG.SPT
+</pre>