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

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(Use plico)
(Avoid "axis," a newly reserved word)
 
(10 intermediate revisions by the same user not shown)
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.  It also allows the user to move an entire chain to nest against another chain.
+
'''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:
 
'''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
 
<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 directory 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
 
<pre>#  tug - Jmol script by Ron Mignery
−
#  v1.8 beta    3/26/2014 for Jmol 14 - use plicoCommon
+
#  v1.20 beta    4/12/2016 -axis is now a reserved word
 
#
 
#
 
#  Translate or rotate a stretch of a polypeptide against itself
 
#  Translate or rotate a stretch of a polypeptide against itself
 
#    or against other chains by mouse actions
 
#    or against other chains by mouse actions
 
#
 
#
−
var gCanchorIdx = -1
+
kTug = 3
−
var gCanchorNo = -1
+
gCanchorIdx = -1
−
var gPlico = "TUG"
+
gCanchorNo = -1
−
var gNanchorIdx = -1
+
gPlico = "TUG"
−
var gNanchorNo = -1
+
gNanchorIdx = -1
−
var gCcargoIdx = -1
+
gNanchorNo = -1
−
var gNcargoIdx = -1
+
gCcargoIdx = -1
−
var gCcargoNo = -1
+
gNcargoIdx = -1
−
var gNcargoNo = -1
+
gCcargoNo = -1
−
var gDestAtomIdx = -1
+
gNcargoNo = -1
−
var g1pivotIdx = -1
+
gDestAtomIdx = -1
−
var g2pivotIdx = -1
+
g1pivotIdx = -1
−
var gSelSaves = ({})
+
g2pivotIdx = -1
−
var gCrotors = array()
+
gSelSaves = ({})
−
var gNrotors = array()
+
gCrotors = array()
−
var gMouseX = 0
+
gNrotors = array()
−
var gMouseY = 0
+
gOkCollide = ({})
−
var gOkCollide = ({})
+
gChain = ""
−
var gChain = ""
+
gMinNo = 1
−
var gMinNo = 1
+
gMaxNo = 9999
−
var gMaxNo = 9999
+
gCargoSet = ({})
−
var gScheme = "Jmol"
+
gMovingSet = ({})
−
var gAltScheme = "Rasmol"
+
gBusy = false
−
var gCargoSet = ({})
+
gSCidx = -1
−
var gMovingSet = ({})
+
gSCcircle = -1
−
var gBusy = FALSE
+
gSCpt = {0 0 0}
−
var gSCidx = -1
+
gTargetPt = {0 0 0}
−
var gSCcircle = -1
+
gNewDrag = false
−
var gSCpt = {0 0 0}
+
gTow = false
−
var gOK = TRUE # global return value to work around jmol *feature*
+
g1dynamicIdx = -1
−
var gOk2 = TRUE # "    "
+
g2dynamicIdx = -1
−
var gTargetPt = {0 0 0}
+
gSCcheck = true
−
var gNewDrag = FALSE
+
gBondPicking = false
−
var gEcho = ""
+
gFreeze = array()
−
var gZoom = ""
+
gToab = false
−
var gRotate = ""
 
−
var gTow = FALSE
 
−
var g1dynamicIdx = -1
 
−
var g2dynamicIdx = -1
 
−
var gSCcheck = TRUE
 
−
var gBondPicking = FALSE
 
  
  
−
function getCAmNo (iNo) {
+
function get_cp_idx (idx) {
−
     while ((iNo > 0) and ({(atomno=iNo) and (chain=gChain)}.atomName != "CA")) {
+
    var no = {atomIndex=idx}.atomno
−
         iNo--
+
     while ((no < gMaxNo) and ({(atomno=no) and (chain=gChain)
 +
        and thisModel}.atomName != "C")) {
 +
         no++
 
     }
 
     }
−
     return iNo
+
     return ({(atomno=no) and (chain=gChain) and thisModel}.atomIndex)
 
}
 
}
  
−
function getCAmIdx (idx) {
+
function get_cm_no (iNo) {
−
    var no = {atomIndex=idx and (chain=gChain)}.atomno
+
     while ((iNo > 0) and ({(atomno=iNo) and (chain=gChain)
−
    no = getCAmNo( no)
+
        and thisModel}.atomName != "C")) {
−
    return ({(atomno=no) and (chain=gChain)}.atomIndex)
+
         iNo--
−
}
 
−
 
 
−
function getCApNo (iNo) {
 
−
     while ((iNo < gMaxNo) and ({(atomno=iNo) and (chain=gChain)}.atomName != "CA")) {
 
−
         iNo++
 
 
     }
 
     }
 
     return iNo
 
     return iNo
 
}
 
}
  
−
function getCpIdx (idx) {
+
function get_nm_idx (idx) {
−
     var no = {atomIndex=idx and (chain=gChain)}.atomno
+
     var no = {atomIndex=idx}.atomno
−
     no = getCpNo( no)
+
    while ((no > 0) and ({(atomno=no) and (chain=gChain)
−
     return ({(atomno=no) and (chain=gChain)}.atomIndex)
+
        and thisModel}.atomName != "N")) {
 +
        no--
 +
     }
 +
     return ({(atomno=no) and (chain=gChain) and thisModel}.atomIndex)
 
}
 
}
  
−
function getCpNo (iNo) {
+
function get_np_no (iNo) {
−
     while ((iNo < gMaxNo) and ({(atomno=iNo) and (chain=gChain)}.atomName != "C")) {
+
     while ((iNo < gMaxNo) and ({(atomno=iNo) and (chain=gChain)
 +
        and thisModel}.atomName != "N")) {
 
         iNo++
 
         iNo++
 
     }
 
     }
Line 89: Line 84:
 
}
 
}
  
−
function getCApIdx (idx) {
+
function get_cb_idx (BBidx) {
−
     var no = {atomIndex=idx and (chain=gChain)}.atomno
+
     var no = {atomIndex=BBidx}.atomno
−
     no = getCApNo( no)
+
    var i = 1
−
     return ({(atomno=no) and (chain=gChain)}.atomIndex)
+
    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 getCmNo (iNo) {
+
function get_o_idx (BBidx) {
−
     while ((iNo > 0) and ({(atomno=iNo) and (chain=gChain)}.atomName != "C")) {
+
     var no = {atomIndex=BBidx}.atomno
−
         iNo--
+
    var i = 1
 +
    for (; i < 4; i++) {
 +
        if ({(atomno=@{no+i}) and (chain=gChain)
 +
            and thisModel}.atomName == "O") {
 +
            break
 +
         }
 
     }
 
     }
−
     return iNo
+
     return {(atomno=@{no+i}) and (chain=gChain) and thisModel}.atomIndex
 
}
 
}
  
−
function getCmIdx (idx) {
+
function get_nward_bb_idx (idx, iChain) {
−
     var no = {atomIndex=idx and (chain=gChain)}.atomno
+
     var no = {atomIndex=idx}.atomno - 1
−
    no = getCmNo( no)
+
    for (; no >= 0; no--) {
−
     return ({(atomno=no) and (chain=gChain)}.atomIndex)
+
        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 getNmNo (iNo) {
+
function get_cward_bb_idx (idx, iChain) {
−
     while ((iNo > 0) and ({(atomno=iNo) and (chain=gChain)}.atomName != "N")) {
+
     var no = {atomIndex=idx}.atomno + 1
−
         iNo--
+
    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 iNo
+
     return ((no >= 0) ? ({(atomno=no) and (chain=iChain)
 +
        and thisModel}.atomIndex) : -1)
 
}
 
}
  
−
function getNmIdx (idx) {
+
function get_sc_set (scIdx, iChain) {
−
     var no = {atomIndex=idx and (chain=gChain)}.atomno
+
     var scSet = ({})
−
     no = getNmNo( no)
+
     var idx = get_sc_bb_idx(scIdx, iChain)
−
     return ({(atomno=no) and (chain=gChain)}.atomIndex)
+
     var iNo = {atomIndex=idx}.atomno + 3
−
}
 
  
−
function getNpNo (iNo) {
+
    for (var i = 1; i < 20; i++) {
−
    while ((iNo < gMaxNo) and ({(atomno=iNo) and (chain=gChain)}.atomName != "N")) {
+
        idx = {(atomno=@{iNo+i}) and (chain=iChain)
−
         iNo++
+
            and thisModel}.atomIndex
 +
        if (is_bb_idx(idx)) {
 +
            break
 +
        }
 +
         scSet = scSet or {atomIndex=idx}
 
     }
 
     }
−
     return iNo
+
     return scSet
 
}
 
}
  
−
function getNpIdx (idx) {
+
function get_sc_bb_idx (idx, iChain) {
 
     var no = {atomIndex=idx}.atomno
 
     var no = {atomIndex=idx}.atomno
−
     no = getNpNo( no)
+
     for (; no > 0; no--) {
−
    return ({(atomno=no) and (chain=gChain)}.atomIndex)
+
        if ({(atomno=no) and (chain=iChain)
−
}
+
            and thisModel}.atomName == "CA") {
−
 
+
            break
−
function getCBidx (BBidx) {
+
        }
−
    var no = {atomIndex=BBidx}.atomno
+
         else if ({(atomno=no) and (chain=iChain)
−
    var i = 1
+
            and thisModel}.atomName == "C") {
−
    for (; i < 5; i++) {
 
−
         if ({(atomno=@{no+i}) and (chain=gChain)}.atomName == "CB") {
 
 
             break
 
             break
 
         }
 
         }
−
    }
+
        else if ({(atomno=no) and (chain=iChain)
−
    return {(atomno=@{no+i}) and (chain=gChain)}.atomIndex
+
            and thisModel}.atomName == "N") {
−
}
+
            break
−
 
+
        }
−
function getOidx (BBidx) {
+
         else if ({(atomno=no) and (chain=iChain)
−
    var no = {atomIndex=BBidx}.atomno
+
            and thisModel}.atomName == "CB") {
−
    var i = 1
+
            no -= 3
−
    for (; i < 4; i++) {
 
−
         if ({(atomno=@{no+i}) and (chain=gChain)}.atomName == "O") {
 
 
             break
 
             break
 
         }
 
         }
 
     }
 
     }
−
     return {(atomno=@{no+i}) and (chain=gChain)}.atomIndex
+
     return {(atomno=no) and (chain=iChain) and thisModel}.atomIndex
 
}
 
}
  
−
function getNwardBBno (iNo, iChain) {
+
function is_bb_idx(aIdx) {
−
     while ((iNo >= 0) and (
+
     var ret = false
−
        ({(atomno=iNo) and (chain=iChain)}.atomName != "N")
+
    switch({atomIndex=aIdx}.atomName) {
−
        and ({(atomno=iNo) and (chain=iChain)}.atomName != "C")
+
    case "N":
−
         and ({(atomno=iNo) and (chain=iChain)}.atomName != "CA"))) {
+
    case "CA":
−
         iNo--
+
    case "C":
 +
         ret = true
 +
         break
 
     }
 
     }
−
     return iNo
+
     return ret
 
}
 
}
  
−
function getNwardBBidx (idx, iChain) {
+
function is_sc_idx(aIdx) {
−
     var no = {atomIndex=idx}.atomno - 1
+
 
−
     no = getNwardBBno( no, iChain)
+
     var ret = false
−
    return ((no >= 0) ? ({(atomno=no) and (chain=iChain)}.atomIndex) : -1)
+
     if (not is_bb_idx(aIDx)) {
−
}
 
  
−
function getCwardBBno (iNo, iChain) {
+
        ret = true
−
    while ((iNo < gMaxNo) and (
+
         switch({atomIndex=aIdx}.atomName) {
−
         ({(atomno=iNo) and (chain=iChain)}.atomName != "N")
+
         case "O":
−
         and ({(atomno=iNo) and (chain=iChain)}.atomName != "C")
+
         case "CB":
−
         and ({(atomno=iNo) and (chain=iChain)}.atomName != "CA"))) {
+
            ret = false
−
         iNo++
+
            break
 +
         }
 
     }
 
     }
−
     return iNo
+
     return ret
 
}
 
}
  
−
function getCwardBBidx (idx, iChain) {
+
function select_add_sc(fromIdx) {
−
     var no = {atomIndex=idx}.atomno + 1
+
     var iNo = {atomIndex=fromIdx}.atomno
−
     no = getCwardBBno( no, iChain)
+
     var iChain = {atomIndex=fromIdx}.chain
−
     return ((no >= 0) ? ({(atomno=no) and (chain=iChain)}.atomIndex) : -1)
+
    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++
 +
    }
 
}
 
}
  
−
function getScSet (scIdx, iChain) {
+
# Resolve collisions on selection
−
     var scSet = ({})
+
function handle_collisions( targetIdx) {
−
     var idx = getScBBidx(scIdx, iChain)
+
 
−
    var iNo = {atomIndex=idx}.atomno + 3
+
     # For all selected atoms
−
   
+
     for (var iNo = {selected}.min.atomno; iNo <= {selected}.max.atomno; iNo++) {
−
    for (var i = 1; i < 20; i++) {
+
         var idx = {(atomno=iNo) and (chain=gchain)
−
         idx = {(atomno=@{iNo+i}) and (chain=iChain)}.atomIndex
+
            and thisModel}.atomIndex
−
         if (isBBidx(idx)) {
+
         if ({atomindex=idx}.selected) {
−
            break
 
−
        }
 
−
        scSet = scSet or {atomIndex=idx}
 
−
    }
 
−
    return scSet
 
−
}
 
  
−
function getScBBidx (idx, iChain) {
+
            # Collect local colliders
−
    var no = {atomIndex=idx}.atomno
+
            var lcAtoms = (within(kCtolerance, false, {atomIndex=idx})
−
    for (; no > 0; no--) {
+
                and not {atomIndex=idx}
−
        if ({(atomno=no) and (chain=iChain)}.atomName == "CA") {
+
                and not {gOkCollide}
−
             break
+
                and not connected({atomIndex=idx}))
−
        }
+
             if (lcAtoms) {
−
        else if ({(atomno=no) and (chain=iChain)}.atomName == "C") {
+
                # Ignore kinked BB
−
            break
+
                try {
−
        }
+
                    if (is_bb_idx(idx) and (angle(
−
        else if ({(atomno=no) and (chain=iChain)}.atomName == "N") {
+
                        {atomIndex=@{get_cward_bb_idx(idx, gChain)}}, {atomIndex=idx},
−
            break
+
                        {atomIndex=@{get_nward_bb_idx(idx, gChain)}}) < 100.0)) {
−
        }
+
                        continue
−
        else if ({(atomno=no) and (chain=iChain)}.atomName == "CB") {
+
                    }
−
            no -= 3
+
                }
−
            break
+
                catch {
−
        }
+
                }
−
    }
 
−
    return {(atomno=no) and (chain=iChain)}.atomIndex
 
−
}
 
  
−
function isBBidx(aIdx) {
+
                # For all local colliders
−
    var ret = FALSE
+
                for (var c = 1; c <= lcAtoms.size; c++ ) {
−
    switch({atomIndex=aIdx}.atomName) {
+
                    var cidx = lcAtoms[c].atomIndex
−
    case "N":
 
−
    case "CA":
 
−
    case "C":
 
−
        ret = TRUE
 
−
        break
 
−
    }
 
−
    return ret
 
−
}
 
  
−
function isSCidx(aIdx) {
+
                    # If it is with water, delete it
 +
                    if (lcAtoms[c].group = "HOH") {
 +
                        delete {atomIndex=cidx}
 +
                    }
  
−
    var ret = FALSE
+
                    # else if it is with side chain not proline, fix it
−
    if (not isBBidx(aIDx)) {
+
                    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)
 +
                        }
 +
                    }
  
−
        ret = TRUE
+
                    # else if it is itself a side chain not proline, fix it
−
        switch({atomIndex=aIdx}.atomName) {
+
                    else if (is_sc_idx(idx) and ({atomIndex=idx}.group != "PRO")) {
−
        case "O":
+
                        fix_sc_collision_2(idx)
−
        case "CB":
 
−
            ret = FALSE
 
−
            break
 
−
        }
 
−
    }
 
−
    return ret
 
−
}
 
  
−
function addSideChainToSelection(CAno, isAdd, addOXT, iChain) {
+
                        # If not fixed, exit fail
−
    var iNo = CAno+3
+
                        if (not gOk2) {
−
    while ({(atomno=iNo) and (chain=iChain)}.resno == {(atomno=CAno) and (chain=iChain)}.resno) {
+
                            return # early exit (break n jmol bug)
−
        {(atomno=iNo) and (chain=iChain)}.selected = isAdd
+
                        }
−
        if ({(atomno=iNo) and (chain=iChain)}.atomName == "OXT") {
+
                    }
−
            {(atomno=iNo) and (chain=iChain)}.selected = addOXT
 
−
        }
 
−
        iNo++
 
−
    }
 
−
}
 
  
−
function selectAddSideChain(fromIdx) {
+
                    # Else if it is with O, counter-rotate
−
    var iNo = {atomIndex=fromIdx}.atomno
+
                    else if (lcAtoms[c].atomName = "O") {
−
    var iChain = {atomIndex=fromIdx}.chain
+
                        counter_rotate_2(lcAtoms[c].atomIndex,
−
    select none
+
                            {atomIndex=idx}.xyz, targetIdx, false)
−
    while ({(atomno=iNo) and (chain=iChain)}.atomName != "N") {
 
−
        {(atomno=iNo) and (chain=iChain)}.selected = TRUE
 
−
        iNo++
 
−
        if (iNo > {chain=iChain}.atomno.max) {
 
−
            break
 
−
        }
 
−
    }
 
−
}
 
  
−
# First and last are BB atoms
+
                        # If not fixed, exit fail
−
# Any side atoms in the range are also selected
+
                        if (not gOk2) {
−
function selectNwardIdx (firstIdx, lastIdx) {
+
                            return # early exit (break n jmol bug)
−
    var firstno = ((firstIdx < 0) ? {atomIndex=lastIdx}.atomno : {atomIndex=firstIdx}.atomno)
+
                        }
−
    var lastno = ((lastIdx < 0) ? firstno : {atomIndex=lastIdx}.atomno)
+
                    }
−
    var iChain = ((firstIdx < 0)
 
−
        ? {atomIndex=lastIdx}.chain : {atomIndex=firstIdx}.chain)
 
  
−
    select (atomno <= firstno) and (atomno >= lastno) and (chain = iChain)
+
                    # Else if it is itself O, counter-rotate
 +
                    else if ({atomIndex=idx}.atomName = "O") {
 +
                        counter_rotate_2(idx, lcAtoms[c].xyz, targetIdx, false)
  
−
    if ({(atomno=firstno) and (chain=gChain)}.atomName == "C") { # if psi
+
                        # If not fixed, exit fail
−
        addSideChainToSelection(firstno-1, TRUE, TRUE, iChain)
+
                        if (not gOk2) {
−
        {(atomno=@{firstno+1}) and (chain=iChain)}.selected = TRUE # add O
+
                            return # early exit (break n jmol bug)
−
    }
+
                        }
−
    if ({(atomno=firstno) and (chain=iChain)}.atomName == "CA") {
+
                    }
−
        addSideChainToSelection(firstno, TRUE, FALSE, iChain)
 
−
    }
 
−
    if ({(atomno=lastno) and (chain=iChain)}.atomName == "C") { # if psi
 
−
        addSideChainToSelection(lastno-1, FALSE, FALSE, iChain)
 
−
    }
 
−
}
 
  
−
# First and last are BB atoms
+
                    else {    # Else not fixed, exit fail
−
# Any side atoms in the range are also selected
+
                        gOk2 = false
−
function selectCwardIdx (firstIdx, lastIdx) {
+
                        return # early exit (break n jmol bug)
−
    var firstno = ((firstIdx < 0) ? gMaxNo : {atomIndex=firstIdx}.atomno)
+
                    }
−
    var lastno = ((lastIdx < 0) ? 1 : {atomIndex=lastIdx}.atomno)
+
                } # endfor
−
    var iChain = ((firstIdx < 0)
+
            }
−
        ? {atomIndex=lastIdx}.chain : {atomIndex=firstIdx}.chain)
 
−
 
 
−
    # If nWard anchor in range, begin selection with it
 
−
    if ((gNanchorIdx >= 0) and ({atomIndex=gNanchorIdx}.chain == iChain))  {
 
−
        var aNo = {atomIndex=gNanchorIdx}.atomno
 
−
        if (aNo > firstNo) {
 
−
            firstno = aNo
 
 
         }
 
         }
−
     }
+
     } # endfor iNo
 +
}
  
−
    # If cWard anchor in range, end selection with it
+
# Rotate rotor set to move target atom to its proper place
−
    if ((gCanchorIdx >= 0) and ({atomIndex=gCanchorIdx}.chain == iChain))  {
+
function tug_track_idx(targetIdx, targetPt, nWard, cDetect) {
−
        var aNo = {atomIndex=gCanchorIdx}.atomno
+
    gOK = false
−
        if (aNo < lastNo) {
+
    var pt = targetPt
−
            lastno = aNo
+
    var dist = distance(pt, {atomIndex=targetIdx}.xyz)
−
        }
 
−
    }
 
  
−
     select (atomno >= firstno) and (atomno <= lastno) and (chain = iChain)
+
     var rotors = (nWard ? gNrotors : gCrotors)
  
−
     if ({(atomno=firstno) and (chain=iChain)}.atomName == "C") { # if psi
+
     # For a number of passes
−
         addSideChainToSelection(firstno-1, FALSE, FALSE, iChain)
+
    for (var pass1 = 0; pass1 < 20; pass1++) {
−
    }
+
         var blocked = ({})
−
    if ({(atomno=lastno) and (chain=iChain)}.atomName == "CA") {
+
         for (var pass2 = 0; pass2 < (rotors.size/4); pass2++) {
−
         addSideChainToSelection(lastno, TRUE, FALSE, iChain)
 
−
    }
 
−
    if ({(atomno=lastno) and (chain=iChain)}.atomName == "C") { # if psi
 
−
        addSideChainToSelection(lastno-1, TRUE, TRUE, iChain)
 
−
        {(atomno=@{lastno+1}) and (chain=iChain)}.selected = TRUE # add O
 
−
    }
 
−
}
 
  
 +
            var v1 = {atomIndex=targetIdx}.xyz - pt
  
−
# Resolve collisions
+
            # Find the most orthgonal unused rotor
−
function handleCollisions2( targetIdx) {
+
            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
  
−
    # For all selected atoms
+
                        var s = sin(abs(angle(v1, {0 0 0}, v2)))
−
    for (var iNo = {selected}.min.atomno; iNo <= {selected}.max.atomno; iNo++) {
+
                        if (s > smax) {
−
        var idx = {(atomno=iNo) and (chain=gchain)}.atomIndex
+
                            smax = s
−
        if ({atomindex=idx}.selected) {
+
                            imax = i
 +
                        }
 +
                    }
 +
                }
 +
            }
  
−
             # Collect local colliders
+
             # If no more rotors, break to next full try
−
             var lcAtoms = (within(kCtolerance, FALSE, {atomIndex=idx})
+
            if (imax == 0) {
−
                and not {atomIndex=idx}
+
              break
−
                and not {gOkCollide}
+
            }
−
                and not connected({atomIndex=idx}))
+
            var i1 = rotors[imax+0]
−
             if (lcAtoms.size > 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
  
−
                # Ignore kinked BB
+
            # Compute resultant psi and phi
−
                 if (isBBidx(idx) and angle({atomIndex=@{getCwardBBidx(idx, gChain)}},
+
            # and select from target atom to first half of rotor
−
                     {atomIndex=idx} , {atomIndex=@{getNwardBBidx(idx, gChain)}}) < 100) {
+
            var movePt = false
−
                    continue
+
            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
 
                 }
 
                 }
  
−
                 # For all local colliders
+
                 if ({atomIndex=i2}.atomno > {atomIndex=targetIdx}.atomno) {
−
                 for (var c = 1; c <= lcAtoms.size; c++ ) {
+
                    movePt = true
−
                     var cidx = lcAtoms[c].atomIndex
+
                    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 it is with water, delete it
+
                if ({atomIndex=i2}.atomno < {atomIndex=targetIdx}.atomno) {
−
                    if (lcAtoms[c].group = "HOH") {
+
                    movePt = true
−
                        delete {atomIndex=cidx}
+
                    select_cward_idx(i3, get_nward_bb_idx(targetIdx, gChain))
−
                     }
+
                    {atomIndex=targetIdx}.selected = true
 +
                }
 +
                else {
 +
                     select_nward_idx(i2, targetIdx)
 +
                }
 +
            }
  
−
                    # else if it is with side chain not proline, fix it
+
            # Relax rules if desperate
−
                    else if (isSCidx(cidx) and ({atomIndex=cidx}.group != "PRO")) {
+
            if (pass1 > 10) {
−
                        fixSCcollision2(cidx)
+
                phi = -50
−
                        recollect = TRUE
+
            }
−
 
 
−
                        # If not fixed, exit fail
 
−
                        if (not gOk2) {
 
−
                            return # early exit (break n jmol bug)
 
−
                        }
 
−
                    }
 
  
−
                    # else if it is itself a side chain not proline, fix it
+
            # If rotation within ramachandran limits
−
                    else if (isSCidx(idx) and ({atomIndex=idx}.group != "PRO")) {
+
            if ((abs(dt) >= 0.1) and
−
                        fixSCcollision2(idx)
+
                (({atomIndex=i2}.group=="GLY") or (phi < 0))) {
−
                        recollect = TRUE
 
  
−
                        # If not fixed, exit fail
+
                # If moving target point, put the target atom there
−
                        if (not gOk2) {
+
                var cp = {atomIndex=targetIdx}.xyz
−
                            return # early exit (break n jmol bug)
+
                if (movePt) {
−
                        }
+
                    dt = -dt
−
                    }
+
                    {atomIndex=targetIdx}.xyz = pt
 +
                }
  
−
                    # Else if it is with O, counter-rotate
+
                # Rotate to minimize vector ====================
−
                    else if (lcAtoms[c].atomName = "O") {
+
                rotateSelected {atomIndex=i2} {atomIndex=i3} @dt
−
                        counterRotate2(lcAtoms[c].atomIndex,
 
−
                            {atomIndex=idx}.xyz, targetIdx, FALSE)
 
  
−
                        # If not fixed, exit fail
+
                # 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) {
 
                         if (not gOk2) {
−
                             return # early exit (break n jmol bug)
+
                             wasCollision = true
 +
                            rotateSelected {atomIndex=i2} {atomIndex=i3} @{-dt}
 +
                        }
 +
                        else if (wasCollision) {
 +
                            if (ci <3) {
 +
                                rotateSelected {atomIndex=i2} {atomIndex=i3} @{dt}
 +
                            }
 
                         }
 
                         }
−
                    }
+
                        else {
−
 
+
                             break
−
                    # Else if it is itself O, counter-rotate
 
−
                    else if ({atomIndex=idx}.atomName = "O") {
 
−
                        counterRotate2(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
+
                         if (dt < 0.01) {
−
                         gOk2 = FALSE
+
                            break
−
                        return # early exit (break n jmol bug)
+
                        }
−
                    }
+
                    } # endfor
−
                } # endfor
+
                }
−
            }
 
−
        }
 
−
    } # endfor iNo
 
−
}
 
  
−
# Rotate rotor set to move target atom to its proper place
+
                # If moving target point, put the target atom back
−
function tugTrackIdx(targetIdx, targetPt, nWard, cDetect) {
+
                if (movePt) {
−
    gOK = FALSE
+
                    pt = {atomIndex=targetIdx}.xyz
−
    var pt = targetPt
+
                    {atomIndex=targetIdx}.xyz = cp
−
    var dist = distance(pt, {atomIndex=targetIdx}.xyz)
+
                }
  
−
    var rotors = (nWard ? gNrotors : gCrotors)
+
            }
  
−
    # For a number of passes
+
            # If close enough, stop
−
    for (var pass1 = 0; pass1 < 20; pass1++) {
+
            if (distance(pt, {atomIndex=targetIdx}) < kDtolerance) {
−
        var blocked = ({})
+
                gOK = true
−
        for (var pass2 = 0; pass2 < (rotors.size/4); pass2++) {
+
                gTargetPt = pt
 +
                break
 +
            }
  
−
             var v1 = {atomIndex=targetIdx}.xyz - pt
+
             # Block rotor
 +
            blocked |= {atomIndex=i2}
  
−
            # Find the most orthgonal unused rotor
+
        }  # endfor num rotors passes
−
            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 (gOK) {
−
                        if (s > smax) {
+
            break
−
                            smax = s
+
        }
−
                            imax = i
+
    }   # endfor 20 passes
−
                        }
+
}
−
                    }
 
−
                }
 
−
            }
 
  
−
            # If no more rotors, break to next full try
+
# Counter rotate bonds on either side of a BB O
−
            if (imax == 0) {
+
function do_counter_rotate(caPhiIdx, nIdx, cIdx, oIdx, caPsiIdx, dir, nWard) {
−
              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
+
    # Rotate psi
−
            var dt = angle({atomIndex=targetIdx}, {atomIndex=i2}, {atomIndex=i3}, pt)
+
    {atomIndex=nIdx}.selected = nWard
−
            var dh = angle({atomIndex=i1}, {atomIndex=i2}, {atomIndex=i3}, {atomIndex=i4})
+
    {atomIndex=cIdx}.selected = nWard
−
            if (dh == "NaN") {
+
    {atomIndex=oIdx}.selected = nward
−
                dh = -50
+
    rotateSelected {atomIndex=caPsiIdx} {atomIndex=cIdx} @{dir}
−
            }
+
 
−
            var psi = dh + dt
+
    # Counter-rotate phi
−
            var phi = dh + dt
+
    {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) {
  
−
            # Compute resultant psi and phi
+
    var iChain = {atomIndex=oIdx}.chain
−
            #  and select from target atom to first half of rotor
+
    var selsave = {selected}
−
            var movePt = FALSE
+
    var cIdx = get_sc_bb_idx(oIdx, iChain)
−
            if (nWard) {
+
    var nIdx = get_cward_bb_idx(cIdx, iChain)
−
                if ({atomIndex=i2}.atomName="CA") {
+
    var caPhiIdx = get_cward_bb_idx(nIdx, iChain)
−
                    psi = angle({atomIndex=@{getCwardBBidx(i1, gChain)}}, {atomIndex=i1},
+
    var caPsiIdx = get_nward_bb_idx(cIdx, iChain)
−
                        {atomIndex=i2}, {atomIndex=i3}) + dt
 
−
                }
 
−
                else {
 
−
                    phi = angle({atomIndex=i1}, {atomIndex=i2},
 
−
                        {atomIndex=i3}, {atomIndex=@{getNwardBBidx(i3, gChain)}}) + dt
 
−
                }
 
  
−
                if ({atomIndex=i2}.atomno > {atomIndex=targetIdx}.atomno) {
+
    if (nWard) {
−
                    movePt = TRUE
+
        var nNo = {(chain=iChain) and thisModel}.atomno.min
−
                    selectNwardIdx(i3, getCwardBBidx(targetIdx, gChain))
+
        select_nward_idx(caPsiIdx, {(atomno=nNo) and (chain=iChain)
−
                    {atomIndex=targetIdx}.selected = TRUE
+
            and thisModel}.atomIndex)
−
                }
+
    }
−
                else {
+
    else {
−
                    selectCwardIdx(i2, targetIdx)
+
        var cNo = {(chain=iChain) and thisModel}.atomno.max
−
                }
+
        select_cward_idx(caPhiIdx, {(atomno=cNo) and (chain=iChain)
−
            }
+
            and thisModel}.atomIndex)
−
            else {
+
    }
−
                if (({atomIndex=i2}.atomName="CA")) {
 
−
                    phi = angle({atomIndex=@{getNwardBBidx(i1, gChain)}}, {atomIndex=i1},
 
−
                        {atomIndex=i2}, {atomIndex=i3}) + dt
 
−
                }
 
−
                else {
 
−
                    psi = angle({atomIndex=i2}, {atomIndex=i3},
 
−
                        {atomIndex=i4}, {atomIndex=@{getCwardBBidx(i4, gChain)}}) + dt
 
−
                }
 
  
−
                if ({atomIndex=i2}.atomno < {atomIndex=targetIdx}.atomno) {
+
    # Counter-rotate
−
                    movePt = TRUE
+
    do_counter_rotate(caPhiIdx, nIdx, cIdx, oIdx, caPsiIdx, dir, not nWard)
−
                    selectCwardIdx(i3, getNwardBBidx(targetIdx, gChain))
+
    select selsave
−
                    {atomIndex=targetIdx}.selected = TRUE
+
}
−
                }
 
−
                else {
 
−
                    selectNwardIdx(i2, targetIdx)
 
−
                }
 
−
            }
 
  
−
            # Relax rules if desperate
+
function counter_rotate_2(oIdx, toPt, terminalIdx, oDrag) {
−
            if (pass1 > 10) {
 
−
                phi = -50
 
−
            }
 
  
−
            # If rotation within ramachandran limits
+
    var iChain = {atomIndex=oIdx}.chain
−
            if ((abs(dt) >= 0.1) and
+
    var selsave = {selected}
−
                (({atomIndex=i2}.group=="GLY") or (phi < 0))) {
+
    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)
  
−
                # If moving target point, put the target atom there
+
    var nTward = ({atomIndex=oIdx}.atomno < {atomIndex=terminalIdx}.atomno)
−
                var cp = {atomIndex=targetIdx}.xyz
+
    if (nTward) {
−
                if (movePt) {
+
        select_cward_idx(cIdx, terminalIdx)
−
                    dt = -dt
+
    }
−
                    {atomIndex=targetIdx}.xyz = pt
+
    else {
−
                }
+
        select_nward_idx(nIdx, terminalIdx)
 +
    }
  
−
                # Rotate to minimize vector ====================
+
    # Until all collisions cancelled
−
                rotateSelected {atomIndex=i2} {atomIndex=i3} @dt
+
    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)) {
  
−
                # If collision checking
+
        # Counter-rotate
−
                if (cDetect) {
+
        do_counter_rotate(caPhiIdx, nIdx, cIdx, oIdx, caPsiIdx, dir, nTward)
 +
        var newang = angle(toPt, {atomIndex=oIdx}, {atomIndex=cIdx})
  
−
                    # If collision, back off by eighths
+
        # If wrong direction once, undo and reverse
−
                    var wasCollision = FALSE
+
        if (newang > ang) {
−
                    for (var ci = 0; ci < 4; ci++) {
+
            do_counter_rotate(caPhiIDx, nIdx, cIdx, oIdx, caPsiIdx, -dir, nTward)
−
                        if (ci < 3) {
 
−
                            dt /= 2
 
−
                        }
 
−
                        handleCollisions2( 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 first time, continue in opposite direction
 +
            dir *= -1
 +
            if (dir < 0) {
 +
                continue
 
             }
 
             }
 +
        }
  
−
            # If close enough, stop
+
         if (oDrag) {
−
            if (distance(pt, {atomIndex=targetIdx}) < kDtolerance) {
 
−
                gOK = TRUE
 
−
                gTargetPt = pt
 
−
                break
 
−
            }
 
−
 
 
−
            # Block rotor
 
−
            blocked |= {atomIndex=i2}
 
−
 
 
−
        }  # endfor num rotors passes
 
−
 
 
−
         if (gOK) {
 
 
             break
 
             break
 
         }
 
         }
−
    }  # endfor 20 passes
 
−
}
 
  
−
# Counter rotate bonds on either side of a BB O
+
        # If no go, undo and exit
−
function docounterRotate(caPhiIdx, nIdx, cIdx, oIdx, caPsiIdx, dir, nWard) {
+
        tcount++
 +
        if (tcount > (360/abs(dir))) {
 +
            gOk2 = false
 +
            break
 +
        }
  
−
     # Rotate psi
+
     } # endwhile
−
    {atomIndex=nIdx}.selected = nWard
+
     select selsave
−
     {atomIndex=cIdx}.selected = nWard
+
}
−
    {atomIndex=oIdx}.selected = nward
 
−
    rotateSelected {atomIndex=caPsiIdx} {atomIndex=cIdx} @{dir}
 
  
−
     # Counter-rotate phi
+
# Repair proline
−
     {atomIndex=nIdx}.selected = not nWard
+
function repair_proline(BBidx) {
−
     {atomIndex=cIdx}.selected = not nWard
+
     var cbidx = get_cb_idx(BBidx)
−
     {atomIndex=oIdx}.selected = not nward
+
     var cbno = {atomIndex=cbidx}.atomno
−
     rotateSelected {atomIndex=nIdx} {atomIndex=caPhiIdx} @{-dir}
+
     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
  
−
function counterRotate(oIdx, dir, nWard) {
+
    select {atomIndex=cbidx}
 +
    set_angle_idx(nidx, caidx, cbidx, 109.5)
  
−
     var iChain = {atomIndex=oIdx}.chain
+
     select {atomIndex=cdidx}
−
    var selsave = {selected}
+
     set_distance_idx(nidx, cdidx, 1.47)
−
     var cIdx = getScBBidx(oIdx, iChain)
+
     set_angle_idx(caidx, nidx, cdidx, 102.7)
−
     var nIdx = getCwardBBidx(cIdx, iChain)
+
     set_dihedral_idx(cbidx, caidx, nidx, cdidx, 16.2)
−
     var caPhiIdx = getCwardBBidx(nIdx, iChain)
 
−
    var caPsiIdx = getNwardBBidx(cIdx, iChain)
 
  
−
     if (nWard) {
+
     select {atomIndex=cgidx}
−
        nNo = {chain=iChain}.atomno.min
+
    set_distance_idx(cdidx, cgidx, 1.51)
−
        selectNwardIdx(caPsiIdx, {(atomno=nNo) and (chain=iChain)}.atomIndex)
+
     set_angle_idx(nidx, cdidx, cgidx, 106.4)
−
     }
+
     set_dihedral_idx(caidx, nidx, cdidx, cgidx, 16.2)
−
    else {
 
−
        cNo = {chain=iChain}.atomno.max
 
−
        selectCwardIdx(caPhiIdx, {(atomno=cNo) and (chain=iChain)}.atomIndex)
 
−
     }
 
−
 
 
−
    # Counter-rotate
 
−
    docounterRotate(caPhiIdx, nIdx, cIdx, oIdx, caPsiIdx, dir, not nWard)
 
−
    select selsave
 
 
}
 
}
  
−
function counterRotate2(oIdx, toPt, terminalIdx, oDrag) {
+
# Repair side chain
 +
function repair_sc(targetIdx, nWard) {
  
−
     var iChain = {atomIndex=oIdx}.chain
+
     var idx = (nWard ? get_cward_bb_idx(targetIdx, gChain) : get_nward_bb_idx(targetIdx, gChain))
−
    var selsave = {selected}
 
−
    var gOk2 = TRUE
 
−
    var cIdx = getScBBidx(oIdx, iChain)
 
−
    var nIdx = getCwardBBidx(cIdx, iChain)
 
−
    var caPhiIdx = getCwardBBidx(nIdx, iChain)
 
−
    var caPsiIdx = getNwardBBidx(cIdx, iChain)
 
  
−
     var nTward = ({atomIndex=oIdx}.atomno < {atomIndex=terminalIdx}.atomno)
+
     if (({atomIndex=targetIdx}.atomName == "CA")
−
    if (nTward) {
+
        and ({atomIndex=targetIdx}.group != "GLY")) {
−
        selectCwardIdx(cIdx, terminalIdx)
+
        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 {
+
 
−
         selectNwardIdx(nIdx, terminalIdx)
+
     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)
 +
                }
 +
            }
 +
        }
 
     }
 
     }
 +
}
  
−
    # Until all collisions cancelled
+
# Rebuild Cward rotors set
−
    var dir = 5
+
function tug_track_c() {
−
    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
+
    # For all bb atoms cWard of cargo
−
        docounterRotate(caPhiIdx, nIdx, cIdx, oIdx, caPsiIdx, dir, nTward)
+
    var targetIdx = gCcargoIdx
−
        var newang = angle(toPt, {atomIndex=oIdx}, {atomIndex=cIdx})
+
    var okCount = 0
  
−
        # If wrong direction once, undo and reverse
+
    # Allow collisions with cargo
−
        if (newang > ang) {
+
    gOkCollide = gCargoSet
−
            docounterRotate(caPhiIDx, nIdx, cIdx, oIdx, caPsiIdx, -dir, nTward)
+
    var tcount = 0
 +
    while (targetIdx != gNanchorIdx) {
  
−
            # If first time, continue in opposite direction
+
        # Step to next atom
−
            dir *= -1
+
        targetIdx = get_cward_bb_idx(targetIdx, gChain)
−
            if (dir < 0) {
+
        if (targetIdx < 0) {
−
                continue
+
             break
−
             }
 
 
         }
 
         }
  
−
         if (oDrag) {
+
        # No collision with cargo allowed after two atoms placed
−
            break
+
         if (tcount == 2) {
 +
          gOkCollide = ({})
 
         }
 
         }
−
 
−
        # If no go, undo and exit
 
 
         tcount++
 
         tcount++
−
        if (tcount > (360/abs(dir))) {
 
−
            gOk2 = FALSE
 
−
            break
 
−
        }
 
  
−
     } # endwhile
+
        # Compute targets desired coords
−
     select selsave
+
        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 {
 +
        }
  
−
# Repair proline
+
        # If successful
−
function repairProline(BBidx) {
+
        if (gOK == true) {
−
    var cbidx = getCBidx(BBidx)
 
−
    var cbno = {atomIndex=cbidx}.atomno
 
−
    var cgidx = {(atomno=@{cbno+1}) and (chain=gChain)}.atomIndex
 
−
    var cdidx = {(atomno=@{cbno+2}) and (chain=gChain)}.atomIndex
 
−
    var caidx = {(atomno=@{cbno-3}) and (chain=gChain)}.atomIndex
 
−
    var nidx = {(atomno=@{cbno-4}) and (chain=gChain)}.atomIndex
 
  
−
    select {atomIndex=cbidx}
+
            # Adust any side atoms
−
    setAngleIdx(nidx, caidx, cbidx, 109.5)
+
            repair_sc(targetIdx, false)
 +
        }
  
−
    select {atomIndex=cdidx}
+
        # Else fail
−
    setDistanceIdx(nidx, cdidx, 1.47)
+
        else {
−
    setAngleIdx(caidx, nidx, cdidx, 102.7)
+
            break
−
    setDihedralIdx(cbidx, caidx, nidx, cdidx, 16.2)
+
        }
  
−
    select {atomIndex=cgidx}
+
        # If no movement in 4 tries, we are done
−
    setDistanceIdx(cdidx, cgidx, 1.51)
+
        if (okCount > 3) {
−
    setAngleIdx(nidx, cdidx, cgidx, 106.4)
+
            break
−
     setDihedralIdx(caidx, nidx, cdidx, cgidx, 16.2)
+
        }
 +
     } # endwhile (targetIdx != gCanchorIdx) {
 
}
 
}
  
−
# Repair side chain
+
# Rebuild Nward rotors set
−
function repairSideChain(targetIdx, nWard) {
+
function tug_track_n() {
  
−
     var idx = (nWard ? getCwardBBidx(targetIdx, gChain) : getNwardBBidx(targetIdx, gChain))
+
     gOK = true
  
−
     if (({atomIndex=targetIdx}.atomName == "CA")
+
     # For all bb atoms nWard of cargo
−
        and ({atomIndex=targetIdx}.group != "GLY")) {
+
    var targetIdx = gNcargoIdx
−
        var cbidx = getCBidx(targetIdx)
+
    var okCount = 0
−
        select none
+
 
−
         selectAddSideChain(cbidx)
+
    # Allow collisions with cargo
−
         setAngleIdx(idx, targetIdx, cbidx, 110.0)
+
    gOkCollide = gCargoSet
−
        setDistanceIdx(targetIdx, cbidx, 1.5)
+
    var tcount = 0
−
         if ({atomIndex=targetIdx}.group != "PRO") {
+
    while (targetIdx != gNanchorIdx) {
−
            var colliders = (within(kCtolerance, FALSE, {selected})
+
 
−
                and not {atomIndex=targetIdx} and not {selected})
+
         # Step to next atom
−
            if (colliders.size > 0) {
+
         targetIdx = get_nward_bb_idx(targetIdx, gChain)
−
                if ({atomIndex=targetIdx}.group != "ALA") {
+
         if (targetIdx < 0) {
−
                    fixSCcollision2(cbidx)
+
             break
−
                }
 
−
             }
 
 
         }
 
         }
−
         else {
+
          
−
            if (nWard) {
+
        # No collision with cargo allowed after two atoms placed
−
            }
+
        if (tcount == 2) {
−
            else {
+
          gOkCollide = ({})
−
                setDihedralIdx(getNwardBBidx(idx, gChain), idx, targetIdx, cbidx, 174.2)
 
−
            }
 
 
         }
 
         }
−
    }
+
        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") {
  
−
    else if ({atomIndex=targetIdx}.atomName == "C") {
+
            # Desired target location is trigonal O
−
        var oidx = getOidx(targetIdx)
+
            var oidx = get_o_idx(c1idx)
−
        select {atomIndex=oidx}
+
            select {atomIndex=oidx}
−
        setAngleIdx(idx, targetIdx, oidx, 120.0)
+
            set_distance_idx(c1idx, oidx, 1.39)
−
        setDistanceIdx(targetIdx, oidx, 1.21)
+
            pt = get_trigonal_idx(c2idx, c1idx, oidx, 1.41)
−
        if (nWard) {
+
             set_distance_idx(c1idx, oidx, 1.21)
−
             setDihedralIdx(getCwardBBidx(idx, gChain), idx, targetIdx, oidx, 0.0)
 
 
         }
 
         }
−
         if ({atomIndex=idx}.group == "PRO") {
+
         else if (({atomIndex=targetIdx}.atomName == "N")
−
             repairProline(idx)
+
             and ({atomIndex=targetIdx}.group != "GLY")) {
−
            var dNo = {atomIndex=targetIdx}.atomno + 4
+
 
−
            var dIdx = {(atomno=dNO) and (chain=gChain)}.atomIndex
+
            # Desired target location is r-tetragonal CB
−
            var colliders = (within(kCtolerance, FALSE, {atomIndex=dIdx})
+
             var cbidx = get_cb_idx(c1idx)
−
                and not connected({atomIndex=dIdx})
+
            pt = get_tet_idx(cbidx, c1idx, c2idx, 1.5)
−
                and not {atomIndex=dIdx})
 
−
             for (var i = 1; i <= colliders.size; i++) {
 
−
                if (colliders[i].atomName == "O") {
 
−
                    counterRotate2(colliders[i].atomIndex,
 
−
                        {atomIndex=dIdx}.xyz, targetIdx, FALSE)
 
−
                }
 
−
            }
 
 
         }
 
         }
−
    }
+
        else { # C
−
}
 
  
−
# Rebuild Cward rotors set
+
            # Save current target coords
−
function tugTrackC() {
+
            var cp = {atomIndex=targetIdx}.xyz
  
−
    # For all bb atoms cWard of cargo
+
            # Set target atom at desired distance and angle
−
    var targetIdx = gCcargoIdx
+
            select {atomIndex=targetIdx}
−
    var okCount = 0
+
            set_distance_idx(c1idx, targetIdx, 1.37)
 +
            set_angle_idx(c2idx, c1idx, targetIdx, 110.0)
  
−
    # Allow collisions with cargo
+
            if ({atomIndex=targetIdx}.group == "PRO") {
−
    gOkCollide = gCargoSet
+
                set_dihedral_idx(c3idx, c2idx, c1idx, targetIdx, -57.0)
−
    var tcount = 0
+
            }
−
    while (targetIdx != gCanchorIdx) {
 
  
−
        # Step to next atom
+
            # Record and restore target
−
        targetIdx = getCwardBBidx(targetIdx, gChain)
+
            pt = {atomIndex=targetIdx}.xyz
−
 
+
            {atomIndex=targetIdx}.xyz = cp
−
        # No collision with cargo allowed after two atoms placed
 
−
        if (tcount == 2) {
 
−
          gOkCollide = ({})
 
 
         }
 
         }
−
        tcount++
 
  
−
         # Compute targets desired coords
+
         # If target not at desired location
−
         var c1idx = getCwardBBidx(targetIdx, gChain)
+
         if (distance(pt, {atomIndex=targetIdx}) > kDtolerance) {
−
        var n1idx = getNwardBBidx(targetIdx, gChain )
+
            var okCount = 0
−
        var n2idx = getNwardBBidx(n1Idx, gChain)
+
            gTargetPt = pt
−
        var n3idx = getNwardBBidx(n2Idx, gChain)
+
            var xcount = 0
−
        var pt = {0 0 0}
+
            gOK = false
−
        if ({atomIndex=targetIdx}.atomName == "N") {
+
             while ((xcount < 20) and (not gOK)) {
−
             var oidx = getOidx(n1idx)
 
−
            select {atomIndex=oidx}
 
  
−
            # Desired target location is trigonal O
+
                # Rotate on nWard rotor set to move it there
−
            setDistanceIdx(n1idx, oidx, 1.5)
+
                tug_track_idx(targetIdx, pt, true, false)
−
            pt = getTrigonalIdx(n2idx, n1idx, oidx, 1.37)
+
                xcount++
−
             setDistanceIdx(n1idx, oidx, 1.21)
+
             }
 
         }
 
         }
−
         else if (({atomIndex=targetIdx}.atomName == "C")
+
         else {
−
             and ({atomIndex=targetIdx}.group != "GLY")) {
+
             gOK = true
−
 
+
             okCount++
−
             # Desired target location is tetragonal CB
 
−
            var cbidx = getCBidx(n1idx)
 
−
            pt = getTetIdx(n2idx, n1idx, cbidx, 1.5)
 
 
         }
 
         }
−
        else { # CA (or GLY C)
 
  
−
            # Save current target coords
+
        # If sucessful
−
            var cp = {atomIndex=targetIdx}.xyz
+
        if (gOK == true) {
  
−
             # Set target atom at desired distance and angle
+
             # Adust any side atoms
−
             select {atomIndex=targetIdx}
+
             repair_sc(targetIdx, true)
−
            setDistanceIdx(n1idx, targetIdx, 1.5)
+
        }
−
            setAngleIdx(n2idx, n1idx, targetIdx, 120.0)
 
−
            if ({atomIndex=targetIdx}.atomName == "CA") {
 
−
                setDihedralIdx(n3idx, n2idx, n1idx, targetIdx, 180)
 
−
            }
 
  
−
            # Record and restore target
+
        # Else fail
−
            pt = {atomIndex=targetIdx}.xyz
+
        else {
−
             {atomIndex=targetIdx}.xyz = cp
+
             break
 
         }
 
         }
  
−
         # If target not at desired location
+
         # If no movement in 4 tries, we are done
−
         if (distance(pt, {atomIndex=targetIdx}) > kDtolerance) {
+
         if (okCount > 3) {
−
             okCount = 0
+
             break
−
            gTargetPt = pt
 
−
            var xcount = 0
 
−
            gOK = FALSE
 
−
            while ((xcount < 20) and (not gOK)) {
 
−
 
 
−
                # Rotate on cWard rotor set to move it there
 
−
                tugTrackIdx(targetIdx, pt, FALSE, FALSE)
 
−
                xcount++
 
−
            }
 
−
        }
 
−
        else {
 
−
            gOK = TRUE
 
−
            okCount++
 
 
         }
 
         }
  
−
        # If successful
+
    }  # endwhile (targetIdx != gNanchorIdx) {
−
        if (gOK == TRUE) {
+
}
  
−
            # Adust any side atoms
+
# gPlicoRecord is maintained by the macro pilcoRecord
−
            repairSideChain(targetIdx, FALSE)
+
function translate_selected_record(pt) {
−
        }
+
    if (gPlicoRecord != "") {
 +
        plico_record(format("select %s;translateSelected %s;", {selected}, pt))
 +
    }
 +
    translateSelected @pt
 +
}
  
−
         # Else fail
+
# gPlicoRecord is maintained by the macro pilcoRecord
−
         else {
+
function rotate_selected_record(pivotIdx, caxis, a) {
−
             break
+
    if (gPlicoRecord != "") {
−
        }
+
         plico_record(format("select %s;", {selected}))
 +
         plico_record(format("rotateSelected {atomIndex=%d} @%s @%s;",
 +
             pivotIdx, caxis, a))
 +
    }
 +
    rotateSelected {atomIndex=pivotIdx} @caxis @a
 +
}
  
−
         # If no movement in 4 tries, we are done
+
function collect_sc_rotors(no, iChain) {
−
        if (okCount > 3) {
+
    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
 
             break
 
         }
 
         }
−
     } # endwhile (targetIdx != gCanchorIdx) {
+
 
 +
     }
 +
 
 +
    return scBondIdxs
 
}
 
}
  
−
# Rebuild Nward rotors set
+
# Drag Side Chain
−
function tugTrackN() {
+
function drag_sc() {
 +
    var iNo = {atomIndex=gSCidx}.atomno
 +
    var iChain  = {atomIndex=gSCidx}.chain
 +
    if ({atomIndex=gSCidx}.group != "PRO") {
  
−
    gOK = TRUE
+
        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 bb atoms nWard of cargo
+
        # For all rotor combinations
−
    var targetIdx = gNcargoIdx
+
        var dh = array()
−
    var okCount = 0
+
        for (var i = 0; i < numChi; i++) {
−
 
+
            dh += angle({atomIndex=@{scBondIdxs[4+(4*i)]}},
−
    # Allow collisions with cargo
+
                {atomIndex=@{scBondIdxs[3+(4*i)]}},
−
    gOkCollide = gCargoSet
+
                {atomIndex=@{scBondIdxs[2+(4*i)]}},
−
    var tcount = 0
+
                {atomIndex=@{scBondIdxs[1+(4*i)]}})
−
    while (targetIdx != gNanchorIdx) {
+
        }
 +
        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
 +
                    }
 +
                }
  
−
        # Step to next atom
+
                # Find the best
−
        targetIdx = getNwardBBidx(targetIdx, gChain)
+
                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)]}})
 +
                    }
 +
                }
 +
            }
 +
        }
  
−
         # No collision with cargo allowed after two atoms placed
+
         # Now set the best
−
         if (tcount == 2) {
+
        for (var i = 0; i < numChi; i++) {
−
          gOkCollide = ({})
+
            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)
 
         }
 
         }
−
         tcount++
+
    }
 +
    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}
  
−
         # Compute targets desired coords
+
         if (angle({atomIndex=ica}, {atomIndex=in},
−
        var n1idx = getNwardBBidx(targetIdx, gChain)
+
            {atomIndex=icd}, {atomIndex=gSCidx}) < -10.0) {
−
        var c1idx = getCwardBBidx(targetIdx, gChain)
+
             set_dihedral_idx(ica, in, icd, gSCidx, 8.7)
−
        var c2idx = getCwardBBidx(c1idx, gChain)
+
             set_angle_idx(in, icd, gSCidx, 110.0)
−
        var c3idx = getCwardBBidx(c2idx, gChain)
+
             set_distance_idx(icd, gSCidx, 1.5)
−
        var pt = {0 0 0}
 
−
        if ({atomIndex=targetIdx}.atomName == "CA") {
 
−
 
 
−
            # Desired target location is trigonal O
 
−
             var oidx = getOidx(c1idx)
 
−
            select {atomIndex=oidx}
 
−
            setDistanceIdx(c1idx, oidx, 1.39)
 
−
             pt = getTrigonalIdx(c2idx, c1idx, oidx, 1.41)
 
−
             setDistanceIdx(c1idx, oidx, 1.21)
 
 
         }
 
         }
−
         else if (({atomIndex=targetIdx}.atomName == "N")
+
         else {
−
             and ({atomIndex=targetIdx}.group != "GLY")) {
+
             set_dihedral_idx(ica, in, icd, gSCidx, -29.5)
−
 
+
             set_angle_idx(in, icd, gSCidx, 108.8)
−
            # Desired target location is r-tetragonal CB
+
             set_distance_idx(icd, gSCidx, 1.5)
−
             var cbidx = getCBidx(c1idx)
 
−
             pt = getTetIdx(cbidx, c1idx, c2idx, 1.5)
 
 
         }
 
         }
−
        else { # C
+
    }
  
−
            # Save current target coords
+
    draw gSCcircle CIRCLE {atomIndex=gSCidx} MESH NOFILL
−
            var cp = {atomIndex=targetIdx}.xyz
+
    gSCpt = {atomIndex=gSCidx}.xyz
 +
}
  
−
            # Set target atom at desired distance and angle
+
# Fix side chain collisions
−
            select {atomIndex=targetIdx}
+
function fix_sc_collision_2(idx) {
−
            setDistanceIdx(c1idx, targetIdx, 1.37)
+
    gOk2 = false
−
            setAngleIdx(c2idx, c1idx, targetIdx, 110.0)
+
    var iNo = {atomIndex=idx}.atomno
 +
    var iChain = {atomIndex=idx}.chain
 +
    var resno = {(atomno=iNo) and (chain=iChain)
 +
        and thisModel}.resno
  
−
            if ({atomIndex=targetIdx}.group == "PRO") {
+
    # Get SC terminus
−
                setDihedralIdx(c3idx, c2idx, c1idx, targetIdx, -57.0)
+
    while (resno == {(atomno=iNo) and (chain=iChain)
−
            }
+
        and thisModel}.resno) {
 +
        iNo++
 +
    }
 +
    iNo--
  
−
            # Record and restore target
+
    var sc = array()
−
            pt = {atomIndex=targetIdx}.xyz
+
    var iBno = iNo
−
             {atomIndex=targetIdx}.xyz = cp
+
    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
  
−
        # If target not at desired location
+
    var scBondIdxs = collect_sc_rotors( iNo, iChain)
−
        if (distance(pt, {atomIndex=targetIdx}) > kDtolerance) {
+
    var numChi = scBondIdxs.size / 4
−
            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
+
    # For all rotor combinations
−
                tugTrackIdx(targetIdx, pt, TRUE, FALSE)
+
    for (var i = 0; i < numChi; i++) {
−
                xcount++
+
         var rot = -120
−
            }
+
         for (var j = 0; j < 6; j++) {
−
         }
+
             rot += 60
−
         else {
+
             select_add_sc(scBondIdxs[1+(4*i)])
−
             gOK = TRUE
+
            set_dihedral_idx(scBondIdxs[1+(4*i)], scBondIdxs[2+(4*i)],
−
             okCount++
+
                scBondIdxs[3+(4*i)], scBondIdxs[4+(4*i)], rot)
−
        }
 
  
−
        # If sucessful
+
            # If no collision, exit
−
        if (gOK == TRUE) {
+
            var colliders = (within(kCtolerance, false, {sc})
 +
                and not {atomIndex=cbidx} and not {sc})
  
−
             # Adust any side atoms
+
             # If it is with water, delete the water
−
             repairSideChain(targetIdx, TRUE)
+
             for (var c = 1; c < colliders.size; c++ ) {
−
        }
+
                if (colliders[c].group = "HOH") {
 +
                    delete {atomIndex=@{colliders[c].atomIndex}}
 +
                    colliders = {colliders and not @{colliders[c]}}
 +
                }
 +
            }
  
−
        # Else fail
+
            if (colliders.size == 0) {
−
        else {
+
                gOk2 = true
−
            break
+
                return # Early exit since break 1 appears broken
−
        }
+
            }
  
−
        # 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) {
 
−
    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 is_moveable_sc(aIdx) {
−
function translateSelectedRecord(pt) {
 
−
    if (gPlicoRecord != "") {
 
−
        plicoRecord(format("select %s;translateSelected %s;", {selected}, pt))
 
−
    }
 
−
    translateSelected @pt
 
−
}
 
  
−
# gPlicoRecord is maintained by the macro pilcoRecord
+
    var ret = (({atomIndex=aIdx}.group != "PRO")
−
function rotateSelectedRecord(pivotIdx, axis, a) {
+
         or ({atomIndex=aIdx}.atomName == "CG"))
−
    if (gPlicoRecord != "") {
+
    switch({atomIndex=aIdx}.atomName) {
−
         plicoRecord(format("select %s;", {selected}))
+
    case "N":
−
        plicoRecord(format("rotateSelected {atomIndex=%d} @%s @%s;",
+
    case "CA":
−
            pivotIdx, axis, a))
+
    case "C":
 +
    case "CB":
 +
    case "O":
 +
    case "O4\'":
 +
        ret = false
 +
        break
 
     }
 
     }
−
     rotateSelected {atomIndex=pivotIdx} @axis @a
+
     return ret
 
}
 
}
  
−
function collectSCrotors(no, iChain) {
+
function is_rotor_avail(i1idx, i2idx) {
−
     var scBondIdxs = array()
+
     var ret = true
−
     for (var iNo = no; iNo >= 0; iNo--) {
+
     if (i1idx > i2idx) { # frozen bonds are kept as lo-hi
−
         var ile = 0
+
         var idx = @i1idx
−
         switch ({(atomno=iNo) and (chain=iChain)}.atomName) {
+
         i1idx = @i2idx
−
         case "CA" :
+
         i2idx = @idx
−
            return scBondIdxs # Early exit since break 1 appears broken
+
    }
−
        case "CZ" :
+
 
−
            if ({(atomno=iNo) and (chain=iChain)}.group == "TYR") {
+
    for (var i = 1; i <= gFreeze.size; i += 2) {
−
                break
+
         if ((gFreeze[i] == i1idx) and (gFreeze[i+1] == i2idx)) {
−
            }
+
             ret = false
−
        case "CE" :
+
             break
−
            if ({(atomno=iNo) and (chain=iChain)}.group == "MET") {
 
−
                break
 
−
            }
 
−
         case "CG1" :
 
−
            if ({(atomno=iNo) and (chain=iChain)}.group == "VAL") {
 
−
                break
 
−
            }
 
−
            if ({(atomno=iNo) and (chain=iChain)}.group == "ILE") {
 
−
                ile = 1
 
−
            }
 
−
        case "NE" :
 
−
        case "CD" :
 
−
        case "SD" :
 
−
        case "CG" :
 
−
        case "CB" :
 
−
            scBondIdxs += {(atomno=@{iNo+1+ile}) and (chain=iChain)}.atomIndex
 
−
            scBondIdxs += {(atomno=@{iNo+0}) and (chain=iChain)}.atomIndex
 
−
            if ({(atomno=iNo) and (chain=iChain)}.atomName%2 == "CG") {
 
−
                scBondIdxs += {(atomno=@{iNo-1}) and (chain=iChain)}.atomIndex
 
−
                scBondIdxs += {(atomno=@{iNo-4}) and (chain=iChain)}.atomIndex
 
−
            }
 
−
             else if ({(atomno=iNo) and (chain=iChain)}.atomName == "CB") {
 
−
                scBondIdxs += {(atomno=@{iNo-3}) and (chain=iChain)}.atomIndex
 
−
                scBondIdxs += {(atomno=@{iNo-4}) and (chain=iChain)}.atomIndex
 
−
            }
 
−
            else {
 
−
                scBondIdxs += {(atomno=@{iNo-1}) and (chain=iChain)}.atomIndex
 
−
                scBondIdxs += {(atomno=@{iNo-2}) and (chain=iChain)}.atomIndex
 
−
            }
 
−
             break
 
 
         }
 
         }
−
 
 
     }
 
     }
  
−
     return scBondIdxs
+
     return ret
 
}
 
}
  
−
# Drag Side Chain
+
function xcollect_bb_rotors(nWard) {
−
function dragSC() {
+
     var anchorNo = (nWard
−
 
+
        ? ((gNanchorIdx >= 0) ? {atomIndex=gNanchorIdx}.atomno : gMinNo)
−
     var iNo = {atomIndex=gSCidx}.atomno
+
        : ((gCanchorIdx >= 0) ? {atomIndex=gCanchorIdx}.atomno : gMaxNo))
−
     var iChain  = {atomIndex=gSCidx}.chain
+
     var cargoNo = (nWard
 +
        ? ((gNcargoIdx >= 0) ? {atomIndex=gNcargoIdx}.atomno
 +
        : {atomIndex=gCcargoIdx}.atomno)
 +
        : {atomIndex=gCcargoIdx}.atomno)
 +
    var rotors = array()
 +
    if (cargoNo < anchorNo) {
  
−
    if ({atomIndex=gSCidx}.group != "PRO") {
+
        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 {
  
−
         var scBondIdxs = collectSCrotors( iNo, iChain)
+
         for (var iNo = cargoNo; iNo >= anchorNo; iNo--) {
−
        var numChi = scBondIdxs.size / 4
+
            if ({(atomno=iNo) and (chain=gChain)
−
        var dist = distance({atomIndex=gSCidx}.xyz, gSCpt)
+
                and thisModel}.atomName == "CA") {
−
 
+
                if (is_rotor_avail(iNo)) {
−
        var scSet = ({})
+
                    if ((iNo != (anchorNo-1)) and (iNo < cargoNo)) { # psi
−
        if (gSCcheck) {
+
                        rotors += [{(atomno=@{get_np_no(iNo+2)}) and (chain=gChain)
−
            scSet = getScSet(gSCidx, iChain)
+
                            and thisModel}.atomIndex,
−
        }
+
                            {(atomno=@{iNo+1}) and (chain=gChain)
−
       
+
                                and thisModel}.atomIndex]
−
        # For all rotor combinations
+
                        rotors += [{(atomno=@{iNo}) and (chain=gChain)
−
        var dh = array()
+
                            and thisModel}.atomIndex,
−
        for (var i = 0; i < numChi; i++) {
+
                            {(atomno=@{iNo-1}) and (chain=gChain)
−
            dh += angle({atomIndex=@{scBondIdxs[4+(4*i)]}},
+
                                and thisModel}.atomIndex]
−
                {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
 
−
                selectAddSideChain(scBondIdxs[1+(4*i)])
 
−
                setDihedralIdx(scBondIdxs[4+(4*i)], scBondIdxs[3+(4*i)],
 
−
                    scBondIdxs[2+(4*i)], scBondIdxs[1+(4*i)], rot)
 
−
                var newDist = distance({atomIndex=gSCidx}.xyz, gSCpt)
 
−
                if (gSCcheck) {
 
−
                    var colliders = (within(kCtolerance, FALSE, scSet)
 
−
                        and not connected(scSet) and not {scSet})
 
−
                    if (colliders.size > 0) {
 
−
                        continue
 
 
                     }
 
                     }
−
                }
+
                    if ({(atomno=iNo) and (chain=gChain)
−
               
+
                        and thisModel}.group != "PRO") { # phi
−
                # Find the best
+
                         rotors += [{(atomno=@{iNo+1}) and (chain=gChain)
−
                if (newDist < dist) {
+
                            and thisModel}.atomIndex,
−
                    dist = newDist
+
                            {(atomno=@{iNo}) and (chain=gChain)
−
                    for (var k = 0; k < numChi; k++) {
+
                                and thisModel}.atomIndex]
−
                         dh[k+1] = angle({atomIndex=@{scBondIdxs[4+(4*k)]}},
+
                         rotors += [{(atomno=@{iNo-1}) and (chain=gChain)
−
                        {atomIndex=@{scBondIdxs[3+(4*k)]}},
+
                            and thisModel}.atomIndex,
−
                         {atomIndex=@{scBondIdxs[2+(4*k)]}},
+
                            {(atomno=@{get_cm_no(iNo-1)}) and (chain=gChain)
−
                        {atomIndex=@{scBondIdxs[1+(4*k)]}})
+
                                and thisModel}.atomIndex]
 
                     }
 
                     }
 
                 }
 
                 }
 
             }
 
             }
 
         }
 
         }
 +
    }
  
−
        # Now set the best
+
    if (nWard) {
−
        for (var i = 0; i < numChi; i++) {
+
         gNrotors = rotors
−
            selectAddSideChain(scBondIdxs[1+(4*i)])
 
−
            setDihedralIdx(scBondIdxs[4+(4*i)], scBondIdxs[3+(4*i)],
 
−
                scBondIdxs[2+(4*i)], scBondIdxs[1+(4*i)], dh[i+1])
 
−
         }
 
 
     }
 
     }
−
     else { # PRO - toggle between puckers up and down
+
     else {
−
         var icd = {(atomno=@{iNo+1}) and (chain=iChain)}.atomIndex
+
        gCrotors = rotors
−
         var icb = {(atomno=@{iNo-1}) and (chain=iChain)}.atomIndex
+
    }
−
        var ica = {(atomno=@{iNo-4}) and (chain=iChain)}.atomIndex
+
}
−
        var in = {(atomno=@{iNo-5}) and (chain=iChain)}.atomIndex
+
function collect_bb_rotors(nWard) {
−
        select {atomIndex=gSCidx}
+
    if (nWard) {
−
 
+
        gNrotors = array()
−
         if (angle({atomIndex=ica}, {atomIndex=in},
+
         var nres = {atomIndex=gNcargoIdx}.resno
−
             {atomIndex=icd}, {atomIndex=gSCidx}) < -10.0) {
+
        var nname = {atomIndex=gNcargoIdx}.atomName
−
             setDihedralIdx(ica, in, icd, gSCidx, 8.7)
+
        var ares = get_resno_min(gChain)
−
             setAngleIdx(in, icd, gSCidx, 110.0)
+
        var aA = get_atom_rcn( ares, gChain, "N")
−
             setDistanceIdx(icd, gSCidx, 1.5)
+
        if (gNanchorIdx >= 0) {
−
        }
+
            aA = {atomIndex=gNanchorIdx}
−
        else {
+
        }
−
             setDihedralIdx(ica, in, icd, gSCidx, -29.5)
+
        var aname = aA.atomName
−
            setAngleIdx(in, icd, gSCidx, 108.8)
+
         for (var r = nres; r >= ares; r--) {
−
             setDistanceIdx(icd, gSCidx, 1.5)
+
            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
 
     }
 
     }
−
 
−
    draw gSCcircle CIRCLE {atomIndex=gSCidx} MESH NOFILL
 
−
    gSCpt = {atomIndex=gSCidx}.xyz
 
 
}
 
}
  
−
# Fix side chain collisions
+
function collect_rotors() {
−
function fixSCcollision2(idx) {
+
     collect_bb_rotors(false)
−
     gOk2 = FALSE
+
     collect_bb_rotors(true)
−
    var iNo = {atomIndex=idx}.atomno
+
}
−
     var iChain = {atomIndex=idx}.chain
 
−
    var resno = {(atomno=iNo) and (chain=iChain)}.resno
 
  
−
    # Get SC terminus
+
function tug_sc(pt) {
−
    while (resno == {(atomno=iNo) and (chain=iChain)}.resno) {
 
−
        iNo++
 
−
    }
 
−
    iNo--
 
  
−
     var sc = array()
+
     # If destination atom defined
−
    var iBno = iNo
+
    if (gDestAtomIdx >= 0) {
−
    while ({(atomno=iBno) and (chain=iChain)}.atomName != "CB") {
+
        var v = {atomIndex=gDestAtomIdx}.xyz - {atomIndex=gSCidx}.xyz
−
         sc += {(atomno=iBno) and (chain=iChain)}
+
        if (abs(angle({atomIndex=gDestAtomIdx}.xyz, {0 0 0}, pt)) < 90) {
−
         iBno--
+
            pt = -v/20.0
 +
        }
 +
         else {
 +
            pt = v/20.0
 +
         }
 
     }
 
     }
−
     var cbidx = {(atomno=iBno) and (chain=iChain)}.atomIndex
+
     gSCpt += pt
 +
    draw arrow {atomIndex=gSCidx} @gSCpt
 +
}
  
−
     var scBondIdxs = collectSCrotors( iNo, iChain)
+
function set_colors() {
−
     var numChi = scBondIdxs.size / 4
+
    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
 +
}
  
−
    # For all rotor combinations
+
function clear_atom_idxs() {
−
    for (var i = 0; i < numChi; i++) {
+
    gCcargoIdx = -1
−
        var rot = -120
+
    gNcargoIdx = -1
−
        for (var j = 0; j < 6; j++) {
+
    gCanchorIdx = -1
−
            rot += 60
+
    gNanchorIdx = -1
−
            selectAddSideChain(scBondIdxs[1+(4*i)])
+
    g1pivotIdx = -1
−
            setDihedralIdx(scBondIdxs[1+(4*i)], scBondIdxs[2+(4*i)],
+
    g2pivotIdx = -1
−
                scBondIdxs[3+(4*i)], scBondIdxs[4+(4*i)], rot)
+
    g1dynamicIdx = -1
−
               
+
    g2dynamicIdx = -1
−
            # If no collision, exit
+
    gDestAtomIdx = -1
−
            colliders = (within(kCtolerance, FALSE, {sc})
+
    gSCidx = -1
−
                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 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 isMovableSideChain(aIdx) {
+
function record_drag() {
−
 
+
     var ls = format("select %s;", {selected})
−
     var ret = (({atomIndex=aIdx}.group != "PRO")
+
    ls += format("gCanchorIdx = %d;", gCanchorIdx)
−
        or ({atomIndex=aIdx}.atomName == "CG"))
+
    ls += format("gCanchorNo = %d;", gCanchorNo)
−
     switch({atomIndex=aIdx}.atomName) {
+
    ls += format("gNanchorIdx = %d;", gNanchorIdx)
−
     case "N":
+
    ls += format("gNanchorNo = %d;", gNanchorNo)
−
     case "CA":
+
    ls += format("gCcargoIdx = %d;", gCcargoIdx)
−
     case "C":
+
    ls += format("gNcargoIdx = %d;", gNcargoIdx)
−
     case "CB":
+
     ls += format("gCcargoNo = %d;", gCcargoNo)
−
     case "O":
+
     ls += format("gNcargoNo = %d;", gNcargoNo)
−
     case "O4\'":
+
     ls += format("gDestAtomIdx = %d;", gDestAtomIdx)
−
        ret = FALSE
+
     ls += format("g1pivotIdx = %d;", g1pivotIdx)
−
        break
+
     ls += format("g2pivotIdx = %d;", g2pivotIdx)
−
     }
+
     ls += format("gOkCollide = %s;", gOkCollide)
−
     return ret
+
     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)
 
}
 
}
  
−
function isRotorAvailable(i1idx, i2idx) {
+
# Pick call-back for freeze
−
    var ret = TRUE
+
function tug_pick_cb() {
−
     if (i1idx > i2idx) {
+
     if (_pickInfo[3][6] == "bond") {
−
         var idx = @i1idx
+
         var sel = {selected}
−
         i1idx = @i2idx
+
         var i = _pickInfo.find(":")
−
         i2idx = @idx
+
         var iChain = _pickInfo[i+1]
−
    }
+
        i = _pickInfo.find("#")
−
   
+
        var a1no = 0 + _pickInfo[i+1][i+3]
−
    for (var i = 1; i <= gFreeze.size; i += 2) {
+
        var j = _pickInfo[i+1][9999].find("#")
−
         if ((gFreeze[i] == i1idx) and (gFreeze[i+1] == i2idx)) {
+
        var a2no = 0 + _pickInfo[i+j+1][i+j+3]
−
            ret = FALSE
+
        var i1idx = {(atomno=a1no) and (chain=iChain)
−
            break
+
            and thisModel}.atomIndex
−
        }
+
        var i2idx = {(atomno=a2no) and (chain=iChain)
−
    }
+
            and thisModel}.atomIndex
−
   
+
         if (({atomIndex=i1idx}.atomName == "CA")
−
    return ret
+
            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}
  
−
function collectBBrotors(nWard) {
+
                for (i = 1; i <= gFreeze.size; i += 2) {
−
    var anchorNo = (nWard
+
                    if ((gFreeze[i] == i1idx) and (gFreeze[i+1] == i2idx)) {
−
        ? ((gNanchorIdx >= 0) ? {atomIndex=gNanchorIdx}.atomno : gMinNo)
+
                        if (i > 1) {
−
        : ((gCanchorIdx >= 0) ? {atomIndex=gCanchorIdx}.atomno : gMaxNo))
+
                            if (gFreeze.size = (i+1)) {
−
    var cargoNo = (nWard
+
                                gFreeze = gFreeze[1][i-1]
−
        ? ((gNcargoIdx >= 0) ? {atomIndex=gNcargoIdx}.atomno
+
                            }
−
        : {atomIndex=gCcargoIdx}.atomno)
+
                             else {
−
        : {atomIndex=gCcargoIdx}.atomno)
+
                                gFreeze = gFreeze[1][i-1] + gFreeze[i+2][0]
−
    var rotors = array()
+
                             }
−
    if (cargoNo < anchorNo) {
+
                        }
−
 
+
                         else {
−
        for (var iNo = cargoNo; iNo <= anchorNo; iNo++) {
+
                             gFreeze = gFreeze[i+2][0]
−
            if ({(atomno=iNo) and (chain=gChain)}.atomName == "CA") {
+
                        }
−
                if (isRotorAvailable(iNo)) {
+
                        color bonds NONE
−
                    if (({(atomno=iNo) and (chain=gChain)}.group != "PRO") and (iNo > cargoNo)) { # phi
+
                        i = 0
−
                        rotors += [{(atomno=@{getCmNo(iNo-1)}) and (chain=gChain)}.atomIndex,
+
                        break
−
                            {(atomno=@{iNo-1}) and (chain=gChain)}.atomIndex]
 
−
                        rotors += [{(atomno=@{iNo}) and (chain=gChain)}.atomIndex,
 
−
                             {(atomno=@{iNo+1}) and (chain=gChain)}.atomIndex]
 
−
                    }
 
−
                    if (iNo != (anchorNo-1)) { # psi
 
−
                        rotors += [{(atomno=@{iNo-1}) and (chain=gChain)}.atomIndex,
 
−
                             {(atomno=@{iNo}) and (chain=gChain)}.atomIndex]
 
−
                         rotors += [{(atomno=@{iNo+1}) and (chain=gChain)}.atomIndex,
 
−
                             {(atomno=@{getNpNo(iNo+2)}) and (chain=gChain)}.atomIndex]
 
 
                     }
 
                     }
 +
                }
 +
                if (i > gFreeze.size) {
 +
                    gFreeze += i1idx
 +
                    gFreeze += i2idx
 +
                    color bonds lightblue
 
                 }
 
                 }
 
             }
 
             }
 
         }
 
         }
 +
        select {sel}
 
     }
 
     }
−
    else {
+
}
  
−
        for (var iNo = cargoNo; iNo >= anchorNo; iNo--) {
+
# Bound to LEFT-UP by tug_enable_drag
−
            if ({(atomno=iNo) and (chain=gChain)}.atomName == "CA") {
+
function tug_drag_done_mb() {
−
                if (isRotorAvailable(iNo)) {
+
    if (not gBusy) {
−
                    if ((iNo != (anchorNo-1)) and (iNo < cargoNo)) { # psi
+
        if (gPlicoRecord != "") {
−
                        rotors += [{(atomno=@{getNpNo(iNo+2)}) and (chain=gChain)}.atomIndex,
+
            record_drag()
−
                            {(atomno=@{iNo+1}) and (chain=gChain)}.atomIndex]
 
−
                        rotors += [{(atomno=@{iNo}) and (chain=gChain)}.atomIndex,
 
−
                            {(atomno=@{iNo-1}) and (chain=gChain)}.atomIndex]
 
−
                    }
 
−
                    if ({(atomno=iNo) and (chain=gChain)}.group != "PRO") { # phi
 
−
                        rotors += [{(atomno=@{iNo+1}) and (chain=gChain)}.atomIndex,
 
−
                            {(atomno=@{iNo}) and (chain=gChain)}.atomIndex]
 
−
                        rotors += [{(atomno=@{iNo-1}) and (chain=gChain)}.atomIndex,
 
−
                            {(atomno=@{getCmNo(iNo-1)}) and (chain=gChain)}.atomIndex]
 
−
                    }
 
−
                }
 
−
            }
 
 
         }
 
         }
−
    }
 
  
−
    if (nWard) {
+
        # Move by rotation on rotor sets, smallest first
−
         gNrotors = rotors
+
         gBusy = true
−
    }
+
        background ECHO pink
−
    else {
+
         refresh
−
         gCrotors = rotors
 
−
    }
 
−
}
 
  
−
function collectRotors() {
+
        # If side chain mode
−
    collectBBrotors(FALSE)
+
        if (gSCidx >= 0) {
−
    collectBBrotors(TRUE)
+
            drag_sc()
−
}
+
        }
  
−
function tugSideChain(pt) {
+
        # Else
−
 
+
        else if (not gTow) {
−
    # If destination atom defined
+
            gOK = true
−
    if (gDestAtomIdx >= 0) {
+
            timeout ID"tug" 20.0 "timed_out(\"Tug timed out\")"
−
        var v = {atomIndex=gDestAtomIdx}.xyz - {atomIndex=gSCidx}.xyz
+
            if ((gCrotors.size < gNrotors.size) or (gNanchorIdx < 0)) {
−
        if (abs(angle({atomIndex=gDestAtomIdx}.xyz, {0 0 0}, pt)) < 90) {
+
                if (gCrotors.size > 4) {
−
             pt = -v/20.0
+
                    tug_track_c()
−
        }
+
                }
−
        else {
+
                if (gOK and (gNrotors.size > 4)) {
−
            pt = v/20.0
+
                    tug_track_n()
−
        }
+
                }
−
    }
+
             }
−
    gSCpt += pt
+
            else {
−
    draw arrow {atomIndex=gSCidx} @gSCpt
+
                if (gNrotors.size > 4) {
−
}
+
                    tug_track_n()
 +
                }
 +
                if (gOK and (gCrotors.size > 4)) {
 +
                    tug_track_c()
 +
                }
 +
            }
 +
            timeout ID"tug" OFF
  
−
function setColors() {
+
            # If anchor angles acute, fail
−
    select all
+
            if (gOK == true) {
−
    color {selected} @gScheme
+
                if (gCanchorIdx >= 0) {
−
    color {atomIndex=g1pivotIdx} green
+
                    var ic = get_cward_bb_idx(gCanchorIdx, gChain)
−
    color {atomIndex=g2pivotIdx} green
+
                    var in = get_nward_bb_idx(gCanchorIdx, gChain)
−
    color @gCargoSet @gAltScheme
+
                    if ((ic >= 0) and
−
    select {(atomIndex=gCcargoIdx) or (atomIndex=gNcargoIdx)
+
                        angle({atomIndex=ic}, {atomIndex=gCanchorIdx}, {atomIndex=in})
−
        or (atomIndex=gCanchorIdx) or (atomIndex=gNanchorIdx)}
+
                        < 100.0) {
−
    halo on
+
                        gOK = false
−
    select {atomIndex=gDestAtomIdx}
+
                    }
−
    star on
+
                }
−
    select none
+
                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
 +
                    }
 +
                }
 +
            }
  
−
function clearAtomIdxs() {
+
            # If too far
−
    gCcargoIdx = -1
+
            if (not gOK) {
−
    gNcargoIdx = -1
+
                timed_out("TUG TOO FAR!")
−
    gCanchorIdx = -1
+
            }
−
    gNanchorIdx = -1
+
 
−
    g1pivotIdx = -1
+
            # Else OK
−
    g2pivotIdx = -1
+
            else {
−
    g1dynamicIdx = -1
+
 
−
    g2dynamicIdx = -1
+
                var idx = {
−
    gDestAtomIdx = -1
+
                    (atomno=@{{(chain=gChain) and thisModel}.atomno.min})
−
    gSCidx = -1
+
                    and (chain=gChain) and thisModel}.atomIndex
−
}
 
  
−
function timedOut (s) {
 
−
    timeout ID"tug" OFF
 
−
    p = prompt(format("%s - Undo?", s), "Yes|No", TRUE)
 
−
    if (p == "Yes") {
 
−
        gBusy = FALSE
 
−
        background ECHO yellow
 
−
        restore state gState
 
−
        connect
 
−
        select gCargoSet
 
−
        refresh
 
−
        quit
 
−
    }
 
−
}
 
  
−
function recordDrag() {
+
                var ihc = 0
−
    var ls = format("select %s;", {selected})
+
                for (ihc = 0; ihc < 10; ihc++) {
−
    ls += format("gCanchorIdx = %d;", gCanchorIdx)
+
                    select ((atomno >= gNanchorNo) and (atomno <= gCanchorNo)
−
    ls += format("gCanchorNo = %d;", gCanchorNo)
+
                        and (chain = gChain) and thisModel)
−
    ls += format("gNanchorIdx = %d;", gNanchorIdx)
+
                    handle_collisions( idx)
−
    ls += format("gNanchorNo = %d;", gNanchorNo)
+
                    if (count_collisions(({})).size == 0) {
−
    ls += format("gCcargoIdx = %d;", gCcargoIdx)
+
                        break
−
    ls += format("gNcargoIdx = %d;", gNcargoIdx)
+
                    }
−
    ls += format("gCcargoNo = %d;", gCcargoNo)
+
                }
−
    ls += format("gNcargoNo = %d;", gNcargoNo)
+
                if (ihc == 10) {
−
    ls += format("gDestAtomIdx = %d;", gDestAtomIdx)
+
                    timed_out("Unable to handle all collisions!")
−
    ls += format("g1pivotIdx = %d;", g1pivotIdx)
+
                }
−
    ls += format("g2pivotIdx = %d;", g2pivotIdx)
+
            }
−
    ls += format("gOkCollide = %s;", gOkCollide)
+
        }
−
    ls += format("gChain = \"%s\";", gChain)
+
        select {gCargoSet}
−
    ls += format("gMinNo = %d;", gMinNo)
+
        gBusy = false
−
    ls += format("gMaxNo = %d;", gMaxNo)
+
        background ECHO yellow
−
    ls += format("gCargoSet = %s;", gCargoSet)
+
        set bondPicking true
−
     ls += format("gSCidx = %d;", gSCidx)
+
        refresh
−
    ls += format("gSCcircle = %d;", gSCcircle)
+
     }
−
    ls += format("gSCpt = %s;", gSCpt)
+
}
−
    ls += "collectRotors();"
+
 
−
    ls += "tugDragDoneMB();"
+
# Bound to ALT-SHIFT-LEFT-DRAG by tug_enable_drag
−
     plicoRecord(ls)
+
function tug_drag_2_mb() {
 +
     tug_drag_mb(true)
 
}
 
}
  
−
# Pick call-back for freeze
+
# Bound to ALT-LEFT-DRAG by tug_enable_drag
−
function tugPickCB() {
+
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)
 +
                }
 +
            }
  
−
    if (_pickInfo[3][6] == "bond") {
+
            # Else
−
        var sel = {selected}
+
             else {
−
        var i = _pickInfo.find(":")
+
 
−
        var iChain = _pickInfo[i+1]
+
                 # If new drag
−
        i = _pickInfo.find("#")
+
                 if (gNewDrag) {
−
        var a1no = _pickInfo[i+1][i+3]
+
                     gNewDrag = false
−
        j = _pickInfo[i+1][9999].find("#")
+
                     save state gState
−
        var a2no = _pickInfo[i+j+1][i+j+3]
 
−
        var i1idx = {(atomno=a1no) and (chain=iChain)}.atomIndex
 
−
        var i2idx = {(atomno=a2no) and (chain=iChain)}.atomIndex
 
−
       
 
−
        if (({atomIndex=i1idx}.atomName == "CA")
 
−
             or ({atomIndex=i2idx}.atomName == "CA")) {
 
−
            if (({atomIndex=i1idx}.atomName != "CB")
 
−
                 and ({atomIndex=i2idx}.atomName != "CB")) {
 
−
                 if (i1idx > i2idx) {
 
−
                     idx = 0 + i1idx
 
−
                     i1idx = 0 + i2idx
 
−
                    i2idx = 0 + idx
 
 
                 }
 
                 }
−
                 select {atomIndex=i1idx} or {atomIndex=i2idx}
+
 
−
               
+
                # If destination atom defined
−
                for (i = 1; i <= gFreeze.size; i += 2) {
+
                 if (gDestAtomIdx >= 0) {
−
                     if ((gFreeze[i] == i1idx) and (gFreeze[i+1] == i2idx)) {
+
                    var v = {atomIndex=gDestAtomIdx}.xyz - {selected}.xyz
−
                         gFreeze[i] == -1
+
                     if (abs(angle({atomIndex=gDestAtomIdx}.xyz, {0 0 0}, pt)) < 90) {
−
                        color bonds NONE
+
                         pt = -v/20.0
−
                         break
+
                    }
 +
                    else {
 +
                         pt = v/20.0
 
                     }
 
                     }
 
                 }
 
                 }
−
                if (i > gFreeze.size) {
 
−
                    gFreeze += i1idx
 
−
                    gFreeze += i2idx
 
−
                    color bonds lightblue
 
−
                }
 
−
            }
 
−
        }
 
−
        select {sel}
 
−
    }
 
−
}
 
  
−
# Bound to LEFT-UP by tugEnableDrag
+
                # Move the cargo
−
function tugDragDoneMB() {
+
                select {gCargoSet}
−
    if (not gBusy) {
 
−
        if (gPlicoRecord != "") {
 
−
            recordDrag()
 
−
        }
 
  
−
        # Move by rotation on rotor sets, smallest first
+
                # If pivots defined, rotate it
−
        gBusy = TRUE
+
                if (g1pivotIdx >= 0) {
−
        background ECHO pink
 
−
        refresh
 
  
−
        # If side chain mode
+
                    # If two pivots
−
        if (gSCidx >= 0) {
+
                    if (g2pivotIdx >= 0) {
−
            dragSC()
+
                        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
 
−
        else if (not gTow) {
 
−
            gOK = TRUE
 
−
            timeout ID"tug" 20.0 "timedOut(\"Tug timed out\")"
 
−
            if ((gCrotors.size < gNrotors.size) or (gNanchorIdx < 0)) {
 
−
                if (gCrotors.size > 4) {
 
−
                    tugTrackC()
 
 
                 }
 
                 }
−
                 if (gOK and (gNrotors.size > 4)) {
+
 
−
                     tugTrackN()
+
                 # Else translate it
 +
                else {
 +
                     translate_selected_record(pt)
 
                 }
 
                 }
−
            }
 
−
            else {
 
−
                if (gNrotors.size > 4) {
 
−
                    tugTrackN()
 
−
                }
 
−
                if (gOK and (gCrotors.size > 4)) {
 
−
                    tugTrackC()
 
−
                }
 
−
            }
 
−
            timeout ID"tug" OFF
 
  
−
            # If anchor angles acute, fail
+
                # If collisions
−
            if (gOK == TRUE) {
+
                 var cNotSels = (within(kCtolerance, false, {selected})
−
                 if (gCanchorIdx >= 0) {
+
                     and not {gMovingSet})
−
                    var ic = getCwardBBidx(gCanchorIdx, gChain)
+
                if ((cNotSels) and (not alt)) {
−
                     var in = getNwardBBidx(gCanchorIdx, gChain)
+
                    gOk2 = true
−
                    if ((ic >= 0) and
+
                     for (var i = 1; i <= cNotSels.size;  i++) {
−
                        angle({atomIndex=ic}, {atomIndex=gCanchorIdx}, {atomIndex=in})
+
 
−
                        < 100.0) {
+
                        # If net collision vector same as move vector
−
                        gOK = FALSE
+
                        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 (gNanchorIdx >= 0) {
+
                            if (abs(angle(v1, {0 0 0}, pt)) < 90) {
−
                    var ic = getCwardBBidx(gNanchorIdx, gChain)
 
−
                    var in = getNwardBBidx(gNanchorIdx, gChain)
 
−
                    if ((in >= 0) and
 
−
                        angle({atomIndex=ic}, {atomIndex=gNanchorIdx}, {atomIndex=in})
 
−
                        < 100.0) {
 
−
                        gOK = FALSE
 
−
                    }
 
−
                }
 
−
            }
 
  
−
            # If too far
+
                                # If tow mode
−
            if (not gOK) {
+
                                if (gTow) {
−
                timedOut("TUG TOO FAR!")
 
−
            }
 
  
−
            # Else OK
+
                                    # Make a dynamic pivot
−
            else {
+
                                    if (g1pivotIdx < 0) {
−
 
+
                                        g1pivotIdx = cSels[j].atomIndex
−
                select ((atomno >= gNanchorNo) and (atomno <= gCanchorNo)
+
                                        g1dynamicIdx = cNotSels[i].atomIndex
−
                    and (chain = gChain))
+
                                        color {atomIndex=g1pivotIdx} lightgreen
−
                var idx = {(atomno=@{{chain=gChain}.atomno.min})
+
                                        set_distance_idx(cNotSels[i].atomIndex,
−
                    and (chain=gChain)}.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
  
−
                var ihc = 0
+
                    # If unable
−
                for (ihc = 0; ihc < 10; ihc++) {
+
                    if (not gOk2) {
−
                    handleCollisions2( idx)
+
 
−
                    if (countCollisions(({})) == 0) {
+
                        # Back off
−
                         break
+
                        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 (ihc == 10) {
 
−
                    timedOut("Unable to handle all collisions!")
 
 
                 }
 
                 }
 
             }
 
             }
−
         }
+
 
−
         select {gCargoSet}
+
            # If dynamic pivots
−
         gBusy = FALSE
+
            if (g1dynamicIdx >= 0) {
−
        background ECHO yellow
+
                var v1 = {atomIndex=g1dynamicIdx}.xyz - {atomIndex=g1pivotIdx}.xyz
−
        refresh
+
                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-SHIFT-LEFT-DRAG by tugEnableDrag
+
# Bound to ALT-LEFT-DOWN by tug_enable_drag
−
function tugDrag2MB() {
+
function tug_mark_mb() {
−
     tugDragMB(TRUE)
+
     gMouseX = _mouseX
 +
    gMouseY = _mouseY
 +
    gNewDrag = true
 
}
 
}
  
−
# Bound to ALT-LEFT-DRAG by tugEnableDrag
+
# Called by tug_cargo_mb
−
function tugDragMB(alt) {
+
function tug_enable_drag() {
−
     if (not gBusy) {
+
     gEcho = "__________TUG__________|ALT-CLICK=mark block|SHIFT-CLICK=anchors" +
−
        gBusy = TRUE
+
         "|ALT-CTRL-CLICK=pivots|ALT-SHIFT-CLICK=dest atom|ALT-DRAG=move" +
−
         var dx = (40.0 * (_mouseX - gMouseX))/_width
+
         "|ALT-SHIFT-DRAG=alt move|CLICK bond=freeze|ALT-DOUBLE-CLICK=undo" +
−
        var dy = (40.0 * (_mouseY - gMouseY))/_height
+
         "|SHIFT-DOUBLE-CLICK=exit"
−
         var q = quaternion()
+
    echo @gEcho
−
        var ptd = {@dx @dy 0}
+
 
−
         var pt = (!q)%ptd
+
    # Allow atoms to be dragged
−
        var axis = {0 0 0}
+
    bind "ALT-LEFT-DOWN" "tug_mark_mb";
−
        if (distance(pt,  {0 0 0}) > 0.004) {
+
    bind "ALT-LEFT-UP" "tug_drag_done_mb";
−
            # If sidechain mode
+
    bind "ALT-SHIFT-LEFT-DOWN" "tug_mark_mb";
−
            if (gSCidx >= 0) {
+
    bind "ALT-LEFT-DRAG" "tug_drag_mb";
−
                if ({atomIndex=gSCidx}.atomName == "O") {
+
    bind "ALT-SHIFT-LEFT-DRAG" "tug_drag_2_mb";
−
                    dir = ((abs(dx) > abs(dy))
 
−
                        ? ((dx < 0) ? 10 : -10)
 
−
                        : ((dy < 0) ? 1 : -1))
 
−
                    counterRotate(gSCidx, dir, not alt)
 
−
                }
 
−
                else {
 
−
                    gSCcheck = not alt
 
−
                    tugSideChain(pt)
 
−
                }
 
−
            }
 
  
−
            # Else
+
    unbind "SHIFT-LEFT-CLICK"
−
            else {
+
    bind "SHIFT-LEFT-CLICK" "_pickAtom";
 +
    bind "SHIFT-LEFT-CLICK" "+:tug_anchor_mb";
  
−
                # If new drag
+
    bind "ALT-CTRL-LEFT-CLICK" "_pickAtom";
−
                if (gNewDrag) {
+
    bind "ALT-CTRL-LEFT-CLICK" "+:tug_pivot_mb";
−
                    gNewDrag = FALSE
 
−
                    save state gState
 
−
                }
 
  
−
                # If destination atom defined
+
    bind "ALT-SHIFT-LEFT-CLICK" "_pickAtom";
−
                if (gDestAtomIdx >= 0) {
+
    bind "ALT-SHIFT-LEFT-CLICK" "+:tug_dest_atom_mb";
−
                    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
+
# Bound to SHIFT-LEFT-CLICK by tug_cargo_mb
−
                select {gCargoSet}
+
function tug_anchor_mb() {
 +
    if ({atomIndex=_atomPicked}.chain == gChain) {
 +
        var aPidx = get_sc_bb_idx( _atomPicked, gChain)
  
−
                # If pivots defined, rotate it
+
        var pno = {atomIndex=aPidx}.atomno
−
                if (g1pivotIdx >= 0) {
+
        if (pno > {atomIndex=gCcargoIdx}.atomno) {
−
 
+
            select {atomIndex=gCanchorIdx}
−
                    # If two pivots
+
            halo off
−
                    if (g2pivotIdx >= 0) {
+
            if (gCanchorIdx == aPidx) {
−
                        axis = {atomIndex=g2pivotIdx}
+
                gCanchorIdx = -1
−
                    }
+
                gCanchorNo = gMaxNo + 1
−
 
+
            }
−
                    # Else
+
            else {
−
                    else {
+
                gCanchorIdx = aPidx
−
                        axis = cross(pt, {0 0 0}) + {atomIndex=g1pivotIdx}.xyz
+
                gCanchorNo = {atomIndex=gCanchorIdx}.atomno
−
                    }
+
                select {atomIndex=gCanchorIdx}
−
 
+
                halo on
−
                    dir = ((abs(dx) > abs(dy))
+
            }
−
                        ? ((dx < 0) ? 2 : -2)
+
            collect_bb_rotors(false)
−
                        : ((dy < 0) ? 2 : -2))
+
        }
−
                    rotateSelectedRecord(g1pivotIdx, axis, dir)
+
        else if (pno < {atomIndex=gNcargoIdx}.atomno) {
−
 
+
            select {atomIndex=gNanchorIdx}
−
                 }
+
            halo off
−
 
+
            if (gNanchorIdx == aPidx) {
−
                 # Else translate it
+
                gNanchorIdx = -1
−
                else {
+
                gNanchorNo = gMinNo - 1
−
                    translateSelectedRecord(pt)
+
            }
−
                }
+
            else {
 +
                gNanchorIdx = aPidx
 +
                 gNanchorNo = {atomIndex=gNanchorIdx}.atomno
 +
                select {atomIndex=gNanchorIdx}
 +
                 halo on
 +
            }
 +
            collect_bb_rotors(true)
 +
        }
 +
        else {
 +
            tow_cargo_mb()
 +
        }
  
−
                # If collisions
+
        # Get moving atoms set
−
                var cNotSels = (within(kCtolerance, FALSE, {selected})
+
        gMovingSet = {((atomno < gCanchorNo) and (atomno > gNanchorNo)
−
                    and not {gMovingSet})
+
            and (chain=gChain) and thisModel)}
−
                if ((cNotSels.size > 0) and (not alt)) {
+
    }
−
                    gOk2 = TRUE
+
    select {gCargoSet}
−
                    for (var i = 1; i <= cNotSels.size;  i++) {
+
}
  
−
                        # If net collision vector same as move vector
+
# Bound to ALT-SHIFT-LEFT-CLICK by tug_cargo_mb
−
                        cSels = (within(kCtolerance, FALSE, cNotSels[i]) and {selected})
+
function tug_dest_atom_mb() {
−
                        for (var j = 1; j <= cSels.size;  j++) {
+
    var aOk = true
−
                            var v1 = cNotSels[i].xyz - cSels[j].xyz
+
    if ({atomIndex=_atomPicked}.chain == gChain) {
−
                            if (abs(angle(v1, {0 0 0}, pt)) < 90) {
 
  
−
                                # If tow mode
+
        var pno = {atomIndex=_atomPicked}.atomno
−
                                if (gTow) {
+
        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}
 +
    }
 +
}
  
−
                                    # Make a dynamic pivot
+
# Bound to CTRL-LEFT-CLICK by tug_cargo_mb
−
                                    if (g1pivotIdx < 0) {
+
function tug_pivot_mb() {
−
                                        g1pivotIdx = cSels[j].atomIndex
+
    if (g1pivotIdx == _atomPicked) {
−
                                        g1dynamicIdx = cNotSels[i].atomIndex
+
        color {atomIndex=g1pivotIdx} @gScheme
−
                                        color {atomIndex=g1pivotIdx} lightgreen
+
        if (g2pivotIdx >= 0) {
−
                                        setDistanceIdx(cNotSels[i].atomIndex,
+
            g1pivotIdx = g2pivotIdx
−
                                            cSels[j].atomIndex,
+
            g2pivotIdx = -1
−
                                            kCtolerance + kDtolerance)
+
            g2dynamicIdx = -1
−
                                    }
+
        }
−
                                    else if (g2pivotIdx < 0) {
+
        else {
−
                                        g2pivotIdx = cSels[j].atomIndex
+
            g1pivotIdx = -1
−
                                        g2dynamicIdx = cNotSels[i].atomIndex
+
            g1dynamicIdx = -1
−
                                        color {atomIndex=g2pivotIdx} lightgreen
+
        }
−
                                        setDistanceIdx(cNotSels[i].atomIndex,
+
    }
−
                                            cSels[j].atomIndex,
+
    else if (g2pivotIdx == _atomPicked) {
−
                                            kCtolerance + kDtolerance)
+
        color {atomIndex=g2pivotIdx} @gScheme
−
                                    }
+
        g2pivotIdx = -1
−
                                    else {
+
        g2dynamicIdx = -1
−
                                        gOk2 = FALSE
+
    }
−
                                    }
+
    else if (g1pivotIdx >= 0) {
−
                                }
+
        if (g2pivotIdx >= 0) {
−
                                else {
+
            color {atomIndex=g2pivotIdx} @gScheme
 +
        }
  
−
                                    # Try to resolve
+
        g2pivotIdx = _atomPicked
−
                                    select cSels[j]
+
        g2dynamicIdx = -1
−
                                    var idx = {(atomno=@{{chain=gChain}.atomno.min})
+
        color {atomIndex=g2pivotIdx} green
−
                                        and (chain=gChain)}.atomIndex
+
    }
−
                                    handleCollisions2( idx)
+
    else {
−
                                }
+
        g1pivotIdx = _atomPicked
−
                            }
+
        g1dynamicIdx = -1
−
                        } # endfor
+
        color {atomIndex=g1pivotIdx} green
−
                        if (not gOk2) {
+
    }
−
                            break
+
    select {gCargoSet}
−
                        }
+
}
−
                    } # endfor
 
  
−
                    # If unable
+
# Bound to SHIFT-LEFT-CLICK by plico_tug
−
                    if (not gOk2) {
+
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
  
−
                        # Back off
+
    # Highlight cargo cluster
−
                        background ECHO pink
+
    select {(chain=gChain) and thisModel}
−
                        delay 1
+
    gCargoSet = {selected}
−
                        if (g1pivotIdx >= 0) {
+
    gMovingSet = {selected}
−
                            rotateSelectedRecord(g1pivotIdx, axis, -a)
+
    set_colors()
−
                        }
 
−
                        else {
 
−
                            translateSelectedRecord(-pt)
 
−
                        }
 
−
                        background ECHO yellow
 
−
                    }
 
−
                }
 
−
            }
 
  
−
            # If dynamic pivots
+
    # Enable dragging
−
            if (g1dynamicIdx >= 0) {
+
    tug_enable_drag()
−
                var v1 = {atomIndex=g1dynamicIdx}.xyz - {atomIndex=g1pivotIdx}.xyz
+
    select {gCargoSet}
−
                if (abs(angle(v1, {0 0 0}, pt)) > 90) {
+
    halo off
−
                    color {atomIndex=g1pivotIdx} @gAltScheme
+
    var es = gEcho.replace("anchors","mark chain")
−
                    g1pivotIdx = -1
+
    echo @es
−
                    g1dynamicIdx = -1
+
    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 (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
+
    # If O or movable side chain atom picked
−
             gMouseY = _mouseY
+
    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
 
         }
 
         }
−
        select {gCargoSet}
 
−
        gBusy = FALSE
 
 
     }
 
     }
−
}
+
    else {
−
 
+
        if ({atomIndex=_atomPicked}.chain != gChain) {
−
# Bound to ALT-LEFT-DOWN by tugEnableDrag
+
            if (gTow) {
−
function tugMarkMB() {
+
                select {(chain=gChain) and thisModel}
−
    gMouseX = _mouseX
+
                color {selected} @gScheme
−
    gMouseY = _mouseY
+
            }
−
    gNewDrag = TRUE
+
            gChain = {atomIndex=_atomPicked}.chain
−
}
+
            select ({atomIndex=gCcargoIdx} or {atomIndex=gNcargoIdx}
−
 
+
                or {atomIndex=gCanchorIdx} or {atomIndex=gNanchorIdx})
−
# Called by tugCargoMB
+
            halo off
−
function tugEnableDrag() {
+
            gCcargoIdx = -1
−
    gEcho = "__________TUG__________|ALT-CLICK=mark block|SHIFT-CLICK=anchors" +
+
            gNcargoIdx = -1
−
         "|ALT-CTRL-CLICK=pivots|ALT-SHIFT-CLICK=dest atom|ALT-DRAG=move" +
+
            gCanchorIdx = -1
−
         "|SHIFT-ALT-DRAG=alt move|CLICK bond=freeze|DOUBLE-CLICK=exit"
+
            gNanchorIdx = -1
−
    echo @gEcho
+
        }
 +
        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)
  
−
    # Allow atoms to be dragged
+
        gSCidx = -1
−
    bind "ALT-LEFT-DOWN" "tugMarkMB";
+
        draw gSCcircle DELETE
−
    bind "ALT-LEFT-UP" "tugDragDoneMB";
 
−
    bind "ALT-SHIFT-LEFT-DOWN" "tugMarkMB";
 
−
    bind "ALT-SHIFT-LEFT-UP" "tugDragDoneMB";
 
−
    bind "ALT-LEFT-DRAG" "tugDragMB";
 
−
    bind "ALT-SHIFT-LEFT-DRAG" "tugDrag2MB";
 
  
−
    unbind "SHIFT-LEFT-CLICK"
+
        # If existing cWard cargo picked
−
    bind "SHIFT-LEFT-CLICK" "_pickAtom";
+
        if (gCcargoIdx == aPidx) {
−
    bind "SHIFT-LEFT-CLICK" "+:tugAnchorMB";
 
  
−
    bind "ALT-CTRL-LEFT-CLICK" "_pickAtom";
+
            # Clear the highlight
−
    bind "ALT-CTRL-LEFT-CLICK" "+:tugPivotMB";
+
            select {atomIndex=gCcargoIdx}
 +
            halo off
  
−
    bind "ALT-SHIFT-LEFT-CLICK" "_pickAtom";
+
            # If nWard cargo exists, mark it as the cWard cargo
−
    bind "ALT-SHIFT-LEFT-CLICK" "+:tugDestAtomMB";
+
            if (gNcargoIdx != gCcargoIdx) {
−
}
+
                gCcargoIdx = get_cp_idx(gNcargoIdx)
−
 
+
                gCcargoNo = {atomIndex=gCcargoIdx}.atomno
−
# Bound to SHIFT-LEFT-CLICK by tugCargoMB
 
−
function tugAnchorMB() {
 
−
    if ({atomIndex=_atomPicked}.chain == gChain) {
 
−
        var aPidx = getScBBidx( _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 {
 
             else {
−
                 gCanchorIdx = aPidx
+
                 gCcargoIdx = -1
−
                 gCanchorNo = {atomIndex=gCanchorIdx}.atomno
+
                 gNcargoIdx = -1
−
                select {atomIndex=gCanchorIdx}
 
−
                halo on
 
 
             }
 
             }
−
            collectBBrotors(FALSE)
 
 
         }
 
         }
−
         else if (pno < {atomIndex=gNcargoIdx}.atomno) {
+
         else if (gNcargoIdx == aPidx) {
−
             select {atomIndex=gNanchorIdx}
+
             select {atomIndex=gNcargoIdx}
 
             halo off
 
             halo off
−
             if (gNanchorIdx == aPidx) {
+
             gNcargoIdx = get_nm_idx(gCcargoIdx)
−
                gNanchorIdx = -1
+
             gNcargoNo = {atomIndex=gNcargoIdx}.atomno
−
                gNanchorNo = gMinNo - 1
 
−
            }
 
−
             else {
 
−
                gNanchorIdx = aPidx
 
−
                gNanchorNo = {atomIndex=gNanchorIdx}.atomno
 
−
                select {atomIndex=gNanchorIdx}
 
−
                halo on
 
−
            }
 
−
            collectBBrotors(TRUE)
 
−
        }
 
−
        else {
 
−
            towCargoMB()
 
 
         }
 
         }
 +
        else if (gCcargoIdx >= 0) {
  
−
        # Get moving atoms set
+
            var no = {atomIndex=aPidx}.atomno
−
        gMovingSet = {((atomno < gCanchorNo) and (atomno > gNanchorNo)
 
−
            and (chain=gChain))}
 
−
    }
 
−
    select {gCargoSet}
 
−
}
 
  
−
# Bound to ALT-SHIFT-LEFT-CLICK by tugCargoMB
+
            # If pick is nWard of it
−
function tugDestAtomMB() {
+
            if (no < {atomIndex=gCcargoIdx}.atomno) {
−
    var aOk = TRUE
 
−
    if ({atomIndex=_atomPicked}.chain == gChain) {
 
  
−
        var pno = {atomIndex=_atomPicked}.atomno
+
                # If exists, clear its highlight
−
        if ((pno <= {atomIndex=gCcargoIdx}.atomno) and (pno >= {atomIndex=gNcargoIdx}.atomno)) {
+
                if (gNcargoIdx != gCcargoIdx) {
−
            aOk = FALSE
+
                    select {atomIndex=gNcargoIdx}
−
        }
+
                    halo off
−
    }
+
                }
−
    if (aOk) {
+
 
−
        select {atomIndex=gDestAtomIdx}
+
                # Set new nWard cargo and highlight it
−
        star off
+
                gNcargoIdx = get_nm_idx(aPidx)
−
        if (gDestAtomIdx == _atomPicked) {
+
                gNcargoNo = {atomIndex=gNcargoIdx}.atomno
−
             gDestAtomIdx = -1
+
             }
−
        }
+
 
−
        else {
+
             # Else cWard
−
            gDestAtomIdx = _atomPicked
+
             else {
−
             select {atomIndex=gDestAtomIdx}
 
−
             star on
 
−
        }
 
−
        select {gCargoSet}
 
−
    }
 
−
}
 
  
−
# Bound to CTRL-LEFT-CLICK by tugCargoMB
+
                # Clear its old highlight
−
function tugPivotMB() {
+
                select {atomIndex=gCcargoIdx}
−
    if (g1pivotIdx == _atomPicked) {
+
                if (gNcargoIdx != gCcargoIdx) {
−
        color {atomIndex=g1pivotIdx} @gScheme
+
                    halo off
−
        if (g2pivotIdx >= 0) {
+
                }
−
            g1pivotIdx = g2pivotIdx
+
 
−
            g2pivotIdx = -1
+
                # Set new cWard cargo and highlight
−
             g2dynamicIdx = -1
+
                gCcargoIdx = get_cp_idx(aPidx)
 +
                gCcargoNo = {atomIndex=gCcargoIdx}.atomno
 +
             }
 
         }
 
         }
 +
 +
        # Else no cWard cargo
 
         else {
 
         else {
−
             g1pivotIdx = -1
+
 
−
             g1dynamicIdx = -1
+
            # Set new cWard cargo and highlight
 +
             gCcargoIdx = get_cp_idx(aPidx)
 +
             gCcargoNo = {atomIndex=gCcargoIdx}.atomno
 +
            gNcargoIdx = get_nm_idx(gCcargoIdx)
 +
            gNcargoNo = {atomIndex=gNcargoIdx}.atomno
 
         }
 
         }
−
    }
+
 
−
    else if (g2pivotIdx == _atomPicked) {
+
        # If any anchor now inside cargo cluster, kill it
−
        color {atomIndex=g2pivotIdx} @gScheme
+
        if ({atomIndex=gCanchorIdx}.atomno <= {atomIndex=gCcargoIdx}.atomno) {
−
        g2pivotIdx = -1
+
            gCanchorIdx = -1
−
        g2dynamicIdx = -1
+
            gCanchorNo = gMaxNo + 1
−
    }
+
        }
−
    else if (g1pivotIdx >= 0) {
+
        if ({atomIndex=gNanchorIdx}.atomno >= {atomIndex=gNcargoIdx}.atomno) {
−
        if (g2pivotIdx >= 0) {
+
            gNanchorIdx = -1
−
             color {atomIndex=g2pivotIdx} @gScheme
+
             gNanchorNo = gMinNo - 1
 
         }
 
         }
  
−
         g2pivotIdx = _atomPicked
+
         # Highlight cargo cluster
−
         g2dynamicIdx = -1
+
        select_nward_idx(gCcargoIdx, gNcargoIdx)
−
         color {atomIndex=g2pivotIdx} green
+
        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 {
 
     else {
−
         g1pivotIdx = _atomPicked
+
         tug_enable_drag()
−
        g1dynamicIdx = -1
 
−
        color {atomIndex=g1pivotIdx} green
 
 
     }
 
     }
 +
 
     select {gCargoSet}
 
     select {gCargoSet}
 
}
 
}
  
−
# Bound to SHIFT-LEFT-CLICK by plicoTug
+
function tug_undo_mb() {
−
function towCargoMB() {
+
     if (prompt("Undo", "Yes|No", true) == "Yes") {
−
     gTow = TRUE
+
        restore state gState
−
    gChain = {atomIndex=_atomPicked}.chain
+
     }
−
     gMinNo = {chain=gChain}.atomno.min
+
}
−
    gMaxNo = {chain=gChain}.atomno.max
 
−
    gCcargoIdx = -1
 
−
    gNcargoIdx = -1
 
−
    gCanchorIdx = -1
 
−
    gCanchorNo = gMaxNo + 1
 
−
    gNanchorIdx = -1
 
−
    gNanchorNo = gMinNo - 1
 
  
−
    # Highlight cargo cluster
+
# Top level of Tug
−
    select {chain=gChain}
+
function plico_tug() {
−
    gCargoSet = {selected}
 
−
    gMovingSet = {selected}
 
−
    setColors()
 
  
−
     # Enable dragging
+
     # Load common functions if not already
−
     tugEnableDrag()
+
     if (kCommon < 7) {
−
    select {gCargoSet}
+
        script $SCRIPT_PATH$plicoCommon.spt
−
     halo off
+
        if (kCommon < 7) {
−
     var es = gEcho.replace("anchors","mark chain")
+
            prompt ("A newer version of plicoCommon.SPT is required")
−
     echo @es
+
            quit
−
     unbind "SHIFT-LEFT-CLICK"
+
        }
 +
     }
 +
 
 +
     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" "_pickAtom";
−
     bind "SHIFT-LEFT-CLICK" "+:towCargoMB";
+
     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 ALT-LEFT-CLICK by plicoTug or called by plicotoab.toabCargoMB
+
# Bound to DOUBLE by plico_tug
−
function tugCargoMB() {
+
function tug_exit() {
−
 
+
     if (plico_exit()) {
−
    # If O or movable side chain atom picked
+
         set bondPicking gBondPicking
−
     if (({atomIndex=_atomPicked}.atomName = "O")
+
        set PickCallback NONE
−
        or (isMovableSideChain( _atomPicked))) {
+
         select all
−
         if (gSCidx >= 0) {
+
         color bonds none
−
            draw gSCcircle DELETE
+
       
−
         }
+
         reset kTug
−
         if (gSCidx == _atomPicked) {
+
         reset gCanchorIdx 
−
            gSCidx = -1
+
        reset gCanchorNo 
−
         }
+
        reset gPlico     
−
         else {
+
        reset gNanchorIdx 
−
            gSCidx = _atomPicked
+
         reset gNanchorNo 
−
            gSCpt = {atomIndex=gSCidx}.xyz
+
        reset gCcargoIdx 
−
            draw gSCcircle CIRCLE {atomIndex=gSCidx} MESH NOFILL
+
         reset gNcargoIdx  
−
         }
+
        reset gCcargoNo   
−
    }
+
        reset gNcargoNo   
−
    else {
+
        reset gDestAtomIdx
−
         if ({atomIndex=_atomPicked}.chain != gChain) {
+
        reset g1pivotIdx 
−
            if (gTow) {
+
        reset g2pivotIdx 
−
                select {chain=gChain}
+
        reset gSelSaves   
−
                color {selected} @gScheme
+
         reset gCrotors   
−
            }
+
         reset gNrotors   
−
            gChain = {atomIndex=_atomPicked}.chain
+
         reset gOkCollide 
−
            select ({atomIndex=gCcargoIdx} or {atomIndex=gNcargoIdx}
+
         reset gChain      
−
                or {atomIndex=gCanchorIdx} or {atomIndex=gNanchorIdx})
+
         reset gMinNo      
−
            halo off
+
         reset gMaxNo      
−
            gCcargoIdx = -1
+
         reset gCargoSet   
−
            gNcargoIdx = -1
+
         reset gMovingSet 
−
            gCanchorIdx = -1
+
         reset gSCidx      
−
            gNanchorIdx = -1
+
         reset gSCcircle  
−
         }
+
        reset gSCpt       
−
         gTow = FALSE
+
         reset gTargetPt   
−
         gMinNo = {chain=gChain}.atomno.min
+
         reset gNewDrag   
−
         gMaxNo = {chain=gChain}.atomno.max
+
        reset gTow       
−
         if (gNanchorIdx < 0) {
+
        reset g1dynamicIdx
−
            gNanchorNo = gMinNo - 1
+
        reset g2dynamicIdx
−
         }
+
        reset gSCcheck   
−
        if (gCanchorIdx < 0) {
+
        reset gBondPicking
−
            gCanchorNo = gMaxNo + 1
+
        reset gFreeze     
−
         }
+
        reset gToab       
−
         var aPidx = getScBBidx( _atomPicked, gChain)
+
        reset function "get_cp_idx"
−
 
+
        reset function "get_cm_no"
−
         gSCidx = -1
+
        reset function "get_nm_idx"
−
         draw gSCcircle DELETE
+
        reset function "get_np_no"
−
 
+
        reset function "get_cb_idx"
−
         # If existing cWard cargo picked
+
        reset function "get_o_idx"
−
         if (gCcargoIdx == aPidx) {
+
        reset function "get_nward_bb_idx"
−
 
+
         reset function "get_cward_bb_idx"
−
            # Clear the highlight
+
         reset function "get_sc_set"
−
            select {atomIndex=gCcargoIdx}
+
        reset function "get_sc_bb_idx"
−
            halo off
+
        reset function "is_bb_idx"
−
 
+
        reset function "is_sc_idx"
−
            # If nWard cargo exists, mark it as the cWard cargo
+
        reset function "select_add_sc"
−
            if (gNcargoIdx != gCcargoIdx) {
+
         reset function "handle_collisions"
−
                gCcargoIdx = getCpIdx(gNcargoIdx)
+
         reset function "tug_track_idx"
−
                gCcargoNo = {atomIndex=gCcargoIdx}.atomno
+
        reset function "do_counter_rotate"
−
            }
+
        reset function "counter_rotate"
−
            else {
+
        reset function "counter_rotate_2"
−
                gCcargoIdx = -1
+
        reset function "repair_proline"
−
                gNcargoIdx = -1
+
        reset function "repair_sc"
−
            }
+
        reset function "tug_track_c"
−
         }
+
        reset function "tug_track_n"
−
         else if (gNcargoIdx == aPidx) {
+
        reset function "translate_selected_record"
−
            select {atomIndex=gNcargoIdx}
+
        reset function "rotate_selected_record"
−
            halo off
+
        reset function "collect_sc_rotors"
−
            gNcargoIdx = getNmIdx(gCcargoIdx)
+
        reset function "drag_sc"
−
            gNcargoNo = {atomIndex=gNcargoIdx}.atomno
+
        reset function "fix_sc_collision_2"
−
         }
+
        reset function "is_moveable_sc"
−
         else if (gCcargoIdx >= 0) {
+
        reset function "is_rotor_avail"
−
 
+
        reset function "xcollect_bb_rotors"
−
            var no = {atomIndex=aPidx}.atomno
+
        reset function "collect_bb_rotors"
−
 
+
         reset function "collect_rotors"
−
            # If pick is nWard of it
+
         reset function "tug_sc"
−
            if (no < {atomIndex=gCcargoIdx}.atomno) {
+
         reset function "set_colors"
−
 
+
         reset function "clear_atom_idxs"
−
                # If exists, clear its highlight
+
         reset function "timed_out"
−
                if (gNcargoIdx != gCcargoIdx) {
+
         reset function "record_drag"
−
                    select {atomIndex=gNcargoIdx}
+
         reset function "tug_pick_cb"
−
                    halo off
+
         reset function "tug_drag_done_mb"
−
                }
+
         reset function "tug_drag_2_mb"
−
 
+
         reset function "tug_drag_mb"
−
                # Set new nWard cargo and highlight it
+
         reset function "tug_mark_mb"
−
                gNcargoIdx = getNmIdx(aPidx)
+
         reset function "tug_anchor_mb"
−
                gNcargoNo = {atomIndex=gNcargoIdx}.atomno
+
         reset function "tug_enable_drag"
−
            }
+
         reset function "tug_dest_atom_mb"
−
 
+
         reset function "tug_pivot_mb"
−
            # Else cWard
+
         reset function "tow_cargo_mb"
−
            else {
+
         reset function "tug_cargo_mb"
−
 
+
         reset function "tug_undo_mb"
−
                # Clear its old highlight
+
         reset function "plico_tug"
−
                select {atomIndex=gCcargoIdx}
 
−
                if (gNcargoIdx != gCcargoIdx) {
 
−
                    halo off
 
−
                }
 
−
 
 
−
                # Set new cWard cargo and highlight
 
−
                gCcargoIdx = getCpIdx(aPidx)
 
−
                gCcargoNo = {atomIndex=gCcargoIdx}.atomno
 
−
            }
 
−
         }
 
−
 
 
−
         # Else no cWard cargo
 
−
         else {
 
−
 
 
−
            # Set new cWard cargo and highlight
 
−
            gCcargoIdx = getCpIdx(aPidx)
 
−
            gCcargoNo = {atomIndex=gCcargoIdx}.atomno
 
−
            gNcargoIdx = getNmIdx(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
 
−
         }
 
−
 
 
−
         # 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
 
−
         selectNwardIdx(gCcargoIdx, gNcargoIdx)
 
−
         gCargoSet = {selected}
 
−
         setColors()
 
−
 
 
−
         # Collect the rotor sets
 
−
         collectRotors()
 
−
 
 
−
         # Get moving atoms set
 
−
         gMovingSet = {((atomno < gCanchorNo) and (atomno > gNanchorNo)
 
−
            and (chain=gChain))}
 
−
    }
 
−
 
 
−
    # Enable dragging
 
−
    if (gToab) {
 
−
         toabEnableDrag()
 
−
    }
 
−
    else {
 
−
         tugEnableDrag()
 
−
    }
 
−
   
 
−
    select {gCargoSet}
 
−
}
 
  
−
# Top level of Tug
 
−
function plicoTug() {
 
  
−
    # Load common functions if not already
 
−
    if (kCommon < 1) {
 
−
        script $SCRIPT_PATH$plicoCommon.spt
 
−
        if (kCommon < 1) {
 
−
            prompt ("A newer version of plicoCommon.SPT is required")
 
−
            quit
 
−
        }
 
 
     }
 
     }
−
   
 
−
    gPlico = "TUG"
 
−
    plicoPrelim()
 
−
    gBondPicking = bondPicking
 
−
    set bondPicking TRUE
 
−
    set PickCallback "jmolscript:tugPickCB"
 
−
           
 
−
    gEcho = ("_________TUG_________|ALT-CLICK=mark block|SHIFT-CLICK=mark chain" +
 
−
        "|CLICK bond=freeze|DOUBLE-CLICK=exit")
 
−
    echo @gEcho
 
−
    gCrotors = array()
 
−
    gNrotors = array()
 
−
    clearAtomIdxs()
 
−
 
−
    bind "ALT-LEFT-CLICK" "_pickAtom";
 
−
    bind "ALT-LEFT-CLICK" "+:tugCargoMB";
 
−
    bind "SHIFT-LEFT-CLICK" "_pickAtom";
 
−
    bind "SHIFT-LEFT-CLICK" "+:towCargoMB";
 
−
    bind "DOUBLE" "tugExit";
 
−
}
 
−
 
−
# Bound to DOUBLE by plicoTug
 
−
function tugExit() {
 
−
    set bondPicking gBondPicking
 
−
    set PickCallback NONE
 
−
    plicoExit()
 
 
}
 
}
  
−
# End of TUG.SPT</pre>
+
# End of TUG.SPT
 +
</pre>

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

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