User:Remig/plico/modify

Modify allows the user to make common amino acid and nucleotide modification by mouse actions. Hover text above each atom gives the available options including methylation on nucleosides, single-bond oxygens, and nitrogens, hydroxylation of PRO, formylation of MET, ribose/deoxyribose interconversion, phophorylation of SER, THR, TYR and HIS, and conversions to pseudouridine, dihyrouridine, inosine, and xanthine.

Some features unrelated to modification have been placed here as well to serve other Plico functions. Water molecules may be added and moved around to serve as pivot points for Tug when no other atoms are where the pivot point is wanted. Also the Jmol parameters allowMoveAtoms and allowRotateSelected are set true while modify is active to allow free rotation and translation of selected atoms.

Modify is a member of the Plico suite of protein folding tools described here. It may be installed and accessed as a macro with the file:

Title=PLICO Modify
Script=script <path to your scripts folder>/modify.spt;plicoModify

saved as plicoModify.macro in your .jmol/macros folder as described in Macro.

Copy and paste the following to a text editor and save to your scripts folder as modify.spt:

#   modify - Jmol script by Ron Mignery
#   v1.1 beta    2/22/2014 for Jmol 14
#
# See atom hover text for options:
# methyl on nucleosides, single-bond oxygens, and terminal N
# OH on ribose and proline, PO3 on SER, THR, TYR and HIS (2)
# pseudouridine and dihyrouridine, inosine, xanthine
# HOH singlet anywhere for phantom pivot and target atoms
# Enable jmol move for duration

var kCtolerance = 1.85
var gAllowMoveAtoms = allowMoveAtoms
var gAllowRotateSelected = allowRotateSelected
var gSelsave = ({})
var gScheme = defaultColorScheme
var gAltScheme = ((gScheme == "Jmol") ? "Rasmol" : "Jmol")
var gIsPlanar = FALSE

# Return L tetrahedron point if i1<i2<i3, else R point
function getTet(i1, i2, i3, dist) {
    var v1 = {atomIndex=i3}.xyz - {atomIndex=i2}.xyz
    var v2 = {atomIndex=i1}.xyz - {atomIndex=i2}.xyz
    var axis = cross(v1, v2)
    var pma = ({atomIndex=i1}.xyz + {atomIndex=i3}.xyz)/2
    var pmo = {atomIndex=i2}.xyz + {atomIndex=i2}.xyz - pma
    var pt = pmo + (axis/axis)

    var v = pt - {atomIndex=i2}.xyz
    var cdist = distance(pt, {atomIndex=i2})
    var factor = (dist/cdist)
    var lpt = v * factor

    return lpt + {atomIndex=i2}.xyz
}

# return vector parallel to previous bond
function getTet1(pIdx, idx) {
    var cset = connected({atomIndex=pIdx}) and not {atomIndex=idx}
    return {atomIndex=idx}.xyz + {atomIndex=pIdx}.xyz - cset[1].xyz
}

function getTrigonal(i1, i2, i3, dist) {
    var v1 = {atomIndex=i1}.xyz - {atomIndex=i2}.xyz
    var v2 = {atomIndex=i3}.xyz - {atomIndex=i2}.xyz
    var pt = {atomIndex=i2}.xyz - (v1 + v2)

    var v = pt - {atomIndex=i2}.xyz
    var cdist = distance(pt, {atomIndex=i2})
    var factor = (dist/cdist)
    var lpt = (v * factor)

    return lpt + {atomIndex=i2}.xyz
}

function addToIdx(idx, aElement, greek, addOs) {
    var iGroup = {atomIndex=idx}.group
    var iResno = {atomIndex=idx}.resno
    var iChain = {atomIndex=idx}.chain
    var iAtomName = {atomIndex=idx}.atomName
    var iAtomno = {atomIndex=idx}.atomno
    var aAtomno = {chain=iChain}.atomno.max + 1
    var cset = connected({atomIndex=idx})
    var pt = {0 0 0}
    if  ((iGroup = "HIS") or ((({atomIndex=idx} and {amino}).size == 0) 
        and (iAtomName[1][2] != "OP") and (iAtomName[3] != "\'"))) {
        pt = getTrigonal(cSet[1].atomIndex, idx, cSet[2].atomIndex, 1.5) 
    }
    else {
        if ((cSet.size == 2) and not greek.find("\'")) {
            pt = getTet(cSet[1].atomIndex, idx, cSet[2].atomIndex, 1.5) 
        }
        else if (cSet.size > 2) {
            pt = getTet(cSet[2].atomIndex, idx, cSet[1].atomIndex, 1.5) 
        }
        else {
            pt = getTet1(cSet[1].atomIndex, idx) 
        }
    }
    if (greek.size < 2) {
        greek += iAtomName[2]
    }
    var ls = "data \"append addto\"\n"
    ls += format("ATOM  %5d  %-4s%3s ", aAtomno, aElement + greek, iGroup)
    ls += format("%s%4d    %8.3f", iChain, iResno, pt.x)          
    ls += format("%8.3f%8.3f\n", pt.y, pt.z)
    ls += "end \"append addto\""
    script inline @{ls}
        
    var aIdx = {(atomno=aAtomno) and (chain=iChain)}.atomIndex
    connect {atomIndex=idx} {atomIndex=aIdx}

    if (addOs > 0) {    
        for (var i = 1; i <= addOs; i++) {
            aAtomno++
            var ccSet = connected({atomIndex=aIdx})
            if (addOs == 1) {
                pt = ({atomIndex=aIdx}.xyz +
                    ({atomIndex=aIdx}.xyz - {atomIndex=idx}.xyz))
            }
            else if (addOs == 2) {
                pt = getTrigonal(ccSet[1].atomIndex, aIdx, ccSet[2].atomIndex, 1.5) 
            }
            else {
                if (ccSet.size == 2) {
                    pt = getTet(ccSet[1].atomIndex, aIdx, ccSet[2].atomIndex, 1.5) 
                }
                else if (ccSet.size == 3) {
                    pt = getTet(ccSet[2].atomIndex, aIdx, ccSet[1].atomIndex, 1.5) 
                }
                else {
                    pt = getTet1(ccSet[1].atomIndex, aIdx) 
                }
            }
            ls = "data \"append addto\"\n"
            ls += format("ATOM  %5d  O%s%d ", aAtomno,
                {atomIndex=aIdx}.AtomName[1], i)
            ls += format("%3s %s%4d    ", iGroup, iChain, iResno)          
            ls += format("%8.3f%8.3f%8.3f\n",  pt.x, pt.y, pt.z)
            ls += "end \"append addto\""
            script inline @{ls}
            oIdx = {(atomno=aAtomno) and (chain=iChain)}.atomIndex
            connect {atomIndex=aIdx} {atomIndex=oIdx}
        }
    }
    setHoverLabels()
}

function removeFromIdx(idx) {
    var cSet = connected({atomIndex=idx})
    if ({atomIndex=idx}.atomName[2] != "M") {
        for (var i = 1; i <= cSet.size; i++) {
            if ((cSet[i].atomName[2] == "P") or (cSet[i].atomName[2] == "O")) {
                delete @{cSet[i]}
            }
        }
    }
}

function toXidx(idx, newElement, newGroup) {
    var cSet = {resno=@{{atomIndex=idx}.resno}}
    var ls = "data \"append toX\"\n"
    for (var i = 1; i <= cSet.size; i++) {
        var iName = cSet[i].atomName
        if (idx == cSet[i].atomIndex) {
            iName[1] = newElement
        }
        ls += format("ATOM  %5d  %-3s ", cSet[i].atomno, iName)
        ls += format("%3s %s%4d    ", newGroup,
            {atomIndex=idx}.chain, cSet[i].resno)          
        ls += format("%8.3f%8.3f%8.3f\n",  cSet[i].x, cSet[i].y, cSet[i].z)
    }
    ls += "end \"append toX\""
    delete cSet
    script inline @{ls}
    connect
}

function toPUidx(idx, undoIt) {
    var iResno = {atomIndex=idx}.resno
    var a1idx = {(resno=iResno) and (atomName="O2")}.atomIndex    
    var a2idx = {(resno=iResno) and (atomName="O4")}.atomIndex
    var xyz = {0 0 0} + {atomIndex=a1idx}.xyz
    {atomIndex=a1idx}.xyz = {0 0 0} + {atomIndex=a2idx}.xyz    
    {atomIndex=a2idx}.xyz = xyz
    
    a1idx = {(resno=iResno) and (atomName="C2")}.atomIndex
    a2idx = {(resno=iResno) and (atomName="C4")}.atomIndex
    xyz = {0 0 0} + {atomIndex=a1idx}.xyz
    {atomIndex=a1idx}.xyz = {0 0 0} + {atomIndex=a2idx}.xyz    
    {atomIndex=a2idx}.xyz = xyz
    
    a1idx = {(resno=iResno) and (atomName="N1")}.atomIndex
    a2idx = {(resno=iResno) and (atomName="C5")}.atomIndex
    xyz = {0 0 0} + {atomIndex=a1idx}.xyz
    {atomIndex=a1idx}.xyz = {0 0 0} + {atomIndex=a2idx}.xyz    
    {atomIndex=a2idx}.xyz = xyz
    
    var a3idx = {(resno=iResno) and (atomName="c1\'")}.atomIndex
    connect (atomIndex=a3idx) (atomindex=a1idx) DELETE
    connect (atomIndex=a3idx) (atomindex=a2idx)
    
    if (undoit) {
        toXidx(idx, "C", "U")
    }
    else {
        toXidx(idx, "N", "PU")
    }
}

function toDidx(idx) {
    delay
    gIsPlanar = FALSE
    var iResno = {atomIndex=idx}.resno
    var iChain = {atomIndex=idx}.chain
    var rSet = {(resno=iResno) and (chain=iChain)}
    var n1 = {rSet and (atomName="N1")}
    var c2 = {rSet and (atomName="C2")}   
    var o2 = {rSet and (atomName="O2")}   
    var n3 = {rSet and (atomName="N3")}
    var c4 = {rSet and (atomName="C4")}   
    var o4 = {rSet and (atomName="O4")}   
    var c5 = {rSet and (atomName="C5")}
    var c6 = {rSet and (atomName="C6")}

    var a1 = angle(n1, c6, c5, c4)\10
    var a2 = angle(c6, c5, c4, n3)\10
    
    # N1-C6-C5-C4 = 0.5     C6-C5-C4-N3 = 0.8
    if ((a1 == 0) or (a1 == -1)) {
        # Planar to Chair 1    
        axis = (c2.xyz - c6.xyz + n1.xyz)
        select c2 or o2 or n3 or c4 or o4 or c5 or c6
        rotateSelected @n1 @axis 40
        select o2 or n3 or c4 or o4 or c5
        rotateSelected @c2 @c6 40
        select c4 or o4
        rotateSelected @c5 @n3 40
    }
    
    # N1-C6-C5-C4 = -41.0     C6-C5-C4-N3 = -46.0
    else if ((a1 == -5) and ((a2 == 5) or (a2 == 4))) {
        # Chair 1 to boat 1 twist 1 `
        select c4 or o4
        rotateSelected @c5 @n3 -80
        select o2 or n3 or c4 or o4 or c5
        rotateSelected @n1 @c4 25
    }
    
    # N1-C6-C5-C4 = 41.6     C6-C5-C4-N3 = 23.3
    else if (((a1 == 3) or (a1 == 4)) and (a2 == -7)) {
        # Boat 1 twist 1 to boat 1 twist 2
        rotateSelected @n1 @c4 -50
    }
    
    # N1-C6-C5-C4 = -40.2     C6-C5-C4-N3 = 70.0
    else if (((a1 == -4) or (a1 == -5)) and ((a2 == -3) or (a2 == -2))) {
        # Boat1 twist 2 to chair 2    
        rotateSelected @n1 @c4 25
        axis = (c2.xyz - c6.xyz + n1.xyz)
        select c2 or o2 or n3 or c4 or o4 or c5 or c6
        rotateSelected @n1 @axis -80
        select o2 or n3 or c4 or o4 or c5
        rotateSelected @c2 @c6 -80
    }
    
    # N1-C6-C5-C4 = 41.8     C6-C5-C4-N3 = -44.10
    else if ((a1 == 4) and (a2 == -5)) {
        # Chair 2 to boat 2 twist 1` `
        select c4 or o4
        rotateSelected @c5 @n3 80
        select o2 or n3 or c4 or o4 or c5
        rotateSelected @n1 @c4 25
    }
    
    # N1-C6-C5-C4 = 41.2     C6-C5-C4-N3 = -68.5
    else if ((a1 == 4) and ((a2 == 1) or (a2 == 2))) {
        # Boat 2 twist 1 to boat 2 twist 2
        rotateSelected @n1 @c4 -50
    }
    
    # N1-C6-C5-C4 = -41.3     C6-C5-C4-N3 = 64.5
    else if ((a1 == -5) and (a2 == 6)) {
        # Boat 2 twist 2 to planar
        rotateSelected @n1 @c4 25
        select c4 or o4
        rotateSelected @c5 @n3 -40
        axis = (c2.xyz - c6.xyz + n1.xyz)
        select c2 or o2 or n3 or c4 or o4 or c5 or c6
#quit        
        rotateSelected @n1 @axis 40
        select o2 or n3 or c4 or o4 or c5
        rotateSelected @c2 @c6 40
        gIsPlanar = TRUE
    }
    
    else {
        print format("a1=%d a2=%d", a1, a2)
    }
    
}

function setHoverLabels() {
    select all
    set hoverLabel "%U"
    
    select ({(atomName="?O?")} or {(atomName="?P?") and {amino}})
    set hoverLabel "%U|1:  -X"
    
    select (oxygen or sulfur) and not *.O and (bondCount = 1)
    select {selected} or (nitrogen and (bondCount < 3))
    set hoverLabel "%U|1:  -CH3"
    select (not {amino} and not oxygen and (bondCount < 3))
    set hoverLabel "%U|1:  -CH3"
    
    select ({(atomName="?M?")} or {group="HOH"})
    set hoverLabel "%U|1:  -X"
    
    # MET N fMET
    select (MET.N and (bondCount == 1))
    set hoverLabel "%U|1:  -CH3|2: -CO"
    select (MET.N and (bondCount == 2))
    set hoverLabel "%U|1:  -CH3|2: -X"
        
    # ASP OD1 OD2 P
    select ASP.OD1 or ASP.OD2 or HIS.ND1 or SER.OG or THR.OG1 OR TYR.OH
    set hoverLabel "%U|1:  -CH3|2:  -PO3"
    
    # PRO CG HYP
    select PRO.CG
    set hoverLabel "%U|1: -CH3|2:  -OH"
    
    # A N6 I
    select [A].N6 or [I].O6
    set hoverLabel "%U|1:  -CH3|2: A <--> I"
    
    # G N2 X
    select [G].N2 or [X].O2
    set hoverLabel "%U|1:  -CH3|2: G <--> X"
    
    # U N1 PU
    select [U].N1 or [PU].C5
    set hoverLabel "%U|1:  -CH3|2: U <--> PU"
    
    # U C5-6 HU
    select [U].C6
    set hoverLabel "%U|1:  -CH3|2: U --> D"
    
    # U C5-6 HU
    select [D].C6
    set hoverLabel "%U|1:  ->Conformers|2: D --> U"
    
    # U C5 M T
    select [U].C5 OR [T].C5
    set hoverLabel "%U|1:  -CH3|2: U <--> T"
    
    # *.?2' -X
    select ??.?2'
    set hoverLabel "%U|1:  -CH3|2: X <--> DX"
    refresh
 }

function addWaterMB() {
    var idx = _atomPicked
    var iChain = {atomIndex=idx}.chain
    var pt = {0 0 0}
    var cSet = connected({atomIndex=idx})
    if (cSet.size == 2) {
        pt = getTet(cSet[1].atomIndex, idx, cSet[2].atomIndex, 2.3) 
    }
    else if (cSet.size == 3) {
        pt = getTet(cSet[2].atomIndex, idx, cSet[1].atomIndex, 2.3) 
    }
    else {
        var v = {atomIndex=idx}.xyz - cSet[1].xyz
        pt = {atomIndex=idx}.xyz + v + v
    }
    if (within(kCtolerance, FALSE, pt).size == 0) {
        var ls = "data \"append addto\"\n"
        ls += format("ATOM  %5d  O   HOH %s%4d    ",
             {*}.atomno.max + 1, iChain, {*}.resno.max + 1)          
        ls += format("%8.3f%8.3f%8.3f\n", pt.x, pt.y, pt.z)
        ls += "end \"append addto\""
        script inline @{ls}
        setHoverLabels()
    }
}

function modify1MB() {
    var idx = _atomPicked
    var isAmino = ({(atomIndex=idx) and {amino}}.size > 0)
    var iName = {atomIndex=idx}.atomName
    var iGroup = {atomIndex=idx}.group
    
    if (iGroup == "HOH") {
        delete {atomIndex=idx}
    }
    
    else if (iGroup == "D") {
        toDidx(idx)
        if(gIsPlanar) {
            toDidx(idx)
        }
    }
    
    else if ((iName[2]="M") or (iName[2]="O")
        or (isAmino and ((iName[1]="P") or (iName[2]=="P")))) {
        removeFromIdx(idx)
        delete {atomIndex=idx}
    }
    
    else {
        if ({atomIndex=idx}.element="P") {
            if (isAmino) {
                removeFromIdx(idx)
            }
        }
        else if (({atomIndex=idx}.element="O")
            and ({atomIndex=idx}.atomName!="O")
            and ({atomIndex=idx}.bondCount=1)) {
            addToIdx(idx, "C", "M", 0)
        }
        else if (({atomIndex=idx}.element!="O")
            and ({atomIndex=idx}.bondCount < 3)) {
            addToIdx(idx, "C", "M", 0)
        }
        else if (isAmino) {
            removeFromIdx(idx)
        }
    }
}

function modify2MB() {
    var idx = _atomPicked
    var iGroup = {atomIndex=idx}.group
    var iName = {atomIndex=idx}.atomName
    var iResno = {atomIndex=idx}.resno
    var iChain = {atomIndex=idx}.chain
    
    # MET.N fMET
    if ((iGroup="MET") and (iName="N")) {
        if ({atomIndex=idx}.bondCount == 1) {
            addToIdx(idx, "C", "F", 1)
        }
        else {
             delete {(resno=iResno) and (chain=iChain) and (atomName="CF")}
             delete {(resno=iResno) and (chain=iChain) and (atomName="OC1")}
        }
    }
    
    # ASP.OD1 or ASP.O or HIS.ND1 or SER.OG or THR.OG1 OR TYR.OH PO3
    else if (((iGroup="HIS") and (iName="ND1"))
        or ((iGroup="SER") and (iName="OG"))
        or ((iGroup="THR") and (iName="OG1"))
        or ((iGroup="TYR") and (iName="OH"))
        or ((iGroup="ASP") and (iName[1][2]="OD"))) {
        
        if (({atomIndex=idx}.bondCount == 1)
            or ((iName="ND1") and ({atomIndex=idx}.bondCount == 2))) {
            addToIdx(idx, "P", "", 3)
        }
        else {
            removeFromIdx(idx)
        }
    }
    
    # PRO.CG HYP
    else if ((iGroup="PRO") and (iName="CG")) {
        if ({atomIndex=idx}.bondCount == 2) {
            addToIdx(idx, "O", "H", 0)
        }
        else {
            removeFromIdx(idx)
        }
    }
    
    # A.N6 I
    else if ((iGroup="A") and (iName="N6")) {
        toXidx(idx, "O", "I")
    }
    else if ((iGroup="I") and (iName="O6")) {
        toXidx(idx, "N", "A")
    }
    
    # G.N2 X
    else if ((iGroup="G") and (iName="N2")) {
        toXidx(idx, "O", "X")
    }
    else if ((iGroup="X") and (iName="O2")) {
        toXidx(idx, "N", "G")
    }
    
    # U.N1 PU
    else if ((iGroup="U") and (iName="N1")) {
        toPUidx(idx, FALSE)
    }
    else if ((iGroup="PU") and (iName="C5")) {
        toPUidx(idx, TRUE)
    }
    
    # U.C5 T
    else if ((iGroup="U") and (iName="C5")) {
        addToIdx(idx, "C", "7 ", 0)
        toXidx(idx, "C", "T")
    }
    else if ((iGroup="T") and (iName="c5")) {
        delete {(resno=iResno) and (atomName="C7")}
        toXidx(idx, "C", "U")
    }
    
    # U.C6 HU
    else if ((iGroup="U") and ((iName="C5") or (iName="C6"))) {
        toXidx(idx, "C", "D")
        toDidx(idx)
    }
    else if ((iGroup="D") and ((iName="C5") or (iName="C6"))) {
        for (var i = 0; i < 10; i++) {
            toDidx(idx)
            if (gIsPlanar) {
                break
            }
        }
        toXidx(idx, "C", "U")
    }
    
    # O2'
    else if (iName="O2\'") {
        var cIdx = connected({atomIndex=idx})[1].atomIndex
        delete {atomIndex=idx}
        toXidx(cIdx, "C", "D"+iGroup)
    }
    
    # C2'
    else if (iName="C2\'") {
        var ccSet = connected({atomIndex=idx})
        if ((ccSet.size < 3) and (iGroup.size > 1)) {
            addToIdx(idx, "O", "2\'", 0)
            toXidx(idx, "C", iGroup[2])
        }
        else if (iGroup.size == 1) {
            for (var i = 1; i <= ccSet.size; i++) {
                if (ccSet[i].element == "O") {
                    delete {atomIndex=@{ccSet[i].atomIndex}}
                    toXidx(idx, "C", "D"+iGroup)
                }
            }
        }
    }
    setHoverLabels()
    
}

function selectChainMB() {
    var cset = {atomIndex=_atomPicked}
    select cSet
    while (cSet.size > 0) {
        cSet = connected({selected}) and not {selected}
        select {selected} or cSet
    }
    color {selected} @gAltScheme
}

function modifyExitMB() {
    unbind
    set echo TOP LEFT
    echo
    set allowRotateSelected gAllowRotateSelected
    set allowMoveAtoms gAllowMoveAtoms
    set hoverDelay gHoverDelay
    select all
    set hoverLabel = ""
    color {selected} @gScheme
    select {gSelsave}
}
    
# Top level of Modify
function plicoModify() {
    gSelsave = {selected}
    gAllowMoveAtoms = allowMoveAtoms
    gAllowRotateSelected = allowRotateSelected
    gHoverDelay = hoverDelay
    set allowMoveAtoms TRUE    
    set allowRotateSelected TRUE
    
    gPlico = "MODIFY"
    
    gScheme = defaultColorScheme
    gAltScheme = ((gScheme == "Jmol") ? "Rasmol" : "Jmol")
    set echo TOP LEFT
    background ECHO yellow
    
    gEcho = ("________MODIFY________|ALT-CLICK=change 1|SHIFT-CLICK=change 2|" +
        "ALT-SHIFT-CLICK=select chain|ALT-CTRL-CLICK=add water|ALT-DRAG=rotate selected|" +
        "ALT-SHIFT_DRAG=move selected|DOUBLE-CLICK=exit")
    echo @gEcho
    gChain = ""
    unbind
    
    bind "ALT-LEFT-CLICK" "_pickAtom";
    bind "ALT-LEFT-CLICK" "+:modify1MB";
    bind "SHIFT-LEFT-CLICK" "_pickAtom";
    bind "SHIFT-LEFT-CLICK" "+:modify2MB";
    bind "ALT-SHIFT-LEFT-CLICK" "_pickAtom";
    bind "ALT-SHIFT-LEFT-CLICK" "+:selectChainMB";
    bind "ALT-CTRL-LEFT-CLICK" "_pickAtom";
    bind "ALT-CTRL-LEFT-CLICK" "+:addWaterMB";
    bind "DOUBLE" "modifyExitMB";
    
    set hoverDelay 0.001
    hover on
    setHoverLabels()
}

# End of MODIFY.SPT

Contributors

Remig