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, phosphorylation 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 directory>/modify.spt;plico_modify

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

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

#   modify - Jmol script by Ron Mignery
#   v1.4 beta    7/21/2014 -handle multi-frame environment
#
# 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

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

# Return L tetrahedron point if i1<i2<i3, else R point
function get_tet(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 get_tet_1(pIdx, idx) {
    var cset = connected({atomIndex=pIdx}) and not {atomIndex=idx}
    return {atomIndex=idx}.xyz + {atomIndex=pIdx}.xyz - cset[1].xyz
}

function get_trigonal(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 add_to_idx(idx, aElement, greek, addOs) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    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) and (file=f) and (model=m)}.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 = get_trigonal(cSet[1].atomIndex, idx, cSet[2].atomIndex, 1.5)
    }
    else {
        if ((cSet.size == 2) and not greek.find("\'")) {
            pt = get_tet(cSet[1].atomIndex, idx, cSet[2].atomIndex, 1.5)
        }
        else if (cSet.size > 2) {
            pt = get_tet(cSet[2].atomIndex, idx, cSet[1].atomIndex, 1.5)
        }
        else {
            pt = get_tet_1(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)
        and (file=f) and (model=m)}.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 = get_trigonal(ccSet[1].atomIndex, aIdx, ccSet[2].atomIndex, 1.5)
            }
            else {
                if (ccSet.size == 2) {
                    pt = get_tet(ccSet[1].atomIndex, aIdx, ccSet[2].atomIndex, 1.5)
                }
                else if (ccSet.size == 3) {
                    pt = get_tet(ccSet[2].atomIndex, aIdx, ccSet[1].atomIndex, 1.5)
                }
                else {
                    pt = get_tet_1(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\""
            gAppendNew = appendNew
            appendNew = FALSE
            script inline @{ls}
            appendNew = gAppendNew
            oIdx = {(atomno=aAtomno) and (chain=iChain)
                and (file=f) and (model=m)}.atomIndex
            connect {atomIndex=aIdx} {atomIndex=oIdx}
        }
    }
    set_hover_labels()
}

function remove_from_idx(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 to_x_idx(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 to_pu_idx(idx, undoIt) {
    var iResno = {atomIndex=idx}.resno
    var iChain = {atomIndex=idx}.chain
    var a1 = atom_rcn(iResno, iChain, "O2")
    var a2 = atom_rcn(iResno, iChain, "O4")
    var xyz = {0 0 0} + a1.xyz
    a1.xyz = {0 0 0} + a2.xyz
    a2.xyz = xyz

    a1 = atom_rcn(iResno, iChain, "C2")
    a2 = atom_rcn(iResno, iChain, "C4")
    xyz = {0 0 0} + a1.xyz
    a1.xyz = {0 0 0} + a2.xyz
    a2.xyz = xyz

    a1 = atom_rcn(iResno, iChain, "N1")
    a2 = atom_rcn(iResno, iChain, "C5")
    xyz = {0 0 0} + a1.xyz
    a1.xyz = {0 0 0} + a2.xyz
    a2.xyz = xyz

    var a3 = atom_rcn(iResno, iChain, "C1\'")
    connect a3 a1 DELETE
    connect a3 a2

    if (undoit) {
        to_x_idx(idx, "C", "U")
    }
    else {
        to_x_idx(idx, "N", "PU")
    }
}

function to_d_idx(idx) {
    delay
    gIsPlanar = FALSE
    var iResno = {atomIndex=idx}.resno
    var iChain = {atomIndex=idx}.chain
    var n1 = atom_rcn(iResno, iChain, "N1")
    var c2 = atom_rcn(iResno, iChain, "C2")
    var o2 = atom_rcn(iResno, iChain, "O2")
    var n3 = atom_rcn(iResno, iChain, "N3")
    var c4 = atom_rcn(iResno, iChain, "C4")
    var o4 = atom_rcn(iResno, iChain, "O4")
    var c5 = atom_rcn(iResno, iChain, "C5")
    var c6 = atom_rcn(iResno, iChain, "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 set_hover_labels() {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    select ((file=f) and (model=m))
    set hoverLabel "%U"

    select ({(atomName="?O?")} or {(atomName="?P?") and {amino}}
        and (file=f) and (model=m))
    set hoverLabel "%U|1:  -X"

    select ((((oxygen or sulfur) and not *.O and (bondCount = 1))
        or (nitrogen and (bondCount < 3))) and (file=f) and (model=m))
    set hoverLabel "%U|1:  -CH3"
    select (not amino and not oxygen and (bondCount < 3)
        and (file=f) and (model=m))
    set hoverLabel "%U|1:  -CH3"

    select (((atomName="?M?") or (group="HOH")) and (file=f) and (model=m))
    set hoverLabel "%U|1:  -X"

    # MET N fMET
    select (MET.N and (bondCount == 1) and (file=f) and (model=m))
    set hoverLabel "%U|1:  -CH3|2: -CO"
    select (MET.N and (bondCount == 2) and (file=f) and (model=m))
    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)
        and (file=f) and (model=m))
    set hoverLabel "%U|1:  -CH3|2:  -PO3"

    # PRO CG HYP
    select PRO.CG and (file=f) and (model=m)
    set hoverLabel "%U|1: -CH3|2:  -OH"

    # A N6 I
    select ([A].N6 or [I].O6) and (file=f) and (model=m)
    set hoverLabel "%U|1:  -CH3|2: A <--> I"

    # G N2 X
    select ([G].N2 or [X].O2) and (file=f) and (model=m)
    set hoverLabel "%U|1:  -CH3|2: G <--> X"

    # U N1 PU
    select ([U].N1 or [PU].C5) and (file=f) and (model=m)
    set hoverLabel "%U|1:  -CH3|2: U <--> PU"

    # U C5-6 HU
    select [U].C6 and (file=f) and (model=m)
    set hoverLabel "%U|1:  -CH3|2: U --> D"

    # U C5-6 HU
    select [D].C6 and (file=f) and (model=m)
    set hoverLabel "%U|1:  ->Conformers|2: D --> U"

    # U C5 M T
    select ([U].C5 OR [T].C5) and (file=f) and (model=m)
    set hoverLabel "%U|1:  -CH3|2: U <--> T"

    # *.?2' -X
    select ??.?2' and (file=f) and (model=m)
    set hoverLabel "%U|1:  -CH3|2: X <--> DX"
    refresh
 }

function add_water_mb() {
    f = _frameID/1000000
    m = _frameID%1000000
    var idx = _atomPicked
    var iChain = {atomIndex=idx}.chain
    var pt = {0 0 0}
    var cSet = connected({atomIndex=idx})
    if (cSet.size == 2) {
        pt = get_tet(cSet[1].atomIndex, idx, cSet[2].atomIndex, 2.3)
    }
    else if (cSet.size == 3) {
        pt = get_tet(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    ",
             {(file=f) and (model=m)}.atomno.max + 1, iChain, {(file=f) and (model=m)}.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}
        set_hover_labels()
    }
}

function modify_1_mb() {
    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") {
        to_d_idx(idx)
        if(gIsPlanar) {
            to_d_idx(idx)
        }
    }

    else if ((iName[2]="M") or (iName[2]="O")
        or (isAmino and ((iName[1]="P") or (iName[2]=="P")))) {
        remove_from_idx(idx)
        delete {atomIndex=idx}
    }

    else {
        if ({atomIndex=idx}.element="P") {
            if (isAmino) {
                remove_from_idx(idx)
            }
        }
        else if (({atomIndex=idx}.element="O")
            and ({atomIndex=idx}.atomName!="O")
            and ({atomIndex=idx}.bondCount=1)) {
            add_to_idx(idx, "C", "M", 0)
        }
        else if (({atomIndex=idx}.element!="O")
            and ({atomIndex=idx}.bondCount < 3)) {
            add_to_idx(idx, "C", "M", 0)
        }
        else if (isAmino) {
            remove_from_idx(idx)
        }
    }
}

function modify_2_mb() {
    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) {
            add_to_idx(idx, "C", "F", 1)
        }
        else {
             delete atom_rcn(iResno, iChain, "CF")
             delete atom_rcn(iResno, iChain, "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))) {
            add_to_idx(idx, "P", "", 3)
        }
        else {
            remove_from_idx(idx)
        }
    }

    # PRO.CG HYP
    else if ((iGroup="PRO") and (iName="CG")) {
        if ({atomIndex=idx}.bondCount == 2) {
            add_to_idx(idx, "O", "H", 0)
        }
        else {
            remove_from_idx(idx)
        }
    }

    # A.N6 I
    else if ((iGroup="A") and (iName="N6")) {
        to_x_idx(idx, "O", "I")
    }
    else if ((iGroup="I") and (iName="O6")) {
        to_x_idx(idx, "N", "A")
    }

    # G.N2 X
    else if ((iGroup="G") and (iName="N2")) {
        to_x_idx(idx, "O", "X")
    }
    else if ((iGroup="X") and (iName="O2")) {
        to_x_idx(idx, "N", "G")
    }

    # U.N1 PU
    else if ((iGroup="U") and (iName="N1")) {
        to_pu_idx(idx, FALSE)
    }
    else if ((iGroup="PU") and (iName="C5")) {
        to_pu_idx(idx, TRUE)
    }

    # U.C5 T
    else if ((iGroup="U") and (iName="C5")) {
        add_to_idx(idx, "C", "7 ", 0)
        to_x_idx(idx, "C", "T")
    }
    else if ((iGroup="T") and (iName="c5")) {
        delete atom_rcn(iResno, iChain, "C7")
        to_x_idx(idx, "C", "U")
    }

    # U.C6 HU
    else if ((iGroup="U") and ((iName="C5") or (iName="C6"))) {
        to_x_idx(idx, "C", "D")
        to_d_idx(idx)
    }
    else if ((iGroup="D") and ((iName="C5") or (iName="C6"))) {
        for (var i = 0; i < 10; i++) {
            to_d_idx(idx)
            if (gIsPlanar) {
                break
            }
        }
        to_x_idx(idx, "C", "U")
    }

    # O2'
    else if (iName="O2\'") {
        var cIdx = connected({atomIndex=idx})[1].atomIndex
        delete {atomIndex=idx}
        to_x_idx(cIdx, "C", "D"+iGroup)
    }

    # C2'
    else if (iName="C2\'") {
        var ccSet = connected({atomIndex=idx})
        if ((ccSet.size < 3) and (iGroup.size > 1)) {
            add_to_idx(idx, "O", "2\'", 0)
            to_x_idx(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}}
                    to_x_idx(idx, "C", "D"+iGroup)
                }
            }
        }
    }
    set_hover_labels()

}

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

function modify_exit_mb() {
    unbind
    set echo TOP LEFT
    echo
    set allowRotateSelected gAllowRotateSelected
    set allowMoveAtoms gAllowMoveAtoms
    set hoverDelay gHoverDelay
    set AnimFrameCallback none
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    select ((file=f) and (model=m))
    set hoverLabel = ""
    color {selected} @gScheme
    select {gSelsave}
}

# Top level of Modify
function plico_modify() {
    gSelsave = {selected}
    gAllowMoveAtoms = allowMoveAtoms
    gAllowRotateSelected = allowRotateSelected
    gHoverDelay = hoverDelay
    set allowMoveAtoms TRUE
    set allowRotateSelected TRUE
    set AnimFrameCallback "jmolscript:set_hover_labels"

    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" "+:modify_1_mb";
    bind "SHIFT-LEFT-CLICK" "_pickAtom";
    bind "SHIFT-LEFT-CLICK" "+:modify_2_mb";
    bind "ALT-SHIFT-LEFT-CLICK" "_pickAtom";
    bind "ALT-SHIFT-LEFT-CLICK" "+:select_chain_mb";
    bind "ALT-CTRL-LEFT-CLICK" "_pickAtom";
    bind "ALT-CTRL-LEFT-CLICK" "+:add_water_mb";
    bind "DOUBLE" "modify_exit_mb";

    set hoverDelay 0.001
    hover on
    set_hover_labels()
}

# End of MODIFY.SPT

Contributors

Remig