User:Remig/plico/modify

Modify allows the user to make common amino acid and nucleotide modifications by mouse actions. Hover text above each atom gives the available options if any 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 nucleotide modifications to generate pseudouridine, dihyrouridine, inosine, and xanthine.

Modifications indicated with 1: are performed with ALT-CLICK on the atom. Modifications indicated with 2: are performed with SHIFT-CLICK on the atom.

See Convert for a script to replace one amino-acid with another or one nucleotide with another.

After a modification adding atoms, the hover text on those atoms includes 'X' to remove the modification. Note also that the desired modification may be presented in the hover text on only just one or a few of the atoms of the residue to be modified and you may have to look around to find it.

Some features unrelated to modification have been placed here as well to serve other Plico functions. Water molecules may be added and moved around perhaps to serve as pivot points for Tug when no other atoms are where the pivot point is wanted.

Also the Jmol parameters allowMoveAtoms, allowRotateSelected, and dragSelected are set true while modify is active to allow free rotation and translation of selected atoms where ALT-DRAG rotates the selection and ALT-SHIFT-DRAG moves it. Note that the select chain option in Modify selects all atoms connected to the clicked atom, not those sharing the chain label with the clicked atom.

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
#   v1.10 beta    7/27/2015 -add dragSelected
#
# 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

gAllowMoveAtoms = allowMoveAtoms
gAllowRotateSelected = allowRotateSelected
gDragSelected = dragSelected
gSelsave = ({})
gScheme = defaultColorScheme
gAltScheme = ((gScheme == "Jmol") ? "Rasmol" : "Jmol")
gIsPlanar = false
gAppendNew = false
gHoverLabel = ""

# 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 iGroup = {atomIndex=idx}.group
    var iResno = {atomIndex=idx}.resno
    var f = {atomIndex=idx}.file
    var m = {atomIndex=idx}.model
    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] != "\'")
        and (cset.size > 1))) {
        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\""
    gAppendNew = appendNew
    appendNew = false
    script inline @{ls}
    appendNew = gAppendNew

    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 f = {atomIndex=idx}.file
    var m = {atomIndex=idx}.model
    var r = {atomIndex=idx}.resno
    var cSet = {(resno=r) and (file=f) and (model=m)}
    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
    gAppendNew = appendNew
    appendNew = false
    script inline @{ls}
    appendNew = gAppendNew
    
    var aP = get_atom_rcn(r, iChain, "P")
    var aO3p = get_atom_rcn(r-1, iChain, "O3\'")
    connect @aP @aO3p
    var aO3 = get_atom_rcn(r, iChain, "O3\'")
    var aPn = get_atom_rcn(r+1, iChain, "P")
    connect @aO3 @aPn
}

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

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

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

    var a3 = get_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", "PSU")
    }
}

function to_d_idx(idx) {
    delay
    gIsPlanar = false
    var iResno = {atomIndex=idx}.resno
    var iChain = {atomIndex=idx}.chain
    var n1 = get_atom_rcn(iResno, iChain, "N1")
    var c2 = get_atom_rcn(iResno, iChain, "C2")
    var o2 = get_atom_rcn(iResno, iChain, "O2")
    var n3 = get_atom_rcn(iResno, iChain, "N3")
    var c4 = get_atom_rcn(iResno, iChain, "C4")
    var o4 = get_atom_rcn(iResno, iChain, "O4")
    var c5 = get_atom_rcn(iResno, iChain, "C5")
    var c6 = get_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

        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"
    select ((file=f) and (model=m))
    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\""
        gAppendNew = appendNew
        appendNew = false
        script inline @{ls}
        appendNew = gAppendNew
        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 get_atom_rcn(iResno, iChain, "CF")
             delete get_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="PSU") 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 get_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
    color {selected and oxygen} pink
}

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

# Top level of Modify
function plico_modify() {
    gSelsave = {selected}
    gAllowMoveAtoms = allowMoveAtoms
    gAllowRotateSelected = allowRotateSelected
    gDragSelected = dragSelected
    gHoverDelay = hoverDelay
    gHoverLabel = hoverLabel
    set allowMoveAtoms true
    set allowRotateSelected true
    set dragSelected 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 = ""
    gMenuMin = false
    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";
    bind "LEFT-CLICK" "+:plico_menu_toggle";

    set hoverDelay 0.001
    hover on
    set_hover_labels()
}

# End of MODIFY.SPT

Contributors

Remig