[PyMOL] Before the release of PyMol 0.99: Nucleotides and CGO

[<gre...@un...>]

Hello List,

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Maybe useful, maybe not=85 Here is a small py script for filling =
nucleotides
with colored CGO objects. I just tried it on the pdb file 127D.

Of course not as efficient as Nuccyl!!! But I couldn=92t find out how to =
run
perl scripts on my Windows-running PC, and this is exactly (and only) =
what I
needed.

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Just run the script, and type =91DrawNT=92 in the PyMol command line.

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Cheers,


Greg

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from pymol import cmd

from pymol.cgo import *

from Numeric import *

import sys,re

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# COLOR SETTINGS:

AColor=3D[0.2,1,0.2]

TColor=3D[1,0.2,0.2]

CColor=3D[0.3,0.3,1]

GColor=3D[1,0.55,0.15]

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def DrawNT(select=3D"all"):

    CurrentView =3D cmd.get_view(1)

    CurrentResi =3D 0

    FirstRun =3D 1

    NTPlate =3D [BEGIN,TRIANGLE_FAN]

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# THYMINE

    BaseT =3D cmd.get_model("resn T")

    for atoms in BaseT.atom:

        if (CurrentResi !=3D atoms.resi):

            CurrentResi =3D atoms.resi

            if FirstRun =3D=3D 0:

                NTPlate.append(END)

                NTPlate.extend([BEGIN,TRIANGLE_FAN])

                NTPlate.extend([COLOR]+TColor)

            else:

                NTPlate.extend([COLOR]+TColor)

                FirstRun =3D 0

        if (atoms.name =3D=3D "N1") or (atoms.name =3D=3D "C2") or =
(atoms.name =3D=3D
"N3") or (atoms.name =3D=3D "C4") or (atoms.name =3D=3D "C5") or =
(atoms.name =3D=3D
"C6"):       =20

            NTPlate.extend([VERTEX] + atoms.coord)

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# ADENINE

    BaseA =3D cmd.get_model("resn A")

    for atoms in BaseA.atom:

        if (CurrentResi !=3D atoms.resi):

            CurrentResi =3D atoms.resi

            if FirstRun =3D=3D 0:

                NTPlate.append(END)

                NTPlate.extend([BEGIN,TRIANGLE_FAN])

                NTPlate.extend([COLOR]+AColor)

            else:

                NTPlate.extend([COLOR]+AColor)

                FirstRun =3D 0

        if (atoms.name =3D=3D "N1") or (atoms.name =3D=3D "C2") or =
(atoms.name =3D=3D
"N3") or (atoms.name =3D=3D "C4") or (atoms.name =3D=3D "C5") or =
(atoms.name =3D=3D
"C6"):           =20

            NTPlate.extend([VERTEX] + atoms.coord)

            if (atoms.name =3D=3D "C4"):

                TmpC4 =3D atoms.coord

            elif (atoms.name =3D=3D "C5"):

                TmpC5 =3D atoms.coord

        elif (atoms.name =3D=3D "N7"):

            NTPlate.append(END)

            NTPlate.extend([BEGIN,TRIANGLE_FAN])

            NTPlate.extend([COLOR]+AColor)

            NTPlate.extend([VERTEX] + TmpC4)

            NTPlate.extend([VERTEX] + TmpC5)

            NTPlate.extend([VERTEX] + atoms.coord)

        elif (atoms.name =3D=3D "C8") or (atoms.name =3D=3D "N9"):

            NTPlate.extend([VERTEX] + atoms.coord)

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# CYTOSINE

    BaseC =3D cmd.get_model("resn C")

    for atoms in BaseC.atom:

        if (CurrentResi !=3D atoms.resi):

            CurrentResi =3D atoms.resi

            if FirstRun =3D=3D 0:

                NTPlate.append(END)

                NTPlate.extend([BEGIN,TRIANGLE_FAN])

                NTPlate.extend([COLOR]+CColor)

            else:

                NTPlate.extend([COLOR]+CColor)

                FirstRun =3D 0

        if (atoms.name =3D=3D "N1") or (atoms.name =3D=3D "C2") or =
(atoms.name =3D=3D
"N3") or (atoms.name =3D=3D "C4") or (atoms.name =3D=3D "C5") or =
(atoms.name =3D=3D
"C6"):       =20

            NTPlate.extend([VERTEX] + atoms.coord)

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# GUANINE

    BaseG =3D cmd.get_model("resn G")

    for atoms in BaseG.atom:

        if (CurrentResi !=3D atoms.resi):

            CurrentResi =3D atoms.resi

            if FirstRun =3D=3D 0:

                NTPlate.append(END)

                NTPlate.extend([BEGIN,TRIANGLE_FAN])

                NTPlate.extend([COLOR]+GColor)

            else:

                NTPlate.extend([COLOR]+GColor)

                FirstRun =3D 0

        if (atoms.name =3D=3D "N1") or (atoms.name =3D=3D "C2") or =
(atoms.name =3D=3D
"N3") or (atoms.name =3D=3D "C4") or (atoms.name =3D=3D "C5") or =
(atoms.name =3D=3D
"C6"):

            NTPlate.extend([VERTEX] + atoms.coord)

            if (atoms.name =3D=3D "C4"):

                TmpC4 =3D atoms.coord

            elif (atoms.name =3D=3D "C5"):

                TmpC5 =3D atoms.coord

        elif (atoms.name =3D=3D "N7"):

            NTPlate.append(END)

            NTPlate.extend([BEGIN,TRIANGLE_FAN])

            NTPlate.extend([COLOR]+GColor)

            NTPlate.extend([VERTEX] + TmpC4)

            NTPlate.extend([VERTEX] + TmpC5)

            NTPlate.extend([VERTEX] + atoms.coord)

        elif (atoms.name =3D=3D "C8") or (atoms.name =3D=3D "N9"):

            NTPlate.extend([VERTEX] + atoms.coord)

    NTPlate.append(END)

    cmd.load_cgo(NTPlate,"PLAIN_NT")

    cmd.select("chain1", "name C3*+C4*+C5*+O5*+P+O3*")

    cmd.show("cartoon", "chain1")

    cmd.cartoon("dumbbell", "chain1")

    cmd.delete("chain1")

    cmd.set_view(CurrentView)

cmd.extend("DrawNT",DrawNT)