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RE: [PyMOL] Before the release of PyMol 0.99: Nucleotides and CGO
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From: Warren D. <wa...@de...> - 2005-08-10 19:31:29
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> The question is: how can I then delete the created MyColor=20
> object? I tried the cmd.delete command, it does not generate=20
> an error but apparently the color is still defined... Any idea?!
Colors can't be undefined, and that would especially be true if an =
object is still using a given color, since colors in PyMOL are based on =
lookups. MyColor isn't so much an object as an entry in the global =
color table.
Cheers,
Warren
--
Warren L. DeLano, Ph.D. =20
Principal Scientist
. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213 =20
. South San Francisco, CA 94080 USA =20
. Biz:(650)-872-0942 Tech:(650)-872-0834 =20
. Fax:(650)-872-0273 Cell:(650)-346-1154
. mailto:wa...@de... =20
=20
> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Gr=E9gori Gerebtzoff
> Sent: Wednesday, August 10, 2005 10:43 AM
> To: pym...@li...
> Subject: RE: [PyMOL] Before the release of PyMol 0.99:=20
> Nucleotides and CGO
>=20
> Same script, but with hydrogen bonds between nucleotides.
>=20
> Load the pdb file 127D, run the script and type 'DrawNT' in=20
> PyMol command line...
>=20
> =20
>=20
> =20
>=20
> I have a question, maybe Warren you can answer:
>=20
> I wanted to use the set_color command to define a new color=20
> for the Hydrogen bonds (MyRGBColor =3D [x,y,z] and then=20
> cmd.set_color("MyColor", MyRGBColor))
>=20
> And finally apply the created color to the Hydrogen bonds=20
> (cmd.distance('MyDistance', Selection1, Selection2) and then=20
> cmd.color("MyColor", "MyDistance"))
>=20
> The question is: how can I then delete the created MyColor=20
> object? I tried the cmd.delete command, it does not generate=20
> an error but apparently the color is still defined... Any idea?!
>=20
> =20
>=20
> =20
>=20
> =20
>=20
> Cheers,
>=20
>=20
> Greg
>=20
> =20
>=20
> =20
>=20
> =20
>=20
> =20
>=20
> from pymol import cmd
>=20
> from pymol.cgo import *
>=20
> from Numeric import *
>=20
> import sys,re
>=20
> =20
>=20
> # COLOR SETTINGS:
>=20
> AColor=3D[0.2,1,0.2]
>=20
> TColor=3D[1,0.2,0.2]
>=20
> CColor=3D[0.3,0.3,1]
>=20
> GColor=3D[1,0.55,0.15]
>=20
> HColor=3D"magenta"
>=20
> =20
>=20
> def DrawNT(select=3D"all"):
>=20
> CurrentView =3D cmd.get_view(1)
>=20
> CurrentResi =3D 0
>=20
> FirstRun =3D 1
>=20
> NTPlate =3D [BEGIN,TRIANGLE_FAN]
>=20
> =20
>=20
> # THYMINE
>=20
> BaseT =3D cmd.get_model("resn T")
>=20
> for atoms in BaseT.atom:
>=20
> if (CurrentResi !=3D atoms.resi):
>=20
> CurrentResi =3D atoms.resi
>=20
> if FirstRun =3D=3D 0:
>=20
> NTPlate.append(END)
>=20
> NTPlate.extend([BEGIN,TRIANGLE_FAN])
>=20
> NTPlate.extend([COLOR]+TColor)
>=20
> else:
>=20
> NTPlate.extend([COLOR]+TColor)
>=20
> FirstRun =3D 0
>=20
> if (atoms.name =3D=3D "N1") or (atoms.name =3D=3D "C2") or=20
> (atoms.name =3D=3D "N3") or (atoms.name =3D=3D "C4") or (atoms.name=20
> =3D=3D "C5") or (atoms.name =3D=3D "C6"): =20
>=20
> NTPlate.extend([VERTEX] + atoms.coord)
>=20
> if atoms.name =3D=3D "N3":
>=20
> Sel1 =3D=20
> '%s/%s/%s/%s'%(atoms.segi,atoms.chain,atoms.resi,atoms.name)
>=20
> cmd.select('Sel2','%s around 3.1 and name N1 and=20
> not chain %s'%(Sel1,atoms.chain))
>=20
> cmd.distance('Dst', Sel1, "Sel2")
>=20
> elif atoms.name =3D=3D "O4":
>=20
> Sel1 =3D=20
> '%s/%s/%s/%s'%(atoms.segi,atoms.chain,atoms.resi,atoms.name)
>=20
> cmd.select('Sel2','%s around 3.1 and name N6 and=20
> not chain %s'%(Sel1,atoms.chain))
>=20
> cmd.distance('Dst', Sel1, "Sel2")
>=20
> # ADENINE
>=20
> BaseA =3D cmd.get_model("resn A")
>=20
> for atoms in BaseA.atom:
>=20
> if (CurrentResi !=3D atoms.resi):
>=20
> CurrentResi =3D atoms.resi
>=20
> if FirstRun =3D=3D 0:
>=20
> NTPlate.append(END)
>=20
> NTPlate.extend([BEGIN,TRIANGLE_FAN])
>=20
> NTPlate.extend([COLOR]+AColor)
>=20
> else:
>=20
> NTPlate.extend([COLOR]+AColor)
>=20
> FirstRun =3D 0
>=20
> if (atoms.name =3D=3D "N1") or (atoms.name =3D=3D "C2") or=20
> (atoms.name =3D=3D "N3") or (atoms.name =3D=3D "C4") or (atoms.name=20
> =3D=3D "C5") or (atoms.name =3D=3D "C6"): =20
>=20
> NTPlate.extend([VERTEX] + atoms.coord)
>=20
> if (atoms.name =3D=3D "C4"):
>=20
> TmpC4 =3D atoms.coord
>=20
> elif (atoms.name =3D=3D "C5"):
>=20
> TmpC5 =3D atoms.coord
>=20
> elif (atoms.name =3D=3D "N7"):
>=20
> NTPlate.append(END)
>=20
> NTPlate.extend([BEGIN,TRIANGLE_FAN])
>=20
> NTPlate.extend([COLOR]+AColor)
>=20
> NTPlate.extend([VERTEX] + TmpC4)
>=20
> NTPlate.extend([VERTEX] + TmpC5)
>=20
> NTPlate.extend([VERTEX] + atoms.coord)
>=20
> elif (atoms.name =3D=3D "C8") or (atoms.name =3D=3D "N9"):
>=20
> NTPlate.extend([VERTEX] + atoms.coord)
>=20
> =20
>=20
> # CYTOSINE
>=20
> BaseC =3D cmd.get_model("resn C")
>=20
> for atoms in BaseC.atom:
>=20
> if (CurrentResi !=3D atoms.resi):
>=20
> CurrentResi =3D atoms.resi
>=20
> if FirstRun =3D=3D 0:
>=20
> NTPlate.append(END)
>=20
> NTPlate.extend([BEGIN,TRIANGLE_FAN])
>=20
> NTPlate.extend([COLOR]+CColor)
>=20
> else:
>=20
> NTPlate.extend([COLOR]+CColor)
>=20
> FirstRun =3D 0
>=20
> if (atoms.name =3D=3D "N1") or (atoms.name =3D=3D "C2") or=20
> (atoms.name =3D=3D "N3") or (atoms.name =3D=3D "C4") or (atoms.name=20
> =3D=3D "C5") or (atoms.name =3D=3D "C6"): =20
>=20
> NTPlate.extend([VERTEX] + atoms.coord)
>=20
> if atoms.name =3D=3D "O2":
>=20
> Sel1 =3D=20
> '%s/%s/%s/%s'%(atoms.segi,atoms.chain,atoms.resi,atoms.name)
>=20
> cmd.select('Sel2','%s around 3.1 and name N2 and=20
> not chain %s'%(Sel1,atoms.chain))
>=20
> cmd.distance('Dst', Sel1, "Sel2")
>=20
> elif atoms.name =3D=3D "N3":
>=20
> Sel1 =3D=20
> '%s/%s/%s/%s'%(atoms.segi,atoms.chain,atoms.resi,atoms.name)
>=20
> cmd.select('Sel2','%s around 3.1 and name N1 and=20
> not chain %s'%(Sel1,atoms.chain))
>=20
> cmd.distance('Dst', Sel1, "Sel2")
>=20
> elif atoms.name =3D=3D "N4":
>=20
> Sel1 =3D=20
> '%s/%s/%s/%s'%(atoms.segi,atoms.chain,atoms.resi,atoms.name)
>=20
> cmd.select('Sel2','%s around 3.1 and name O6 and=20
> not chain %s'%(Sel1,atoms.chain))
>=20
> cmd.distance('Dst', Sel1, "Sel2")
>=20
> =20
>=20
> # GUANINE
>=20
> BaseG =3D cmd.get_model("resn G")
>=20
> for atoms in BaseG.atom:
>=20
> if (CurrentResi !=3D atoms.resi):
>=20
> CurrentResi =3D atoms.resi
>=20
> if FirstRun =3D=3D 0:
>=20
> NTPlate.append(END)
>=20
> NTPlate.extend([BEGIN,TRIANGLE_FAN])
>=20
> NTPlate.extend([COLOR]+GColor)
>=20
> else:
>=20
> NTPlate.extend([COLOR]+GColor)
>=20
> FirstRun =3D 0
>=20
> if (atoms.name =3D=3D "N1") or (atoms.name =3D=3D "C2") or=20
> (atoms.name =3D=3D "N3") or (atoms.name =3D=3D "C4") or (atoms.name=20
> =3D=3D "C5") or (atoms.name =3D=3D "C6"):
>=20
> NTPlate.extend([VERTEX] + atoms.coord)
>=20
> if (atoms.name =3D=3D "C4"):
>=20
> TmpC4 =3D atoms.coord
>=20
> elif (atoms.name =3D=3D "C5"):
>=20
> TmpC5 =3D atoms.coord
>=20
> elif (atoms.name =3D=3D "N7"):
>=20
> NTPlate.append(END)
>=20
> NTPlate.extend([BEGIN,TRIANGLE_FAN])
>=20
> NTPlate.extend([COLOR]+GColor)
>=20
> NTPlate.extend([VERTEX] + TmpC4)
>=20
> NTPlate.extend([VERTEX] + TmpC5)
>=20
> NTPlate.extend([VERTEX] + atoms.coord)
>=20
> elif (atoms.name =3D=3D "C8") or (atoms.name =3D=3D "N9"):
>=20
> NTPlate.extend([VERTEX] + atoms.coord)
>=20
> NTPlate.append(END)
>=20
> cmd.load_cgo(NTPlate,"PLAIN_NT")
>=20
> cmd.select("chain1", "name C3*+C4*+C5*+O5*+P+O3*")
>=20
> cmd.show("cartoon", "chain1")
>=20
> cmd.cartoon("dumbbell", "chain1")
>=20
> cmd.set("cartoon_nucleic_acid_mode", 1, "chain1")
>=20
> cmd.delete("chain1")
>=20
> cmd.hide("label", "Dst")
>=20
> cmd.color(HColor, "Dst")
>=20
> cmd.delete("Sel2")
>=20
> cmd.set_view(CurrentView)
>=20
> cmd.extend("DrawNT",DrawNT)
>=20
>=20
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