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RE: [PyMOL] Before the release of PyMol 0.99: Nucleotides and CGO
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From: <gre...@un...> - 2005-08-10 00:55:45
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Same script, but with hydrogen bonds between nucleotides.
Load the pdb file 127D, run the script and type =91DrawNT=92 in PyMol =
command
line=85
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I have a question, maybe Warren you can answer:
I wanted to use the set_color command to define a new color for the =
Hydrogen
bonds (MyRGBColor =3D [x,y,z] and then cmd.set_color(=93MyColor=94, =
MyRGBColor))
And finally apply the created color to the Hydrogen bonds
(cmd.distance('MyDistance', Selection1, Selection2) and then
cmd.color("MyColor", "MyDistance"))
The question is: how can I then delete the created MyColor object? I =
tried
the cmd.delete command, it does not generate an error but apparently the
color is still defined=85 Any idea?!
=20
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Cheers,
Greg
=20
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from pymol import cmd
from pymol.cgo import *
from Numeric import *
import sys,re
=20
# 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]
HColor=3D=94magenta=94
=20
def DrawNT(select=3D"all"):
CurrentView =3D cmd.get_view(1)
CurrentResi =3D 0
FirstRun =3D 1
NTPlate =3D [BEGIN,TRIANGLE_FAN]
=20
# 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)
if atoms.name =3D=3D "N3":
Sel1 =3D
'%s/%s/%s/%s'%(atoms.segi,atoms.chain,atoms.resi,atoms.name)
cmd.select('Sel2','%s around 3.1 and name N1 and not chain
%s'%(Sel1,atoms.chain))
cmd.distance('Dst', Sel1, "Sel2")
elif atoms.name =3D=3D "O4":
Sel1 =3D
'%s/%s/%s/%s'%(atoms.segi,atoms.chain,atoms.resi,atoms.name)
cmd.select('Sel2','%s around 3.1 and name N6 and not chain
%s'%(Sel1,atoms.chain))
cmd.distance('Dst', Sel1, "Sel2")
# 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)
=20
# 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)
if atoms.name =3D=3D "O2":
Sel1 =3D
'%s/%s/%s/%s'%(atoms.segi,atoms.chain,atoms.resi,atoms.name)
cmd.select('Sel2','%s around 3.1 and name N2 and not chain
%s'%(Sel1,atoms.chain))
cmd.distance('Dst', Sel1, "Sel2")
elif atoms.name =3D=3D "N3":
Sel1 =3D
'%s/%s/%s/%s'%(atoms.segi,atoms.chain,atoms.resi,atoms.name)
cmd.select('Sel2','%s around 3.1 and name N1 and not chain
%s'%(Sel1,atoms.chain))
cmd.distance('Dst', Sel1, "Sel2")
elif atoms.name =3D=3D "N4":
Sel1 =3D
'%s/%s/%s/%s'%(atoms.segi,atoms.chain,atoms.resi,atoms.name)
cmd.select('Sel2','%s around 3.1 and name O6 and not chain
%s'%(Sel1,atoms.chain))
cmd.distance('Dst', Sel1, "Sel2")
=20
# 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.set("cartoon_nucleic_acid_mode", 1, "chain1")
cmd.delete("chain1")
cmd.hide("label", "Dst")
cmd.color(HColor, "Dst")
cmd.delete("Sel2")
cmd.set_view(CurrentView)
cmd.extend("DrawNT",DrawNT)
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