pymolmyscript
2BIW.pdb2
# my fancy script (assumes cd desktop for these exercises)
# first lets reset everything without need to quit PyMol
delete all
# set some parameters, even if some were done in previous
# white background:
bg_color white
# antialias: 1 for smooth images, 0 for jagged
set antialias = 1
# now reload the PDB file
load 2BIW.pdb2
# hide everything (all lines and so on)
hide everything
# show cartoon ribbon for the protein
show cartoon
# keep standard helix, strand and loops representations.
# other options would be: cartoon loop, cartoon rect,
# cartoon oval, and cartoon tube.
cartoon automatic
# make the helices with edges as in Molcript.
# 1 is on, 0 is off
set cartoon_fancy_helices=1
# color the inside of the helices in gray
set cartoon_highlight_color, gray
# color everything gray, and change other things later
color gray
# make selection of alpha helices and color it
select myhelix, ss h
color red, myhelix
# make selection of beta sheets and color it
select mybeta, ss s
color yellow, mybeta
# The PDB file contains a carotenoid ligand named 3ON
# it carrot when selecting it, show it as stick,
# and color it orange
select carrot, resn 3ON
show stick, carrot
color orange, carrot
# change the stick thickness from the default 0.25 to 0.40
set stick_radius = 0.40
# Inspection of the PDB file reveals there is also an iron
# select it and name it myiron, color it green and show it
# as a sphere. Then increase the sphere look quality.
select myiron, symbol FE
show sphere, myiron
color green, myiron
set sphere_quality = 8
# Select all full amino acids within 4 angstroms of the ligand
# and call this selection locals. Show them as a blue surface.
select locals, byres (chain B and carrot) around 4
show surface, locals
color blue, locals
# make the surface 15% transparent (85% opaque)
set transparency, 0.15
# Rotate about the Y axis to see the inside of the pocket
rotate y, 145, all
rotate z, -45, all
# zoom in on the ligand
zoom carrot
# make sure nothing is selected to avoid the little pink
# squares.
deselect
# end of this script – you could uncomment the next line to
# to make a fancy image: remove the “#” in the next line
# ray
Helicase
show sticks
hide lines, chain a
hide sticks, chain a
color white
color marine, chain y
color firebrick, resi 700
show sphere, resi 700
show cartoon
hide cartoon, chain y or chain z
select prtn, chain a
show cartoon, prtn
color white, chain a
set cartoon_fancy_helices,1
cmd.disable('prtn')
Helicase
show sticks
hide lines, chain a
hide sticks, chain a
color white
color marine, chain y
color firebrick, resi 700
show sphere, resi 700
show cartoon
hide cartoon, chain y or chain z
select prtn, chain a
show cartoon, prtn
color white, chain a
set cartoon_fancy_helices,1
set cartoon_cylindrical_helices,1
cmd.disable('prtn')
Nucleosome
#########################################################################
# #
# PyMol Script to render nucleosome #
# Histones as surface, DNA as sticks #
# #
# Esther Zhuang and Kalju Kahn, UCSB, 2003-2004 #
# #
#########################################################################
# TODO
Alkaline Phosphatase
#########################################################################
# #
# PyMol Script to render alkaline phosphatase active site #
# Showing protein surface with active site metal ions #
# #
# Esther Zhuang and Kalju Kahn, UCSB, 2004 #
# #
#########################################################################
hide
# General style
set transparency=0.4
set sphere_scale=0.22
set stick_radius=0.1
set surface_color=gray
# Show active site residues His331, His370, His412, Arg166 etc.
select active, (resi 327,331,370,412,166,102,51,155,322) and chain a
select his, (resi 331,370,412) and chain a
select asp, resi 327 and chain a
select water, (resi 453-455)
select mg, elem mg and chain a
select zn, (resi 450,451)
select p, resi 456
show sticks, active
show sticks, his
show sticks, p
show sphere, water
show sphere, p
show sphere, zn
show sphere, mg
cmd.disable('active')
cmd.disable('his')
cmd.disable('asp')
cmd.disable('water')
cmd.disable('p')
color hotpink, elem p
color slate, elem zn
color orange, elem mg
color gray, active or his
color marine, elem n
color salmon, elem o
color white, resn hoh
cmd.select('lb',"(1ED8_alk_phosp`6634)")
cmd.select('rb',"(1ED8_alk_phosp`756)")
unbond
cmd.delete("lb")
cmd.delete("rb")
# Hide unimportant stuff
cmd.select('lb',"(1ED8_alk_phosp`750)")
cmd.select('lb',"( ((lb) or ((1ED8_alk_phosp`749))) and not (((1ED8_alk_phosp`749)) in (lb)))")
cmd.select('lb',"( ((lb) or ((1ED8_alk_phosp`747))) and not (((1ED8_alk_phosp`747)) in (lb)))")
cmd.select('lb',"( ((lb) or ((1ED8_alk_phosp`751))) and not (((1ED8_alk_phosp`751)) in (lb)))")
cmd.select('lb',"( ((lb) or ((1ED8_alk_phosp`752))) and not (((1ED8_alk_phosp`752)) in (lb)))")
cmd.select('lb',"( ((lb) or ((1ED8_alk_phosp`6629))) and not (((1ED8_alk_phosp`6629)) in (lb)))")
cmd.select('lb',"( ((lb) or ((1ED8_alk_phosp`6631))) and not (((1ED8_alk_phosp`6631)) in (lb)))")
cmd.select('lb',"( ((lb) or ((1ED8_alk_phosp`6630))) and not (((1ED8_alk_phosp`6630)) in (lb)))")
select extra, lb
hide sticks, extra
cmd.delete("lb")
cmd.disable('extra')
select extra2, active and (name n
or name o or name c)
hide sticks, extra2
# Show coordination of metals and H-bonds
dist (elem o and p) , (resi 166 or zn) , 3.00
dist (resi 450 and zn) , ((active or water) and (elem o or elem n)) , 2.80
dist (resi 451 and zn) , ((active or water) and (elem o or elem n)) , 2.80
dist (resi 462 and mg) , ((active or water) and (elem o or elem n)), 2.80
hide label
# Show protein as grey surface
show surface
# Zoom into the active site
set_view (\
-0.833488882, -0.316700667, -0.452733815,\
-0.163282588, -0.641609192, 0.749432981,\
-0.527827144, 0.698575199, 0.483063161,\
0.002991825, 0.000191273, -83.746078491,\
75.504585266, 32.291461945, 39.612136841,\
32.583885193, 148.937820435, 0.000000000 )
# This is only for the high-quality raytraced image
# util.performance(0)
# rebuild
# set transparency=0.27
# set ambient,0.30000
# set spec_reflect,0.36000
# ray
Helix-Turn-Helix
Motif
in DNA Binding
#########################################################################
# #
# PyMol Script to render ZIF-DNA complex #
# Illustration of helix-turn-helix DNA binding motif #
# #
# Kalju Kahn, UCSB, 2005 #
# #
#########################################################################
hide
# General preferences
set stick_radius=0.17
set sphere_scale=1.0
set cartoon_loop_radius=0.85
set cartoon_tube_radius, 0.15
set cartoon_transparency, 0.1
set two_sided_lighting,1
set ambient,0.32000
set light,[ 0.50000, -0.40000, -1.00000 ]
# Render protein dimer with one DNA molecule
select protein, (chain a or chain c)
select dna, (chain f or chain h)
cmd.disable('dna')
show sticks, dna
show sphere, elem p and dna
color wheat, dna
color orange, elem p
color marine, chain a
color pink, chain c
# Emphasize the helix-turn-helix motif
cartoon loop, dna
cartoon tube, protein
cartoon automatic, resi 190-217
show cartoon, (dna or protein)
# View with DNA raising diagonally
set_view (\
0.824338973, 0.366992146, 0.431021273,\
0.012900007, -0.773375988, 0.633815348,\
0.565947652, -0.516920686, -0.642258346,\
-0.000141710, -0.000013943, -152.460372925,\
57.745296478, -3.173804760, 45.264041901,\
72.646949768, 232.266403198, 0.000000000 )
util.performance(0)
util.ray_shadows('none')
rebuild