Gallery

# first load lipid model
load lipids.pdb; 
# hide the initially loaded representation
hide all; 
# set background color to white
bg_color white; 
# show lipid model as sticks
show sticks, lipids; 
# color the lipids model by element CHNOS #2 (carbon green)
util.cbag lipids; 
 
# select all hydrogens and remove them from the model
select hideme, hydro; 
hide everything, hideme; 
delete hideme;
 
# create phosphate spheres
create phos, elem p; 
hide everything, phos;
show spheres, phos;
 
# load helix model
load helix.pdb; 
# hide the initially loaded representation
hide everything, helix;
# make the helical struct into a cartoon form
show cartoon, helix; 
# style the cartoon form
cartoon putty; 
 
# reposition the helix among the lipids using
# the 3-Button Editing Mouse Mode
# basically
# Shift+Left Mouse to rotate the helix
# Shift+Middle Mouse to move the helix
# also, you may want to make liberal use of the
# get_view and set_view commands.
#
# When you have the scene set like you want,
# continue with...
 
# move the model to find the view you want, 
# and use get_view to get the coordinate description
get_view;
 
# set ray_trace_mode to black and white outline
set ray_trace_mode, 2;

# example script for creation of an image with a slice region
load $PYMOL_PATH/test/dat/1tii.pdb
orient
 
# must disable depth cue and shadows
unset depth_cue
unset ray_shadows
set ray_trace_mode, 0
 
# this controls the z depth of the slice plane
# (sets it halfway between the clipping planes)
fraction = 0.42
view = cmd.get_view()
near_dist = fraction*(view[16]-view[15])
far_dist = (view[16]-view[15]) - near_dist
cmd.clip("near", -near_dist)
 
# render opaque background image
as surface
set ray_interior_color, grey80
set opaque_background
set surface_color, white
ray
save image_back.png
 
cmd.clip("near", near_dist)
cmd.clip("far", far_dist)
 
# render the foreground image
as cartoon
util.cbc
unset opaque_background
ray
save image_front.png
 
# now use Photoshop, Gimp, or ImageMagick to combine the images
system composite image_front.png image_back.png image_merged.png
system display image_merged.png

fetch 1cll 1sra 1ggz 5pnt 1rlw 1cdy;
set grid_mode

load prot.pdb;
zoom i. 46-49 and n. CA
set field_of_view, 60
ray

load $TUT/1hpv.pdb, tmp
extract lig, organic
extract prot, polymer
delete tmp
 
set surface_carve_cutoff, 4.5
set surface_carve_selection, lig
set surface_carve_normal_cutoff, -0.1
 
show surface, prot within 8 of lig
set two_sided_lighting
set transparency, 0.5
show sticks, lig
orient lig
 
set surface_color, white
set surface_type, 2  # mesh
unset ray_shadows

load $TUT/1hpv.pdb
set_color oxygen, [1.0,0.4,0.4]
set_color nitrogen, [0.5,0.5,1.0]
remove solvent
as spheres
util.cbaw
bg white
set light_count,8
set spec_count,1
set shininess, 10
set specular, 0.25
set ambient,0
set direct,0
set reflect,1.5
set ray_shadow_decay_factor, 0.1
set ray_shadow_decay_range, 2
unset depth_cue
# for added coolness
# set field_of_view, 60
ray

fetch 1wld
as surface, poly
as sticks, org
h_add solvent
color grey, poly
orient org
png img.png
# now, go into Photoshop or the GIMP and apply a Gaussian or
# Focus blur to the top and bottom portions of the image

# grey surface
set surface_color, grey
 
# cavity mode
set surface_mode, 3
 
# layered transparency mode
set transparency_mode, 1
 
# surface transparency
set transparency, 0.5
 
# oblique and contrast define the
# look of the surface transparency:
# if the normal vector is 
set ray_transparency_oblique
set ray_transparency_oblique_power, 8
set ray_transparency_contrast, 7
 
# fetch a protein, with a 
# small molecule in a nice
# hidden pocket
fetch 1hpv, async=0
 
hide
 
# show the small molecule as surface
show surface, org
 
# arrange the view
orient org
 
# zoom back a little
zoom org, 1
 
# show the small molecule inside as sticks
show sticks, org
 
# show some nearby sidechains
show lines, poly within 5 of org
 
# enable frame caching for playback
set cache_frames, 1
 
set ray_trace_frames, 1
 
mset 1x120
 
movie.roll 1, 120, 1, x
 
mplay
 
# now sit back and wait 5 minutes...

fetch 3uex, struct, async=0
 
remove solvent
 
# set the B-factors nice and high for smoothness
alter all, b=10
alter all, q=1
 
# 3.5 A map resolution
set gaussian_resolution, 3.5
 
# new gaussian map w/resolution=0.5 Ang
# on just the main chain
map_new map, gaussian, 0.5, n. C+O+N+CA, 5
 
# create a surface from the map
isosurface surf, map, 3.0
 
# color the protein by number
spectrum count, rainbow, struct
 
# now color the map based on the underlying protein
cmd.ramp_new("ramp", "struct", [0,10,10], [-1, -1, 0])
 
# set the surface color
cmd.set("surface_color", "ramp", "surf")
 
# hide the ramp and lines
disable ramp
hide lines
 
bg grey
 
# soften out the image
set light_count,8
set spec_count,1
set shininess, 10
set specular, 0.075
set ambient,0
set direct,0
set reflect, 0.85
set ray_shadow_decay_factor, 0.1
set ray_shadow_decay_range, 4
 
unset depth_cue
 
# ray trace the image
orient
ray

# fetch a protein
 
fetch 1rx1, async=0
 
# setup the cartoon tubes
 
as cartoon
 
cartoon tube
 
set cartoon_tube_radius, 0.7
 
set cartoon_color, brown
 
set cartoon_side_chain_helper, on
 
show sticks, poly
 
color yellow
 
# README
# stop here, or try this for "sloppy sticks"
# beefy video card required!
 
select rep sticks
select sele and not n. C+O+N+CA
 
# set the B-factors nice and high for smoothness
alter all, b=10
alter all, q=1
 
# 2.5 A map resolution
 
set gaussian_resolution, 2.5
 
# 0.2 A sampling; lower=smoother
 
map_new map, gaussian, 0.2, sele, 5
 
# create a surface from the map
 
isosurface surf, map, 5.0
 
color yellow, surf
hide sticks
 
# reconnect the main chain to the blobs
show sticks, n. CA+CB

fetch 3uex, struct, async=0
 
remove solvent
 
# set the B-factors nice and high for smoothness
alter all, b=10
alter all, q=1
 
# 3.5 A map resolution
set gaussian_resolution, 7.6
 
# new gaussian map w/resolution=0.5 Ang
# on just the main chain
map_new map, gaussian, 1, n. C+O+N+CA, 5
 
# create a surface from the map
isosurface surf, map, 1.5
 
# color the protein by number
spectrum count, rainbow, struct
 
# now color the map based on the b-factors of the
# underlying protein
cmd.ramp_new("ramp", "struct", [0,10,10], "rainbow")
 
# set the surface color
cmd.set("surface_color", "ramp", "surf")
 
# hide the ramp and lines
disable ramp
hide lines
 
show sticks, org
show spheres, org
 
color magenta, org
reinit
 
fetch 3uex, struct, async=0
 
remove solvent
 
# set the B-factors nice and high for smoothness
alter all, b=10
alter all, q=1
 
# 3.5 A map resolution
set gaussian_resolution, 7.6
 
# new gaussian map w/resolution=0.5 Ang
# on just the main chain
map_new map, gaussian, 1, n. C+O+N+CA, 5
 
# create a surface from the map
isosurface surf, map, 1.5
 
# color the protein by number
spectrum count, rainbow, struct
 
# now color the map based on the b-factors of the
# underlying protein
cmd.ramp_new("ramp", "struct", [0,10,10], "rainbow")
 
# set the surface color
cmd.set("surface_color", "ramp", "surf")
 
# hide the ramp and lines
disable ramp
hide lines
 
show sticks, org
show spheres, org
 
color magenta, org
set_bond stick_radius, 0.13, org
set sphere_scale, 0.26, org
 
set_bond stick_radius, 0.13, org
set_bond stick_color, white, org
set sphere_scale, 0.26, org
set_view (\
    -0.877680123,    0.456324875,   -0.146428943,\
    0.149618521,   -0.029365506,   -0.988305628,\
    -0.455291569,   -0.889327347,   -0.042500813,\
    -0.000035629,    0.000030629,  -37.112102509,\
    -3.300258160,    6.586110592,   22.637466431,\
     8.231912613,   65.999290466,  -50.000000000 )
 
# ray trace the image
ray

fetch 1eaz, async=0
 
extract oo, org
 
hide everything, solvent
 
set field_of_view, 50
 
preset.ball_and_stick("oo")
 
set_bond stick_color, 0xffff44, oo
 
set_bond stick_transparency, 0.35, oo
 
color grey, oo and e. C
 
set valence, 1, oo
 
ramp_new pRamp, oo, selection=poly, range=[5,30], color=rainbow
 
set surface_color, pRamp, poly
 
show spheres, poly
 
color white, poly
 
color grey30, poly and e. C
 
set sphere_scale, 0.99, poly
 
set ray_transparency_contrast, 0.20
 
set ray_transparency_oblique, 1.0
 
set ray_transparency_oblique_power, 20
 
show surface, poly
 
set surface_quality, 2
 
set light_count, 5
 
set ambient_occlusion_mode, 1
 
set ambient_occlusion_scale, 50
 
set ambient, 0.40
 
set transparency, 0.50
 
disable pRamp
 
set spec_power, 1200
 
set spec_reflect, 0.20
 
set ray_opaque_background, 0
 
set ray_shadow, 0
 
ray

# fetch the protein
 
fetch 1rx1, async=0
 
# show it as blue/magenta spheres
 
as spheres
 
color lightblue, not org
 
color magenta, org
 
remove solvent
 
# set the view
 
orient all within 8 of org
 
# set the lights, ray tracing setttings
# to get the Goodsell-like rendering
 
unset specular
 
set ray_trace_gain, 0
 
set ray_trace_mode, 3
 
bg_color white
 
set ray_trace_color, black
 
unset depth_cue
 
ray

hide everything
show sticks
show spheres
set stick_radius, .07
set sphere_scale, .18
set sphere_scale, .13, elem H
set bg_rgb=[1, 1, 1]
set stick_quality, 50
set sphere_quality, 4
color gray85, elem C
color red, elem O
color slate, elem N
color gray98, elem H
set stick_color, black
set ray_trace_mode, 1
set ray_texture, 2
set antialias, 3
set ambient, 0.5
set spec_count, 5
set shininess, 50
set specular, 1
set reflect, .1
set dash_gap, 0
set dash_color, black
set dash_gap, .15
set dash_length, .05
set dash_round_ends, 0
set dash_radius, .05
python
preset.ball_and_stick("vis")
python end
fetch 1rx1, async=0
remove not org
orient org
ray