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,10
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