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*[[Set]] | *[[Set]] | ||
*[[Property_Selectors |Short form Selectors]] | *[[Property_Selectors |Short form Selectors]] | ||
}} | |||
{{GalleryImage | |||
|image=Tilt shift.png|size=500px|title=Simulating Tilt-shift|description=Tilt shift simulation | |||
|cmdString=<source lang="python"> | |||
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 | |||
</source> | |||
|seeAlso= | |||
*[[fetch]] | |||
*[[show_as]] | |||
*[[h_add]] | |||
*[[color]] | |||
}} | }} | ||
Revision as of 09:21, 9 June 2010
| Cool PyMOL-generated Images and their Scripts. Add Your Own |
| Complex B&W outline representation | What To Type | |||||
|
# 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;
|
| A "Sliced" Image | What To Type | |||||
|
# 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
|
| Grid Mode | What To Type | |||||
|
fetch 1cll 1sra 1ggz 5pnt 1rlw 1cdy;
set grid_mode
|
| Cool Perspective | What To Type | |||||
|
load prot.pdb;
zoom i. 46-49 and n. CA
set field_of_view, 60
ray
|
| Representing a binding pocket | What To Type | |||||
|
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
|
| QuteMol Like | What To Type | |||||
|
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
|
| Simulating Tilt-shift | What To Type | |||||
|
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
|
