Difference between revisions of "Gallery"
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* [[ray_trace_frames]] | * [[ray_trace_frames]] | ||
* [[movie.roll]] | * [[movie.roll]] | ||
+ | }} | ||
+ | |||
+ | |||
+ | {{GalleryImage | ||
+ | | title=Blobby Main Chain | ||
+ | | image=Gallery dark tube mc.png | ||
+ | | description=Main chain as a darkened tube with special shading | ||
+ | | seeAlso= | ||
+ | * [[remove]] | ||
+ | * [[alter]] | ||
+ | * [[gaussian_resolution]] | ||
+ | * [[map_new]] | ||
+ | * [[spectrum]] | ||
+ | * [[light_count]] | ||
+ | * [[spec_count]] | ||
+ | * [[shininess]] | ||
+ | * [[reflect]] | ||
+ | * [[direct]] | ||
+ | * [[ambient]] | ||
+ | * [[ray_shadow_decay_factor]] | ||
+ | * [[ray_shadow_decay_range]] | ||
+ | * [[fetch]] | ||
+ | | cmdString=<source lang="python"> | ||
+ | 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,10 | ||
+ | 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 | ||
+ | </source> | ||
+ | }} | ||
+ | |||
+ | {{GalleryImage | ||
+ | | title=Blobby Side Chains | ||
+ | | image=Gallery blob sc.png | ||
+ | | description=Main chain as tube with gaussian surfaced side chains | ||
+ | | seeAlso= | ||
+ | * [[cartoon]] | ||
+ | * [[show_as]] | ||
+ | * [[fetch]] | ||
+ | * [[cartoon_tube_radius]] | ||
+ | * [[cartoon_color]] | ||
+ | * [[cartoon_side_chain_helper]] | ||
+ | * [[alter]] | ||
+ | * [[gaussian_resolution]] | ||
+ | * [[map_new]] | ||
+ | * [[isosurface]] | ||
+ | * [[color]] | ||
+ | * [[hide]] | ||
+ | | cmdString=<source lang="python"> | ||
+ | # 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 | ||
+ | </source> | ||
}} | }} |
Revision as of 13:01, 18 November 2011
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;
|
Grid Mode | What To Type | |||||
|
fetch 1cll 1sra 1ggz 5pnt 1rlw 1cdy;
set grid_mode
Hint: You may wish to execute the 'reset' command on the command line after running the above commands to get full molecules in view of window and centered in a more useable manner. |
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
|
Ray-normal-based transparency | What To Type | |||||
|
# 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...
|
Blobby Main Chain | What To Type | |||||
|
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,10
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
|
Blobby Side Chains | What To Type | |||||
|
# 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
|