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m (Correct typo "deday"->"decay")
 
m (1 revision)
 
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|-
 
|-
 
|}
 
|}
 +
 +
 +
 +
{{GalleryImage
 +
<!-- This creates a row entry for the Gallery section -->
 +
|<!-- Image -->
 +
image=BW_raytraced_complex_image.jpg|size=200px
 +
|<!-- Title above image -->
 +
title=Complex B&W outline representation
 +
|<!-- 'Description' section (shows up below image)-->
 +
description=Making a B&W outlined image with depth.
 +
|<!-- 'What to Type' section -->
 +
cmdString=<source lang="python">
 +
# 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;
 +
</source>
 +
Now, you'll need to save multiple versions of your model. (use '''ray''', then '''png''' ''<filename>'' to save each version)<ol>
 +
<li> Version A: with all the elements except for the helix. This will become the background.</li>
 +
<li> Version B: with the 'front' elements, and the helix. Basically this is just a few 'layers' of lipid, with the helix among them.  To do this:</li><ol type="a">
 +
<li>move the model around until you visually see the part to remove</li>
 +
<li>switch your Mouse Mode to 3-button viewing, then use the +Box selection (Shift+Left mouse) to select the 'background' portion to hide.</li>
 +
<li>choose Hide>Everything for the selection</li>
 +
<li>use the code from get_view to go back to the original view</li>
 +
</ol></ol>
 +
Finally, you will need to compose the image in Photoshop (or Gimp, here I'll use Photoshop).<ol>
 +
<li>Load the two versions.</li>
 +
<li>Select the white background in Version B, then choose Select>Color Range...</li>
 +
<li>Make sure 'Select' is set to 'Sampled Colors', and 'Fuzziness' is set to 150, then click okay.</li>
 +
<li>delete the white selection, then choose Select>All</li>
 +
<li>copy the picture, then switch to Version A and paste the selection (it should paste into its own layer as 'Layer 1')</li>
 +
<li>Click on 'Layer 0' (which is Version A) and change its opacity to 30%</li>
 +
<li>Create a new layer under 'Layer 0' which is filled with white only (or whatever background color you like)</li>
 +
<li>Click on 'Layer 1' (which is Version B), and using the Move tool (and nudge), align the molecules in 'Layer 1' to 'Layer 0'</li>
 +
<li>Some parts of 'Layer 1' are transparent and shouldn't be.  Using the Paint Bucket tool fill in these areas with white (or whichever color you find appropriate).</li>
 +
<li>Admire your handiwork; put it in a publication, presentation, or poster.</li></ol>
 +
|<!-- 'See Also' section (shows up below image)-->
 +
seeAlso=
 +
* [[Bg_Color|bg_color]]
 +
* [[Get_View|get_view]]
 +
* Mouse Modes (no good reference for this?)
 +
* [[png]]
 +
* [[Cartoon#Sausage_Representation|putty]]
 +
* [[ray]]
 +
* [[Ray#Modes|ray_trace_mode]]
 +
* [[set]]
 +
* [[Set_View|set_view]]
 +
* [[Single-word_Selectors |single word property selectors]]
 +
* [[Advanced_Coloring#Coloring_by_atom_type|util.cbag]]
 +
}}
 +
 +
 +
 +
{{GalleryImage
 +
|image=Image_merged.png|size=200px|title=A "Sliced" Image|description=A more complex example of how to create an image of a slice.
 +
|cmdString=<source lang="python">
 +
# 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
 +
</source>
 +
|seeAlso=
 +
*[[load]]
 +
*[[orient]]
 +
*[[set]]
 +
*[[unset]]
 +
*[[depth_cue]]
 +
*[[ray_shadows]]
 +
*[[Ray#Modes|ray_trace_mode]]
 +
*[[Get_View|get_view]]
 +
*[[clip]]
 +
*[[as]]
 +
*[[surface]]
 +
*[[cartoon]]
 +
*[[ray_interior_color]]
 +
*[[color]]
 +
*[[ray]]
 +
*[[save]]
 +
*[[util.cbc]]
 +
*[[opaque_background]]
 +
*[[save]]
 +
*[[system]]
 +
}}
 +
  
 
{{GalleryImage
 
{{GalleryImage
Line 12: Line 174:
 
set grid_mode
 
set grid_mode
 
</source>
 
</source>
 +
'''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.
 
|seeAlso=
 
|seeAlso=
 
*[[Fetch]]
 
*[[Fetch]]
Line 70: Line 233:
  
 
{{GalleryImage
 
{{GalleryImage
−
|image=QuteMolLike.png|size=400px|title=QuteMol Like|description=QuteMol like image--modern ''feel'' to it.
+
|image=QuteMolLike.png|size=400px|title=QuteMol Like|description=QuteMol like image--modern ''feel'' to it.  Check out the [[Media:Depthmol.mpeg|movie]].
 
|cmdString=<source lang="python">
 
|cmdString=<source lang="python">
 
load $TUT/1hpv.pdb
 
load $TUT/1hpv.pdb
Line 79: Line 242:
 
util.cbaw
 
util.cbaw
 
bg white
 
bg white
−
set light_count,10
+
set light_count,8
 
set spec_count,1
 
set spec_count,1
 
set shininess, 10
 
set shininess, 10
Line 116: Line 279:
 
*[[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]]
 +
}}
 +
 +
 +
{{GalleryImage
 +
|image=Rnt.png|size=500px|title=Ray-normal-based transparency|description=Ray-normal-based transparency
 +
|cmdString=<source lang="python">
 +
# 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...
 +
</source>
 +
|seeAlso=
 +
* [[surface_color]]
 +
* [[surface_mode]]
 +
* [[transparency_mode]]
 +
* [[transparency]]
 +
* [[ray_transparency_oblique]]
 +
* [[ray_transparency_oblique_power]]
 +
* [[ray_transparency_contrast]]
 +
* [[fetch]]
 +
* [[orient]]
 +
* [[zoom]]
 +
* [[show]]
 +
* [[sticks]]
 +
* [[lines]]
 +
* [[cache_frames]]
 +
* [[mset]]
 +
* [[ray_trace_frames]]
 +
* [[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,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
 +
</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>
 +
}}
 +
 +
{{GalleryImage
 +
| title=Smooth surface with ligand
 +
| image=Abs surf.png
 +
| description=Gaussian abstracted surface colored by underlying b-factors and shown with ligand
 +
| seeAlso=
 +
* [[ramp_new]]
 +
* [[show_as]]
 +
* [[gaussian_resolution]]
 +
* [[fetch]]
 +
* [[isosurface]]
 +
* [[spectrum]]
 +
* [[set]]
 +
* [[alter]]
 +
* [[Get_View|get_view]]
 +
* [[set_view]]
 +
| 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, 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
 +
</source>
 +
}}
 +
 +
{{GalleryImage
 +
| title=Complex Stylized Protein
 +
| image=Cool.png
 +
| description=A Cool, Stylized Rendering
 +
| seeAlso=
 +
* [[field_of_view]]
 +
* [[set]]
 +
* [[light_count]]
 +
* [[ambient]]
 +
* [[ramp_new]]
 +
* [[color]]
 +
* [[surface_quality]]
 +
* [[transparency]]
 +
* [[ambient_occlusion_mode]]
 +
* [[spec_reflect]]
 +
* [[spec_direct]]
 +
* [[disable]]
 +
* [[ray_shadows]]
 +
* [[ray_opaque_background]]
 +
* [[ray_transparency_oblique]]
 +
* [[ray_transparency_oblique_power]]
 +
* [[ray_transparency_contrast]]
 +
| cmdString=<source lang="python">
 +
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
 +
</source>
 +
}}
 +
 +
 +
{{GalleryImage
 +
| title=Goodsell-like
 +
| image=Goodsell_like2.png
 +
| description=Create Goodsell-like images in PyMOL
 +
| seeAlso=
 +
* [[set]]
 +
* [[light_count]]
 +
* [[color]]
 +
* [[ray_shadows]]
 +
* [[ray_trace_mode]]
 +
* [[specular]]
 +
* [[orient]]
 +
* [[ray_trace_gain]]
 +
* [[depth_cue]]
 +
| cmdString=<source lang="python">
 +
# 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
 +
</source>
 +
}}
 +
 +
 +
{{GalleryImage
 +
| title=Stylized Ball and Stick
 +
| image=Stylized bns.png
 +
| description=Stylized Ball and Sticks
 +
| seeAlso=
 +
| cmdString=<source lang="python">
 +
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
 +
</source>
 +
}}
 +
 +
{{GalleryImage
 +
| title=Tribute to Irving Geis
 +
| image=Irvinggeis pymol 500px.png
 +
| description=Hemoglobin, image inspired by Irving Geis
 +
| seeAlso=seeAlso
 +
* [[iterate]]
 +
* [[stick_radius]]
 +
* [[sphere_scale]]
 +
* [[gaussian_b_floor]]
 +
* [[gaussian_resolution]]
 +
* [[map_new]]
 +
* [[isosurface]]
 +
* [[set_color]]
 +
* [[pseudoatom]]
 +
* [[ramp_new]]
 +
* [[cartoon_ring_finder]]
 +
* [[cartoon_ring_mode]]
 +
* [[cartoon_ring_width]]
 +
* [[cartoon_ring_transparency]]
 +
* [[bg_color]]
 +
* [[field_of_view]]
 +
* [[set_view]]
 +
* [[ray_trace_mode]]
 +
* [[ray_shadow]]
 +
* [[light_count]]
 +
* [[light]]
 +
* [[ambient]]
 +
* [[direct]]
 +
* [[specular]]
 +
* [[shininess]]
 +
* [[specular_intensity]]
 +
* [[reflect]]
 +
* [[reflect_power]]
 +
* [[depth_cue]]
 +
* [[fog_start]]
 +
* [[antialias]]
 +
* [[ray]]
 +
| cmdString=<source lang="python">
 +
# I've always appreciated the simplicity of Irving Geis's designs.
 +
# Here, I've reproduced one of his famous images of hemoglobin.
 +
 +
fetch 1buw
 +
remove solvent
 +
hide all
 +
 +
# Irving Geis shows only the carbonyl carbon atoms in his structure,
 +
# so build a backbone made up of only those atoms
 +
 +
create bbC_A, n. C in /1buw/A/A
 +
stored.bbC = []
 +
iterate (bbC_A), stored.bbC.append(index)
 +
for i in stored.bbC: cmd.bond("i. %s in bbC_A" % str(i), "i. %s in bbC_A" % str(i+1))
 +
 +
create bbC_B, n. C in /1buw/B/B
 +
stored.bbC = []
 +
iterate (bbC_B), stored.bbC.append(index)
 +
for i in stored.bbC: cmd.bond("i. %s in bbC_B" % str(i), "i. %s in bbC_B" % str(i+1))
 +
 +
create bbC_C, n. C in /1buw/C/C
 +
stored.bbC = []
 +
iterate (bbC_C), stored.bbC.append(index)
 +
for i in stored.bbC: cmd.bond("i. %s in bbC_C" % str(i), "i. %s in bbC_C" % str(i+1))
 +
 +
create bbC_D, n. C in /1buw/D/D
 +
stored.bbC = []
 +
iterate (bbC_D), stored.bbC.append(index)
 +
for i in stored.bbC: cmd.bond("i. %s in bbC_D" % str(i), "i. %s in bbC_D" % str(i+1))
 +
 +
show sticks, /bbC_A or /bbC_B or /bbC_C or /bbC_D
 +
set stick_radius, 0.2
 +
show spheres, bbC_A or bbC_B or bbC_C or bbC_D
 +
set sphere_scale, 0.4
 +
color white, bbC_A or bbC_B or bbC_C or bbC_D
 +
 +
# Create isosurface maps to draw the backbone surface as a tube
 +
 +
set gaussian_b_floor, 40
 +
set gaussian_resolution, 5
 +
 +
map_new mapA, gaussian, 1, bbC_A, 60
 +
isosurface isoA, mapA, 15
 +
map_new mapB, gaussian, 1, bbC_B, 60
 +
isosurface isoB, mapB, 15
 +
map_new mapC, gaussian, 1, bbC_C, 60
 +
isosurface isoC, mapC, 15
 +
map_new mapD, gaussian, 1, bbC_D, 60
 +
isosurface isoD, mapD, 15
 +
 +
set transparency, 0.2
 +
 +
# Create a color gradient with a color ramp from a pseudoatom
 +
 +
set_color tubedark, [67, 45, 133]
 +
set_color tubelight, [178, 177, 204]
 +
 +
pseudoatom pseud, pos=[142.982, 26.505, 86.321]
 +
hide /pseud
 +
 +
ramp_new colorRamp, pseud, range=[0,100,142], color=[tubedark, tubedark, tubelight]
 +
set surface_color, colorRamp, isoA
 +
set surface_color, colorRamp, isoB
 +
set surface_color, colorRamp, isoC
 +
set surface_color, colorRamp, isoD
 +
disable colorRamp
 +
 +
# Represent the heme rings as cartoons
 +
 +
create hemes, /1buw/E/A or /1buw/G/B or /1buw/I/C or /1buw/K/D
 +
# Recreate a lost bond...
 +
bond /hemes/K/D/HEM`147/FE, /hemes/K/D/HEM`147/NC
 +
show_as cartoon, hemes
 +
set cartoon_ring_finder, 4
 +
set cartoon_ring_mode, 3
 +
set cartoon_ring_width, 0.3
 +
set cartoon_ring_transparency, 0
 +
color ruby, hemes
 +
 +
# Represent the heme iron ions as spheres
 +
 +
create irons, e. Fe
 +
show_as spheres, irons
 +
set sphere_scale, 0.6, irons
 +
color darksalmon, irons
 +
 +
# Hide ligands bound to hemes
 +
 +
hide //F or //H or //J or //L
 +
 +
# Hide atoms that stick out of the surface (mostly terminal atoms)
 +
 +
hide /bbC_C/C/C/141
 +
hide /bbC_A/A/A/141
 +
hide /bbC_D/D/D/144
 +
hide /bbC_D/D/D/1
 +
 +
# Display settings
 +
 +
set_color bground, [252, 247, 229]
 +
bg_color bground
 +
set field_of_view, 5
 +
set_view (\
 +
    0.568997085,    0.032208484,    0.821707368,\
 +
    0.172765702,    0.972248971,  -0.157743633,\
 +
    -0.803984761,    0.231720015,    0.547644258,\
 +
    0.000000000,    0.000000000, -691.255310059,\
 +
    48.556941986,  45.649765015,  22.998313904,\
 +
  579.895507812,  802.615112305,    5.000000000 )
 +
 +
set ray_trace_mode, 1
 +
set ray_shadow, 0
 +
set light_count, 2
 +
set light, [0, 0, -100]
 +
set ambient, 0
 +
set direct, 0.7
 +
set specular, 1
 +
set shininess, 5
 +
set specular_intensity, 0.3
 +
set reflect, 0.2
 +
set reflect_power, 1
 +
set depth_cue, 1
 +
set fog_start, 0.45
 +
set antialias, 3
 +
 +
ray 1280, 960
 +
</source>
 
}}
 
}}

Latest revision as of 06:13, 6 March 2017

PyMOLWiki Gallery
Cool PyMOL-generated Images and their Scripts.

Add Your Own



Complex B&W outline representation What To Type
BW raytraced complex image.jpg
Description
Making a B&W outlined image with depth.


See Also
 
# 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;
Now, you'll need to save multiple versions of your model. (use ray, then png <filename> to save each version)
  1. Version A: with all the elements except for the helix. This will become the background.
  2. Version B: with the 'front' elements, and the helix. Basically this is just a few 'layers' of lipid, with the helix among them. To do this:
    1. move the model around until you visually see the part to remove
    2. switch your Mouse Mode to 3-button viewing, then use the +Box selection (Shift+Left mouse) to select the 'background' portion to hide.
    3. choose Hide>Everything for the selection
    4. use the code from get_view to go back to the original view
Finally, you will need to compose the image in Photoshop (or Gimp, here I'll use Photoshop).
  1. Load the two versions.
  2. Select the white background in Version B, then choose Select>Color Range...
  3. Make sure 'Select' is set to 'Sampled Colors', and 'Fuzziness' is set to 150, then click okay.
  4. delete the white selection, then choose Select>All
  5. copy the picture, then switch to Version A and paste the selection (it should paste into its own layer as 'Layer 1')
  6. Click on 'Layer 0' (which is Version A) and change its opacity to 30%
  7. Create a new layer under 'Layer 0' which is filled with white only (or whatever background color you like)
  8. Click on 'Layer 1' (which is Version B), and using the Move tool (and nudge), align the molecules in 'Layer 1' to 'Layer 0'
  9. Some parts of 'Layer 1' are transparent and shouldn't be. Using the Paint Bucket tool fill in these areas with white (or whichever color you find appropriate).
  10. Admire your handiwork; put it in a publication, presentation, or poster.



A "Sliced" Image What To Type
Image merged.png
Description
A more complex example of how to create an image of a slice.


See Also
 
# 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
Gm2.png
Description
This image shows Grid Mode in action.


See Also
 
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
Fov60.png
Description
This image shows a perspective through Field_Of_View.


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


Representing a binding pocket What To Type
Pocket.png
Description
This image shows a nice way to show binding surfaces


See Also
 
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
QuteMolLike.png
Description
QuteMol like image--modern feel to it. Check out the movie.


See Also
 
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


Simulating Tilt-shift What To Type
Tilt shift.png
Description
Tilt shift simulation


See Also
 
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
Rnt.png
Description
Ray-normal-based transparency


See Also
 
# 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
Gallery dark tube mc.png
Description
Main chain as a darkened tube with special shading


See Also
 
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


Blobby Side Chains What To Type
Gallery blob sc.png
Description
Main chain as tube with gaussian surfaced side chains


See Also
 
# 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


Smooth surface with ligand What To Type
Abs surf.png
Description
Gaussian abstracted surface colored by underlying b-factors and shown with ligand


See Also
 
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


Complex Stylized Protein What To Type
Cool.png
Description
A Cool, Stylized Rendering


See Also
 
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


Goodsell-like What To Type
Goodsell like2.png
Description
Create Goodsell-like images in PyMOL


See Also
 
# 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


Stylized Ball and Stick What To Type
Stylized bns.png
Description
Stylized Ball and Sticks


See Also
 
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


Tribute to Irving Geis What To Type
Irvinggeis pymol 500px.png
Description
Hemoglobin, image inspired by Irving Geis


See Also

seeAlso 

# I've always appreciated the simplicity of Irving Geis's designs. 
# Here, I've reproduced one of his famous images of hemoglobin.

fetch 1buw
remove solvent
hide all

# Irving Geis shows only the carbonyl carbon atoms in his structure,
# so build a backbone made up of only those atoms

create bbC_A, n. C in /1buw/A/A
stored.bbC = []
iterate (bbC_A), stored.bbC.append(index)
for i in stored.bbC: cmd.bond("i. %s in bbC_A" % str(i), "i. %s in bbC_A" % str(i+1))

create bbC_B, n. C in /1buw/B/B
stored.bbC = []
iterate (bbC_B), stored.bbC.append(index)
for i in stored.bbC: cmd.bond("i. %s in bbC_B" % str(i), "i. %s in bbC_B" % str(i+1))

create bbC_C, n. C in /1buw/C/C
stored.bbC = []
iterate (bbC_C), stored.bbC.append(index)
for i in stored.bbC: cmd.bond("i. %s in bbC_C" % str(i), "i. %s in bbC_C" % str(i+1))

create bbC_D, n. C in /1buw/D/D
stored.bbC = []
iterate (bbC_D), stored.bbC.append(index)
for i in stored.bbC: cmd.bond("i. %s in bbC_D" % str(i), "i. %s in bbC_D" % str(i+1))

show sticks, /bbC_A or /bbC_B or /bbC_C or /bbC_D
set stick_radius, 0.2
show spheres, bbC_A or bbC_B or bbC_C or bbC_D
set sphere_scale, 0.4
color white, bbC_A or bbC_B or bbC_C or bbC_D

# Create isosurface maps to draw the backbone surface as a tube

set gaussian_b_floor, 40
set gaussian_resolution, 5

map_new mapA, gaussian, 1, bbC_A, 60
isosurface isoA, mapA, 15
map_new mapB, gaussian, 1, bbC_B, 60
isosurface isoB, mapB, 15
map_new mapC, gaussian, 1, bbC_C, 60
isosurface isoC, mapC, 15
map_new mapD, gaussian, 1, bbC_D, 60
isosurface isoD, mapD, 15

set transparency, 0.2

# Create a color gradient with a color ramp from a pseudoatom

set_color tubedark, [67, 45, 133]
set_color tubelight, [178, 177, 204]

pseudoatom pseud, pos=[142.982, 26.505, 86.321]
hide /pseud

ramp_new colorRamp, pseud, range=[0,100,142], color=[tubedark, tubedark, tubelight]
set surface_color, colorRamp, isoA
set surface_color, colorRamp, isoB
set surface_color, colorRamp, isoC
set surface_color, colorRamp, isoD
disable colorRamp

# Represent the heme rings as cartoons

create hemes, /1buw/E/A or /1buw/G/B or /1buw/I/C or /1buw/K/D
# Recreate a lost bond...
bond /hemes/K/D/HEM`147/FE, /hemes/K/D/HEM`147/NC
show_as cartoon, hemes
set cartoon_ring_finder, 4
set cartoon_ring_mode, 3
set cartoon_ring_width, 0.3
set cartoon_ring_transparency, 0
color ruby, hemes

# Represent the heme iron ions as spheres

create irons, e. Fe
show_as spheres, irons
set sphere_scale, 0.6, irons
color darksalmon, irons

# Hide ligands bound to hemes

hide //F or //H or //J or //L

# Hide atoms that stick out of the surface (mostly terminal atoms)

hide /bbC_C/C/C/141
hide /bbC_A/A/A/141
hide /bbC_D/D/D/144
hide /bbC_D/D/D/1

# Display settings

set_color bground, [252, 247, 229]
bg_color bground
set field_of_view, 5
set_view (\
     0.568997085,    0.032208484,    0.821707368,\
     0.172765702,    0.972248971,   -0.157743633,\
    -0.803984761,    0.231720015,    0.547644258,\
     0.000000000,    0.000000000, -691.255310059,\
    48.556941986,   45.649765015,   22.998313904,\
   579.895507812,  802.615112305,    5.000000000 )

set ray_trace_mode, 1
set ray_shadow, 0
set light_count, 2
set light, [0, 0, -100]
set ambient, 0
set direct, 0.7
set specular, 1
set shininess, 5
set specular_intensity, 0.3
set reflect, 0.2
set reflect_power, 1
set depth_cue, 1
set fog_start, 0.45
set antialias, 3

ray 1280, 960
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