Gallery

PyMOLWiki Gallery

Cool PyMOL-generated Images and their Scripts. Add Your Own

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Complex B&W outline representation

What To Type

Description Making a B&W outlined image with depth. See Also bg_color get_view Mouse Modes (no good reference for this?) png putty ray ray_trace_mode set set_view single word property selectors util.cbag

# 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) Version A: with all the elements except for the helix. This will become the background. 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: move the model around until you visually see the part to remove switch your Mouse Mode to 3-button viewing, then use the +Box selection (Shift+Left mouse) to select the 'background' portion to hide. choose Hide>Everything for the selection 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). Load the two versions. Select the white background in Version B, then choose Select>Color Range... Make sure 'Select' is set to 'Sampled Colors', and 'Fuzziness' is set to 150, then click okay. delete the white selection, then choose Select>All copy the picture, then switch to Version A and paste the selection (it should paste into its own layer as 'Layer 1') Click on 'Layer 0' (which is Version A) and change its opacity to 30% Create a new layer under 'Layer 0' which is filled with white only (or whatever background color you like) Click on 'Layer 1' (which is Version B), and using the Move tool (and nudge), align the molecules in 'Layer 1' to 'Layer 0' 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). Admire your handiwork; put it in a publication, presentation, or poster.

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A "Sliced" Image

What To Type

Description A more complex example of how to create an image of a slice. See Also load orient set unset depth_cue ray_shadows ray_trace_mode Get_View clip as surface cartoon ray_interior_color color ray save util.cbc opaque_background save system

# 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

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Grid Mode	What To Type
Description This image shows Grid Mode in action. See Also Fetch Set grid_mode	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.

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Cool Perspective	What To Type
Description This image shows a perspective through Field_Of_View. See Also Load Ray Zoom Set Short form Selectors	load prot.pdb; zoom i. 46-49 and n. CA set field_of_view, 60 ray

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Representing a binding pocket	What To Type
Description This image shows a nice way to show binding surfaces See Also extract delete show set orient surface_carve_cutoff surface_carve_selection surface_carve_normal_cutoff surface_color surface_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

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QuteMol Like	What To Type
Description QuteMol like image--modern feel to it. Check out the movie. See Also Load Set_color Remove Solvent As Util Util.cbaw Bg Light_Count Spec_Count Shininess Specular Ambient Direct Reflect Ray_shadow_decay_factor Ray_shadow_decay_range Unset depth_cue Ray Set Short form Selectors	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

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Simulating Tilt-shift	What To Type
Description Tilt shift simulation See Also fetch show_as h_add color	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

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Ray-normal-based transparency

What To Type

Description Ray-normal-based transparency See Also 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

# 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...

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Blobby Main Chain

What To Type

Description Main chain as a darkened tube with special shading See Also remove alter gaussian_resolution map_new spectrum light_count spec_count shininess reflect direct ambient ray_shadow_decay_factor ray_shadow_decay_range fetch

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

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Blobby Side Chains

What To Type

Description Main chain as tube with gaussian surfaced side chains See Also cartoon show_as fetch cartoon_tube_radius cartoon_color cartoon_side_chain_helper alter gaussian_resolution map_new isosurface color hide

# 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

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Smooth surface with ligand

What To Type

Description Gaussian abstracted surface colored by underlying b-factors and shown with ligand See Also ramp_new show_as gaussian_resolution fetch isosurface spectrum set alter get_view set_view

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