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,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

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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,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

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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

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Complex Stylized Protein

What To Type

Description A Cool, Stylized Rendering See Also 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

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

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Goodsell-like	What To Type
Description Create Goodsell-like images in PyMOL See Also set light_count color ray_shadows ray_trace_mode specular orient ray_trace_gain depth_cue	# 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

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Stylized Ball and Stick

What To Type

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

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Tribute to Irving Geis

What To Type

Description Hemoglobin, image inspired by Irving Geis See Also 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

# 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