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{| align="center" | {| align="center" | ||
− | |+ style=" | + | |+ style="font-size:190%; font-weight: bold; color:#038; padding-bottom: 15px;" |PyMOLWiki Gallery |
|- style="text-align:center; font-weight: bold; font-size:120%; color:#333;" | |- style="text-align:center; font-weight: bold; font-size:120%; color:#333;" | ||
| Cool PyMOL-generated Images and their Scripts.<br/><br/>''[[Talk:Gallery#Adding|Add Your Own]]'' | | Cool PyMOL-generated Images and their Scripts.<br/><br/>''[[Talk:Gallery#Adding|Add Your Own]]'' | ||
+ | |- | ||
|} | |} | ||
+ | |||
+ | |||
+ | |||
+ | {{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 11: | 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 30: | Line 194: | ||
*[[Zoom]] | *[[Zoom]] | ||
*[[Set]] | *[[Set]] | ||
+ | *[[Property_Selectors |Short form Selectors]] | ||
}} | }} | ||
Line 65: | Line 230: | ||
*[[surface_color]] | *[[surface_color]] | ||
*[[surface_type]] | *[[surface_type]] | ||
+ | }} | ||
+ | |||
+ | {{GalleryImage | ||
+ | |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"> | ||
+ | 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 | ||
+ | </source> | ||
+ | |seeAlso= | ||
+ | *[[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]] | ||
+ | *[[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> | ||
}} | }} |
Revision as of 14:14, 1 January 2014
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,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 | |||||
|
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,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 | |||||
|
# 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 | |||||
|
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 | |||||
|
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 | |||||
|
# 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 | |||||
|
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
|