Gallery

PyMOLWiki Gallery

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

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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

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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. 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