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PyMOL Wiki - User contributions [en]
2026-05-14T11:58:36Z
User contributions
MediaWiki 1.35.1
https://wiki.pymol.org/index.php?title=Gallery&diff=5922
Gallery
2008-07-23T12:36:10Z
<p>Marcocamma: Correct typo "deday"->"decay"</p>
<hr />
<div>{| align="center"<br />
|+ style="font-size:190%; font-weight: bold; color:#038; padding-bottom: 15px;" |PyMOLWiki Gallery<br />
|- style="text-align:center; font-weight: bold; font-size:120%; color:#333;"<br />
| Cool PyMOL-generated Images and their Scripts.<br/><br/>''[[Talk:Gallery#Adding|Add Your Own]]''<br />
|-<br />
|}<br />
<br />
{{GalleryImage<br />
|image=Gm2.png|size=200px|title=Grid Mode|description=This image shows [[Grid mode|Grid Mode]] in action.<br />
|cmdString=<source lang="python"><br />
fetch 1cll 1sra 1ggz 5pnt 1rlw 1cdy;<br />
set grid_mode<br />
</source><br />
|seeAlso=<br />
*[[Fetch]]<br />
*[[Set]]<br />
*[[grid_mode]]<br />
}}<br />
<br />
{{GalleryImage<br />
|image=Fov60.png|size=200px|title=Cool Perspective|description=This image shows a perspective through [[Field_Of_View]].<br />
|cmdString=<source lang="python"><br />
load prot.pdb;<br />
zoom i. 46-49 and n. CA<br />
set field_of_view, 60<br />
ray<br />
</source><br />
|seeAlso=<br />
*[[Load]]<br />
*[[Ray]]<br />
*[[Zoom]]<br />
*[[Set]]<br />
*[[Property_Selectors |Short form Selectors]]<br />
}}<br />
<br />
{{GalleryImage<br />
|image=Pocket.png|size=200px|title=Representing a binding pocket|description=This image shows a nice way to show binding surfaces<br />
|cmdString=<source lang="python"><br />
load $TUT/1hpv.pdb, tmp<br />
extract lig, organic<br />
extract prot, polymer<br />
delete tmp<br />
<br />
set surface_carve_cutoff, 4.5<br />
set surface_carve_selection, lig<br />
set surface_carve_normal_cutoff, -0.1<br />
<br />
show surface, prot within 8 of lig<br />
set two_sided_lighting<br />
set transparency, 0.5<br />
show sticks, lig<br />
orient lig<br />
<br />
set surface_color, white<br />
set surface_type, 2 # mesh<br />
unset ray_shadows<br />
</source><br />
|seeAlso=<br />
*[[extract]]<br />
*[[delete]]<br />
*[[show]]<br />
*[[set]]<br />
*[[orient]]<br />
*[[surface_carve_cutoff]]<br />
*[[surface_carve_selection]]<br />
*[[surface_carve_normal_cutoff]]<br />
*[[surface_color]]<br />
*[[surface_type]]<br />
}}<br />
<br />
{{GalleryImage<br />
|image=QuteMolLike.png|size=400px|title=QuteMol Like|description=QuteMol like image--modern ''feel'' to it.<br />
|cmdString=<source lang="python"><br />
load $TUT/1hpv.pdb<br />
set_color oxygen, [1.0,0.4,0.4]<br />
set_color nitrogen, [0.5,0.5,1.0]<br />
remove solvent<br />
as spheres<br />
util.cbaw<br />
bg white<br />
set light_count,10<br />
set spec_count,1<br />
set shininess, 10<br />
set specular, 0.25<br />
set ambient,0<br />
set direct,0<br />
set reflect,1.5<br />
set ray_shadow_decay_factor, 0.1<br />
set ray_shadow_decay_range, 2<br />
unset depth_cue<br />
# for added coolness<br />
# set field_of_view, 60<br />
ray<br />
</source><br />
|seeAlso=<br />
*[[Load]]<br />
*[[Set_color]]<br />
*[[Remove]]<br />
*[[Solvent]]<br />
*[[As]]<br />
*[[Util]]<br />
*[[Util.cbaw]]<br />
*[[Bg]]<br />
*[[Light_Count]]<br />
*[[Spec_Count]]<br />
*[[Shininess]]<br />
*[[Specular]]<br />
*[[Ambient]]<br />
*[[Direct]]<br />
*[[Reflect]]<br />
*[[Ray_shadow_decay_factor]]<br />
*[[Ray_shadow_decay_range]]<br />
*[[Unset]]<br />
*[[depth_cue]]<br />
*[[Ray]]<br />
*[[Set]]<br />
*[[Property_Selectors |Short form Selectors]]<br />
}}</div>
Marcocamma