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*[[Zoom]] | *[[Zoom]] | ||
*[[Set]] | *[[Set]] | ||
}} | |||
{{GalleryImage | |||
|images=pocket.png|size=200px|title=Representing a binding pocket|description=This image shows a nice way to show binding surfaces | |||
|cmdString=<source lang="python"> | |||
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 | |||
</source> | |||
|seeAlso= | |||
*[[extract]] | |||
*[[delete]] | |||
*[[show]] | |||
*[[set]] | |||
*[[orient]] | |||
*[[surface_carve_cutoff]] | |||
*[[surface_carve_selection]] | |||
*[[surface_carve_normal_cutoff]] | |||
*[[surface_color]] | |||
*[[surface_type]] | |||
}} | }} | ||
Revision as of 12:27, 31 May 2008
| Cool PyMOL-generated Images and their Scripts |
| Grid Mode | What To Type | |||||
|
fetch 1cll 1sra 1ggz 5pnt 1rlw 1cdy;
set grid_mode
|
| 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
|