Difference between revisions of "Gallery"
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Marcocamma (talk | contribs) m (Correct typo "deday"->"decay") |
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| + | {{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_trace_mode]] | ||
| + | *[[get_view]] | ||
| + | *[[clip]] | ||
| + | *[[as]] | ||
| + | *[[surface]] | ||
| + | *[[cartoon]] | ||
| + | *[[ray_interior_color]] | ||
| + | *[[color]] | ||
| + | *[[ray]] | ||
| + | *[[save]] | ||
| + | *[[util.cbc]] | ||
| + | *[[opaque_background]] | ||
| + | *[[save]] | ||
| + | *[[system]] | ||
| + | }} | ||
| + | |||
{{GalleryImage | {{GalleryImage | ||
Revision as of 14:51, 25 August 2008
| Cool PyMOL-generated Images and their Scripts. Add Your Own |
| A "Sliced" Image | What To Type | |||||
|
# 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
|
| 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
|
| 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,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
|
