[ Complexity & Simplicity ]

My interactive simulation "Binding & Attraction" at the Concord Consortium. Java plugin needed

 [ Code - Open Source ]

Here, are some useful commands & tips for graphics, rendering & animations under Pymol & VMD: (Try it yourself & Hope you enjoy!)
PyMol
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fetch [yourpdb]
set_color oxygen, [1.0,0.4,0.4]
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
ray 1200, 1200
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ray xxx [xxx=nb pixels]
set antialias, 1
set ray_trace_mode, 0 [value=0, 1, 2, 3]
set ray_opaque_background, off
set cartoon_fancy_helices, 0 [value=0, 1]
set cartoon_side_chain_helper, on [off/on]
set surface_quality, 0 [value up to 2]
set surface_solvent = on
set solvent_radius, 2.0 [or value= 1.0]
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bg_color white
set ray_trace_mode, 1
set ambient, 1
set reflect, 0
set two_sided_lighting, on
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set cartoon_ring_mode, 3
set cartoon_ring_finder, 1
set cartoon_ladder_mode, 1
set cartoon_nucleic_acid_mode, 4
set cartoon_ring_transparency, 0.5
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mset 1, 180
util.mroll 1, 180, 1
set ray_traces_frames, 1
set cache_frames, 0
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  fetch [pdbcode], type=pdb1, multiplex=1, async=1
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Normal Mode for VMD
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vmd_install_extension nmwiz nmwiz_tk "Analysis/Normal Mode Wizard"
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