Pymol Example I

After making a canonical A-RNA base-pair step with 3DNA and centering it on the middle reference frame, one can follow-up with this pymol exercise.

load arna_m.pdb
load arna_mm.r3d 
as surface 
set solvent_radius, 0.6 
set surface_quality, 1 
pseudoatom xx, pos=(0,0,0), label=origin 
ramp_new proximityRamp, xx, selection=all, range=[0,15], color=rainbow 
set surface_color, proximityRamp, all 
recolor; rebuild 
set sphere_scale, 0.3, xx 
as sphere, xx 
set transparency, 0.4 
show cgo 

You can also dowload a bash script to carry out the exercise: