Figure 4. Succession of configurations illustrating the rigid-body motions

[shuxiang]

Figure 4. Succession of configurations illustrating the rigid-body motions that transform the associations of G and A between different pairing modes. Images are of adenine oriented with respect to a common coordinate frame on guanine. Structures are generated with 3DNA(24) using the average rigid-body parameters reported in Table 1. Base pairs are color-coded by interaction mode (Figures 1–3), with the minor (II) substates of m±W and m–M pairs noted by lighter hues. Pathways connect (a) antiparallel m–m, m–WI, m–WII, W–W, m–MI, and m–MII states and (b) parallel m+m, m+WII, m+WI, and m+M states. Note the counterclockwise rotation of ribose C1′ atoms (darkened spheres) along the top-to-bottom transformation of antiparallel pairs and the clockwise rotation along the corresponding progression of parallel pairs. Hydrogen bonds between base atoms are depicted by thin dashed lines.

[shuxiang]

4-a-1.par
   1 # base-pairs
   0 # ***local base-pair & step parameters***
#        Shear    Stretch   Stagger   Buckle   Prop-Tw   Opening     Shift     Slide     Rise      Tilt      Roll      Twist
G-A  -1.880278  7.232870 -0.008889 -3.494259  -12.964537  148.270648   0.000     0.000     0.000     0.000     0.000     0.000


x3dna_utils cp_std rna
rebuild -atomic 4-a-1.par 01_out.pdb
pymol 01_out.pdb
bg_color white
set ray_opaque_background, off
set ray_shadows,off
as sticks
set valence, 0
set stick_radius, 0.1, (all)
set_color mycolor1, [255,51,51]
color mycolor1, 01_out
set_bond stick_color, mycolor1, 01
show spheres, name C1'
color grey20, name C1'
set sphere_scale, 0.0, (all)
set stick_radius, 0.13, (all)
set valence,0
color grey80, 01 and resn G
set_bond stick_color, grey80, 01_out and resn G

Use Photoshop to add labels and dashed lines on each figure.