Figure 1. Comparison of the hydrogen-bonding interactions, chemical structures

[shuxiang]

Figure 1. Comparison of the hydrogen-bonding interactions, chemical structures, and relative spatial arrangements of nucleotides in the six dominant modes of G·A pairing and in a canonical Watson–Crick G–C pair. Hydrogen bonds are shown by thin dashed lines, with arrows directed toward base/backbone atoms capable of accepting protons. Structures were generated with 3DNA(24) and rendered in PyMOL (www.pymol.org) using the average rigid-body parameters in Table 1 and a canonical A-RNA backbone.(34) Structures are depicted in the standard reference frame of G.(30) Color-coding denotes the mode of base association: sheared m–M (dark blue); imino W–W (gray); m+m (pink); m–m (red); m+W (light blue); m–W (magenta); canonical (white), where the combinations of signs and letters denote the orientation (parallel + /antiparallel –) and the approximate sites (minor, m; major, M; Watson–Crick, W edges) of base association.(27) Interestingly, less than 10% of the + states reflect an anti-to-syn sugar–base rearrangement, and these examples all involve adenine.

[shuxiang]

Figure 1.a
x3dna_utils cp_std rna
rebuild -atomic 1-a.par 1-a.pdb
pymol 1-a.pdb
bg_color white
set ray_opaque_background, off
set ray_shadows,off
preset.ball_and_stick(selection='all', mode=1)
set sphere_scale, 0.18, (all)
set_color mycolor, [51,51,255]
set_bond stick_color, mycolor, all
color mycolor, all
ray

[shuxiang]

Figure 1.b
x3dna_utils cp_std rna
rebuild -atomic 1-b.par
pymol 1-b.pdb
bg_color white
set ray_opaque_background, off
set ray_shadows,off
preset.ball_and_stick(selection='all', mode=1)
set sphere_scale, 0.18, (all)
set_color mycolor, [160,160,160]
set_bond stick_color, mycolor, all
color mycolor, all
ray

[shuxiang]

Figure 1.c
x3dna_utils cp_std rna
rebuild -atomic 1-c.par 1-c.pdb
pymol 1-c.pdb
bg_color white
set ray_opaque_background, off
set ray_shadows,off
preset.ball_and_stick(selection='all', mode=1)
set sphere_scale, 0.18, (all)
set_color mycolor, [255,51,153]
set_bond stick_color, mycolor, all
color mycolor, all
ray

[shuxiang]

Figure 1.d
x3dna_utils cp_std rna
rebuild -atomic 1-d.par 1-d.pdb
pymol 1-d.pdb
bg_color white
set ray_opaque_background, off
set ray_shadows,off
preset.ball_and_stick(selection='all', mode=1)
set sphere_scale, 0.18, (all)
set_color mycolor, [255,51,51]
set_bond stick_color, mycolor, all
color mycolor, all
ray

[shuxiang]

Figure 1.e
x3dna_utils cp_std rna
rebuild -atomic 1-e.par 1-e.pdb
pymol 1-e.pdb
bg_color white
set ray_opaque_background, off
set ray_shadows,off
preset.ball_and_stick(selection='all', mode=1)
set sphere_scale, 0.18, (all)
set_color mycolor, [51,153,255]
set_bond stick_color, mycolor, all
color mycolor, all
ray

[shuxiang]

Figure 1.f
x3dna_utils cp_std rna
rebuild -atomic 1-f.par 1-f.pdb
pymol 1-f.pdb
bg_color white
set ray_opaque_background, off
set ray_shadows,off
preset.ball_and_stick(selection='all', mode=1)
set sphere_scale, 0.18, (all)
set_color mycolor, [255,51,255]
set_bond stick_color, mycolor, all
color mycolor, all
ray

[shuxiang]

Figure 1.g
x3dna_utils cp_std rna
rebuild -atomic 1-g.par 1-g.pdb
pymol 1-g.pdb
bg_color white
set ray_opaque_background, off
set ray_shadows,off
preset.ball_and_stick(selection='all', mode=1)
set sphere_scale, 0.18, (all)
set_color mycolor, [255,255,255]
set_bond stick_color, mycolor, all
color mycolor, all
ray

[shuxiang]

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

1-a.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    6.816843 -4.527391  0.343299   5.599746  -2.494629   -8.234822   0.000     0.000     0.000     0.000     0.000     0.000

1-b.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    0.048750  1.525968 -0.338185   7.312177  -9.915202  -16.193871   0.000     0.000     0.000     0.000     0.000     0.000

1-c.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    -2.676827   -7.299808   -0.098718   -10.314647   9.461635   -152.17256   0.000     0.000     0.000     0.000     0.000     0.000

1-d.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

1-e.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    1.798861 -4.956085 -0.004733  -4.433452  11.665907  -94.003630   0.000     0.000     0.000     0.000     0.000     0.000

1-f.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    3.762906  3.367692  0.284957  -7.853162 -13.928718  101.603333   0.000     0.000     0.000     0.000     0.000     0.000

1-g.par
   1 # base-pairs
   0 # ***local base-pair & step parameters***
#        Shear    Stretch   Stagger   Buckle   Prop-Tw   Opening     Shift     Slide     Rise      Tilt      Roll      Twist
G-C   -0.37   -0.44   -0.18   9.31   -10.39   -1.3  0.000     0.000     0.000     0.000     0.000     0.000

[xiangjun]

Hi Shuxiang,

Thank you for posting these details used to create figure 1 of our ACS Biochemistry paper on G.A pairs. Your efforts serve as another concrete example of how to reproduce results published in a scientific journal. Ironically, reproducibility of scientific publications has become a fashionable topic nowadays, even in leading journals.

Best regards,

Xiang-Jun

PS: You may want to use the code tag (represented by # in the tools menu) to delineate the commands to make them stands out (for easy copy-and-paste). For example, for figure 1A, you could get the following results:

Code: Bash

1. x3dna_utils cp_std rna
2. rebuild -atomic 1-a.par 1-a.pdb
3. pymol 1-a.pdb
4. bg_color white
5. set ray_opaque_background, off
6. set ray_shadows,off
7. preset.ball_and_stick(selection='all', mode=1)
8. set sphere_scale, 0.18, (all)
9. set_color mycolor, [51,51,255]
10. set_bond stick_color, mycolor, all
11. color mycolor, all
12. ray

[shuxiang]

There are many versions and modifications of the figures. For some figures, I don't remember exactly what the codes I once used. I need some time to figure them out.