Netiquette · Download · News · Gallery · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL
· Video Overview · DSSR v2.5.1 (DSSR Manual) · Homepage
-
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.
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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:
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
-
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.
Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids
Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University