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General discussions (Q&As) / Re: Opening values and the definition for base-pair parameters
« Last post by xiangjun on February 06, 2025, 11:14:10 am »Hi Jing,
Thanks for your follow up, and for providing images that illustrate G.G pairs with opening around 180 and 90 degrees. It would have been more helpful if you attached the corresponding PDB files. When posting questions in the future, thinks about providing (mininal) examples so others can *reproduce* the cases.
Now I understand the question you're asking. Let's use a G+G pair in G-tetrad of G-quadruplexes as an example, which has an opening around 90 degrees. Assuming you have downloaded the coordinates file `5ua3.pdb` for PDB entry 5ua3 on "Crystal structure of a DNA G-quadruplex with a cytosine bulge". Please try the following DSSR commands:
Load `5ua3-GG-frame1.pml` into PyMOL to see the attached image where the (`slim`) base blocks are nearly perpendicular, corresponding to an opening angle of ~90 degrees.
Analyze `5ua3-GG.pdb` (or `5ua3-GG-frame1.pdb`) with `--more` option to see the six base-pair parameters, including opening.
Note that the opening is reported as `-89.63` --- if you try to align A.DG6 to A.DG1, you need to rotate ~`-90` degrees as can be seen in the attached images. If you swap the pair, the opening would be ~`+90` degrees. See the [2003 3DNA paper in NAR](https://doi.org/10.1093/nar/gkg680), specifically the section "Base pair parameters".
With a clear understand of the above example, you should have little difficult in understanding opening ~180 degrees. You are suggested to follow the above example on one of such cases, and report back your findings.
Note that 3DNA/DSSR report angular parameters in the range of [0, +-180] instead of [0, 360]. So opening of `-175` is not that much a difference from `+175` (vs `+185`). Also notice the opposite sign of opening for M+N vs N+M pairs.
Please read the [DSSR manual](http://docs.x3dna.org/dssr-manual.pdf) and the [practical guide for the DSSR-PyMOL](http://skmatic.x3dna.org/dssr-schematic-guide.pdf) article.
Best regards,
Xiang-Jun
Quote
I have attached several pictures here. They are G and G pairs. The first two are with the opening \~180, the third picture is with \~-180, and the last two are with \~90.
Thanks for your follow up, and for providing images that illustrate G.G pairs with opening around 180 and 90 degrees. It would have been more helpful if you attached the corresponding PDB files. When posting questions in the future, thinks about providing (mininal) examples so others can *reproduce* the cases.
Now I understand the question you're asking. Let's use a G+G pair in G-tetrad of G-quadruplexes as an example, which has an opening around 90 degrees. Assuming you have downloaded the coordinates file `5ua3.pdb` for PDB entry 5ua3 on "Crystal structure of a DNA G-quadruplex with a cytosine bulge". Please try the following DSSR commands:
Code: [Select]
# This extract DG1 and DG6 from chain A into file 5ua3-GG.pdb
x3dna-dssr -i=5ua3.pdb --select-residue='A 1+6' -o=5ua3-GG.pdb
# Set the pair into the base reference frame of A.DG1
x3dna-dssr -i=5ua3-GG.pdb --frame='A.1' -o=5ua3-GG-frame1.pdb
# Generate the schematic with base blocks
x3dna-dssr -i=5ua3-GG-frame1.pdb --cartoon-block=sticks-label --block-file=slim-outline -o=5ua3-GG-frame1.pmlLoad `5ua3-GG-frame1.pml` into PyMOL to see the attached image where the (`slim`) base blocks are nearly perpendicular, corresponding to an opening angle of ~90 degrees.
Analyze `5ua3-GG.pdb` (or `5ua3-GG-frame1.pdb`) with `--more` option to see the six base-pair parameters, including opening.
Code: [Select]
x3dna-dssr -i=5ua3-GG.pdb --more
# With the following detailed information:
List of 1 base pair
nt1 nt2 bp name Saenger LW DSSR
1 A.DG1 A.DG6 G+G -- 06-VI cWH cW+M
[-131.0(anti) ~C2'-endo lambda=62.6] [-128.4(anti) ~C2'-endo lambda=28.0]
d(C1'-C1')=11.59 d(N1-N9)=9.65 d(C6-C8)=9.30 tor(C1'-N1-N9-C1')=10.9
H-bonds[2]: "N1(imino)-O6(carbonyl)[2.95],N2(amino)-N7[2.91]"
interBase-angle=1 Simple-bpParams: Shear=-2.67 Stretch=2.83 Buckle=-0.8 Propeller=0.5
bp-pars: [1.61 3.54 -0.15 0.14 0.94 -89.63]Note that the opening is reported as `-89.63` --- if you try to align A.DG6 to A.DG1, you need to rotate ~`-90` degrees as can be seen in the attached images. If you swap the pair, the opening would be ~`+90` degrees. See the [2003 3DNA paper in NAR](https://doi.org/10.1093/nar/gkg680), specifically the section "Base pair parameters".
With a clear understand of the above example, you should have little difficult in understanding opening ~180 degrees. You are suggested to follow the above example on one of such cases, and report back your findings.
Note that 3DNA/DSSR report angular parameters in the range of [0, +-180] instead of [0, 360]. So opening of `-175` is not that much a difference from `+175` (vs `+185`). Also notice the opposite sign of opening for M+N vs N+M pairs.
Please read the [DSSR manual](http://docs.x3dna.org/dssr-manual.pdf) and the [practical guide for the DSSR-PyMOL](http://skmatic.x3dna.org/dssr-schematic-guide.pdf) article.
Best regards,
Xiang-Jun