1
MD simulations / Re: Gromacs missing ' P ' atom
« on: May 27, 2024, 06:41:08 pm »
No, it is for information only: i.e., the first nucleotide (DG1) does not have the phosphate group.
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what are the criteria for selecting the origin and XYZ axis vectors for the coordinate system?
ATOM 195 C5' U A 10 -15.795 -3.890 -14.824 1.00 0.34 C
C5' atom coordinate C5prime_xyz: [-1.405, 8.313, 1.694]
{"rmsd":0.013,"origin":[-7.546,-2.079,-13.202],
"x_axis":[-0.071,0.233,0.970],
"y_axis":[-0.997,0.020,-0.078],
"z_axis":[-0.037,-0.972,0.231],
"quaternion":[0.543,0.412,-0.464,0.566]}
dd = [-15.795 -3.890 -14.824] - [-7.546,-2.079,-13.202] = [-8.249 -1.811 -1.622]
dd * [ -0.071 -0.997 -0.037
0.233 0.020 -0.972
0.970 -0.078 0.231 ] = [-1.4096 8.3145 1.6908]
x3dna-dssr -i=AATAAA_dna.pdb -o=AATAAA_dna.out
# dssr-2ndstrs.dbn
>AATAAA_dna nts=16 [AATAAA_dna] -- secondary structure derived by DSSR
GCGCGAATAAACGCGC
(((((......)))))
# dssr-2ndstrs.ct
16 ENERGY = 0.0 [AATAAA_dna] -- secondary structure derived by DSSR
1 G 0 2 16 1
2 C 1 3 15 2
3 G 2 4 14 3
4 C 3 5 13 4
5 G 4 6 12 5
6 A 5 7 0 6
7 A 6 8 0 7
8 T 7 9 0 8
9 A 8 10 0 9
10 A 9 11 0 10
11 A 10 12 0 11
12 C 11 13 5 12
13 G 12 14 4 13
14 C 13 15 3 14
15 G 14 16 2 15
16 C 15 0 1 16
******************************************************************
DSSR: an Integrated Software Tool for
Dissecting the Spatial Structure of RNA
v2.4.2-2023may01 by xiangjun@x3dna.org
******************************************************************
1 C ( A.DC1 0.012 anti,~C2'-endo,BI,non-stack,canonical,helix-end,stem-end,coaxial-stack
2 A ( A.DA2 0.020 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack
3 C ( A.DC3 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack
4 A ( A.DA4 0.018 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack
5 A ( A.DA5 0.015 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack
6 A ( A.DA6 0.015 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack
7 C ( A.DC7 0.009 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack
8 A ( A.DA8 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop
9 ? . A.PYP9 --- modified,~C2'-endo,BI,non-stack,internal-loop
10 G ( A.DG10 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop
nt alpha beta gamma delta epsilon zeta e-z chi phase-angle sugar-type ssZp Dp splay
1 C A.DC1 --- --- 59.6 143.0 -178.2 -98.9 -79(BI) -112.1(anti) 162.0(C2'-endo) ~C2'-endo 1.99 2.26 16.42
2 A A.DA2 -92.0 -166.3 54.8 121.4 179.5 -87.3 -93(BI) -112.9(anti) 143.5(C1'-exo) ~C2'-endo 1.97 2.07 18.44
3 C A.DC3 -62.7 166.0 58.6 144.3 -166.0 -165.5 -1(--) -85.4(anti) 156.7(C2'-endo) ~C2'-endo 2.70 2.79 25.63
4 A A.DA4 -75.7 -177.0 60.4 153.3 -175.3 -78.8 -97(BI) -110.7(anti) 185.3(C3'-exo) ~C2'-endo 1.72 1.82 18.57
5 A A.DA5 -80.9 172.3 59.3 107.1 -166.5 -94.1 -72(BI) -126.1(anti) 120.9(C1'-exo) ~C2'-endo 2.48 2.58 18.91
6 A A.DA6 -74.4 171.8 59.7 120.9 179.8 -99.1 -81(BI) -120.3(anti) 134.2(C1'-exo) ~C2'-endo 2.37 2.43 16.58
7 C A.DC7 -74.1 -176.0 59.0 149.2 -164.1 -146.5 -18(--) -93.5(anti) 168.5(C2'-endo) ~C2'-endo 2.04 2.06 24.91
8 A A.DA8 -74.9 176.5 57.1 147.6 -173.6 -100.2 -73(BI) -120.0(anti) 175.2(C2'-endo) ~C2'-endo --- --- ---
9 ? A.PYP9 -63.0 175.7 62.6 135.3 -178.2 -77.7 -101(BI) --- 151.8(C2'-endo) ~C2'-endo --- --- ---
10 G A.DG10 -84.6 171.5 59.9 122.1 -176.2 -130.1 -46(BI) -112.0(anti) 133.5(C1'-exo) ~C2'-endo 2.63 2.71 21.35
2. Be specific with your questions; provide a minimal, reproducible
example if possible; use attachments where appropriate.
Here, we present RNAfitme, a versatile webserver tool for remodeling of nucleobase- and nucleoside residue conformations in the fixed-backbone RNA 3D structures. Our approach makes use of dedicated libraries that define RNA conformational space. They have been built upon torsional angle characteristics of PDB-deposited RNA structures. RNAfitme can be applied to reconstruct full-atom model of RNA from its backbone; remodel user-selected nucleobase/nucleoside residues in a given RNA structure; predict RNA 3D structure based on the sequence and the template of a homologous molecule of the same size; refine RNA 3D model by reducing steric clashes indicated during structure quality assessment. RNAfitme is a publicly available tool with an intuitive interface. It is freely accessible at http://rnafitme.cs.put.poznan.pl/
"To aid the development of novel XNA polymers and the search for possible pre-RNA candidates, this article presents the proto-Nucleic Acid Builder (https://github.com/GT-NucleicAcids/pnab), an open-source program for modeling nucleic acid analogs with alternative backbones and nucleobases. The torsion-driven conformation search procedure implemented here predicts structures with good accuracy compared to experimental structures, and correctly demonstrates the correlation between the helical structure and the backbone conformation in DNA and RNA."
By the 9 torsional angles, I meant the torsional and pseudotorsional angles - alpha, beta, gamma, delta, chi, epsilon, zeta, eta, theta - calculated by 3DNA's `analyze` program.
DSSR would indeed benefit from more modeling features! I'll be following the release notes to see if this particular modeling feature is ever introduced to DSSR.
I apologize if this question is irrelevant for the forum, I wanted to confirm if DSSR Pro could satisfy our requirements before buying the license since the Pro version of the manual is not available.
We have an RNA sequence, and the 9 torsional angles (calculated by 3DNA v2.4) for each residue. Would it be possible to reconstruct the full-atom 3D structure of the RNA using DSSR Pro's rebuild program from just these two pieces of information - the sequence and the 9 torsional angles?
Identification of nucleotides
Note that pseudouridine (PSU) is shortened to ‘P’, due to its special C1′–C5 glycosidic link- age (Figure 2).
The M–N versus M+N relative base orientations
is it safe to freely use the old DSSR version for academic use according to the old license?
Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.