1
RNA structures (DSSR) / Re: How the length of the sequence depends on _pdbx_unobs_or_zero_occ_atoms ???
« on: September 06, 2024, 10:23:46 am »
Thank you, Xiang-Jun.
This section allows you to view all posts made by this member. Note that you can only see posts made in areas you currently have access to.
Netiquette · Download · News · Gallery · Homepage · DSSR Manual · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · DSSR Licensing · Video Overview· RNA Covers
...
17 R.G19 R.C49 G-C WC 19-XIX cWW cW-W
[-155.1(anti) ~C3'-endo lambda=50.2] [-106.9(anti) ~C2'-endo lambda=53.7]
d(C1'-C1')=10.82 d(N1-N9)=9.00 d(C6-C8)=9.90 tor(C1'-N1-N9-C1')=-11.0
H-bonds[3]: "O6(carbonyl)-N4(amino)[2.93],N1(imino)-N3[2.91],N2(amino)-O2(carbonyl)[2.81]"
interBase-angle=8 Simple-bpParams: Shear=-0.21 Stretch=-0.13 Buckle=-2.1 Propeller=-7.6
...
loop_
_pdbx_poly_seq_scheme.asym_id
_pdbx_poly_seq_scheme.entity_id
_pdbx_poly_seq_scheme.seq_id
_pdbx_poly_seq_scheme.mon_id
_pdbx_poly_seq_scheme.ndb_seq_num
_pdbx_poly_seq_scheme.pdb_seq_num
_pdbx_poly_seq_scheme.auth_seq_num
_pdbx_poly_seq_scheme.pdb_mon_id
_pdbx_poly_seq_scheme.auth_mon_id
_pdbx_poly_seq_scheme.pdb_strand_id
_pdbx_poly_seq_scheme.pdb_ins_code
_pdbx_poly_seq_scheme.hetero
B 2 1 U 1 2 ? ? ? B . n
B 2 2 U 2 3 ? ? ? B . n
B 2 3 C 3 4 4 C C B . n
B 2 4 A 4 5 5 A A B . n
B 2 5 C 5 6 6 C C B . n
B 2 6 U 6 7 7 U U B . n
B 2 7 G 7 8 8 G G B . n
B 2 8 C 8 9 9 C C B . n
B 2 9 C 9 10 10 C C B . n
B 2 10 G 10 11 11 G G B . n
B 2 11 U 11 12 12 U U B . n
B 2 12 A 12 13 13 A A B . n
B 2 13 U 13 14 14 U U B . n
B 2 14 A 14 15 15 A A B . n
B 2 15 G 15 16 16 G G B . n
B 2 16 G 16 17 17 G G B . n
B 2 17 C 17 18 18 C C B . n
B 2 18 A 18 19 19 A A B . n
B 2 19 G 19 20 20 G G B . n
B 2 20 C 20 21 21 C C B . n
DSSR: an Integrated Software Tool for
Dissecting the Spatial Structure of RNA
v2.4.2-2023may01 by xiangjun@x3dna.org
...
****************************************************************************
List of 8 base pairs
nt1 nt2 bp name Saenger LW DSSR
1 A.G1 A.C21 G-C WC 19-XIX cWW cW-W
2 A.G2 A.C20 G-C WC 19-XIX cWW cW-W
3 A.C3 A.G19 C-G WC 19-XIX cWW cW-W
4 A.G4 A.U18 G-U Wobble 28-XXVIII cWW cW-W
5 A.U5 A.A17 U-A WC 20-XX cWW cW-W
6 A.A7 A.U16 A-U -- -- cWW cW-W
7 A.G8 A.C15 G-C WC 19-XIX cWW cW-W
8 A.G9 A.C14 G-C WC 19-XIX cWW cW-W
****************************************************************************
...
****************************************************************************
Secondary structures in dot-bracket notation (dbn) as a whole and per chain
>17RA nts=21 [whole]
GGCGUAAGGAUUACCUAUGCC
(((((..((....)).)))))
****************************************************************************
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.