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RNA structures (DSSR) / Bug or feature (?) : residue numbering not understood
« on: May 26, 2021, 12:33:10 pm »
Dear Dr Xiang-Jun,
About residue numberings. After annotating a structure, outputing in JSON, looking at the "nts" section, residues are organized by chain, and within a chain, the "index_chain" field starts at one (expected behavior, very good). However, in some cases, it starts at last chain's last index_chain plus one, is there any reason for that ?
My spotted case is 4w29 (a large ribosome), i am looking at chain BA, which starts with index_chain = 77, following chain AX's index_chain = 76.
I checked, the chains are not contiguous in space, nothing indicates they could be linked together. Other chains in the structure start at 1.
Execution output below (nothing special spotted), using DSSR v1.9.9:
$ x3dna-dssr -i=/home/persalteas/Data/RNA/3D/RNAcifs/4w29.cif --json --auxfile=no > 4w29.json
Thanks,
Louis
About residue numberings. After annotating a structure, outputing in JSON, looking at the "nts" section, residues are organized by chain, and within a chain, the "index_chain" field starts at one (expected behavior, very good). However, in some cases, it starts at last chain's last index_chain plus one, is there any reason for that ?
My spotted case is 4w29 (a large ribosome), i am looking at chain BA, which starts with index_chain = 77, following chain AX's index_chain = 76.
I checked, the chains are not contiguous in space, nothing indicates they could be linked together. Other chains in the structure start at 1.
Execution output below (nothing special spotted), using DSSR v1.9.9:
$ x3dna-dssr -i=/home/persalteas/Data/RNA/3D/RNAcifs/4w29.cif --json --auxfile=no > 4w29.json
Code: [Select]
Processing file '/home/persalteas/Data/RNA/3D/RNAcifs/4w29.cif'
[i] '/home/persalteas/Data/RNA/3D/RNAcifs/4w29.cif' taken as in .cif format by file extension.
1.AA.U.434 0.121
1.AA.U.723 0.121
1.AA.U.1126 0.135
1.AA.U.1301 0.123
1.AW.U.8 0.123
1.BA.U.1939 0.122
1.BA.U.2887 0.121
1.CA.U.68Q 0.126
1.CA.U.669 0.123
total number of nucleotides: 9398
total number of amino acids: 14040
[w] arginine [AD.ARG3] -- NH1/NH2 naming swapped
[w] arginine [AD.ARG118] -- NH1/NH2 naming swapped
[w] arginine [AT.ARG89] -- NH1/NH2 naming swapped
[w] arginine [AY.ARG351] -- NH1/NH2 naming swapped
[w] arginine [AY.ARG354] -- NH1/NH2 naming swapped
[w] arginine [AY.ARG357] -- NH1/NH2 naming swapped
[w] arginine [AY.ARG396] -- NH1/NH2 naming swapped
[w] arginine [AY.ARG484] -- NH1/NH2 naming swapped
[w] arginine [AY.ARG504] -- NH1/NH2 naming swapped
[w] Residue AV.G1 missing planar atom [ C8 ]
total number of base pairs: 4601
total number of multiplets: 620
total number of helices: 263
total number of stems: 601
total number of isolated WC/wobble pairs: 151
total number of atom-base capping interactions: 589
total number of splayed-apart dinucleotides: 1238
consolidated into units: 797
total number of hairpin loops: 228
total number of bulges: 118
total number of internal loops: 245
total number of junctions: 116
total number of non-loop single-stranded segments: 73
total number of kissing loops: 13
total number of A-minor (types I and II) motifs: 191
total number of eXtended A-minor (type X) motifs: 219
total number of ribose zippers: 94
total number of kink turns: 29
[w] number-of-residues=658 -- in shortened form
[w] number-of-residues=658 -- in shortened form
[w] cross-paired segments in separate chains, be *careful* with .dbn
Time used: 00:00:02:56
Thanks,
Louis