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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: 00:00:02:56Due to a lack of funding support, this is the only way my effort on DSSR can be justified. I will ensure that paid users always receive top-notch support.I understand. While i entirely trust you since you have demonstrated efficiency and skills in developping DSSR and quickly replying to questions on this forum, the CTV is not very engaging, since the website regularly has issues. My first visit was in September 2020, blank page, I had to ask techventures<at>columbia.edu by email to fix it. And today i have the same issue. And i could read in the forum that other people faced problems.
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DSSR Pro has more functionality than DSSR Basic, including: (i) homology modeling via in silico base mutations, (ii) easy generation of regular helical models, and (iii) creation of customized structures with user-specific base sequences and rigid-body parameters. DSSR Pro supersedes 3DNA completely while DSSR basic has no modeling capabilities and less analysis/annotation features. DSSR Pro integrates disparate analysis and modeling programs of 3DNA under one umbrella, and offers an easier to use interface. DSSR Pro includes an in-depth user manual, and one year technical support directly from the developer. DSSR basic is provided AS IS, and does not include any support.
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Total Price $1,000.00
I will discuss with my team, but yes, we may go for it.
If the CTV team wants more information on the problem, do not hesitate to ask me (i tried with different browsers, but nothing succeeds).
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.
ATOM 60690 C C8 . A X 24 76 ? 55.433 -163.384 92.500 1.00 140.84 ? 76 A AX C8 1
ATOM 60691 N N7 . A X 24 76 ? 55.656 -163.215 91.217 1.00 141.03 ? 76 A AX N7 1
ATOM 60692 C C5 . A X 24 76 ? 54.538 -162.520 90.779 1.00 141.71 ? 76 A AX C5 1
ATOM 60693 C C6 . A X 24 76 ? 54.160 -162.033 89.512 1.00 142.30 ? 76 A AX C6 1
ATOM 60694 N N6 . A X 24 76 ? 54.901 -162.183 88.412 1.00 143.14 ? 76 A AX N6 1
ATOM 60695 N N1 . A X 24 76 ? 52.983 -161.377 89.410 1.00 142.62 ? 76 A AX N1 1
ATOM 60696 C C2 . A X 24 76 ? 52.240 -161.228 90.513 1.00 142.49 ? 76 A AX C2 1
ATOM 60697 N N3 . A X 24 76 ? 52.490 -161.642 91.754 1.00 142.54 ? 76 A AX N3 1
ATOM 60698 C C4 . A X 24 76 ? 53.665 -162.290 91.829 1.00 141.84 ? 76 A AX C4 1
ATOM 60699 N N . VAL X 24 77 ? 50.042 -163.172 98.420 1.00 50.64 ? 77 VAL AX N 1
ATOM 60700 C CA . VAL X 24 77 ? 51.296 -162.409 98.368 1.00 47.13 ? 77 VAL AX CA 1
ATOM 60701 C C . VAL X 24 77 ? 52.559 -163.283 98.400 1.00 44.56 ? 77 VAL AX C 1
ATOM 60702 O O . VAL X 24 77 ? 52.567 -164.326 99.054 1.00 40.69 ? 77 VAL AX O 1
ATOM 60703 C CB . VAL X 24 77 ? 51.361 -161.302 99.446 1.00 46.79 ? 77 VAL AX CB 1
ATOM 60704 C CG1 . VAL X 24 77 ? 50.129 -160.404 99.438 1.00 47.04 ? 77 VAL AX CG1 1
ATOM 60705 C CG2 . VAL X 24 77 ? 51.655 -161.873 100.828 1.00 46.46 ? 77 VAL AX CG2 1
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