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Questions and answers > RNA structures (DSSR)
Bug or feature (?) : residue numbering not understood
persalteas:
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
--- Code: ---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
--- End code ---
Thanks,
Louis
xiangjun:
Hi Louis,
Thanks for using DSSR and for posting your questions on the 3DNA Forum. I will look into the reported "issue" and get back to you on the Forum, hopefully before long...
Best regards,
Xiang-Jun
xiangjun:
Hi Louis,
The issue has been fixed and will be released in DSSR Pro. Due 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.
Xiang-Jun
persalteas:
Hi,
Thank you for the quick fix !
I have an academic licence for DSSR2, but i can consider "DSSR Pro", what is the difference and how much does it cost ? (The CTV website displays a blank page)
--- Quote ---Due 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.
--- End quote ---
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.
I suggest you summarize the content of the page in a forum post, to provide a reliable source of information about DSSR licensing, maybe ?
xiangjun:
Hi Louis,
Sorry for your difficult experience in accessing the CTV website for DSSR. I've communicated with the supporting staffs, and hopefully situation would improve as a result of your feedback.
Basically, the DSSR Pro academic license charges a one-time fee of $1000 per seat. It comes with a one-year support directly from me. I do not expect another major release of DSSR in the next 4 years. As a result, the annual cost averages $250, or about a tenth of the cost of a journal publication or a two-night hotel stay. Email and video meetings are included in the one-year support. Following your suggestion, I will create a post on DSSR Pro academic license in the "Site announcements" section. [Note added on May 31, 2021: I've added a post titled "Clarification on DSSR licensing".]
Best regards,
Xiang-Jun
Below in the copied from the CTV website on DSSR Pro:
--- Quote ---License Name
DSSR-Pro Academic ($1000, 1 seat)
Description
This academic license is for one user and includes the DSSR Pro software (macOS, linux, and windows) along with the Pro Manual. It is for people working on open academic research at, or for, an academic institution or similar non-profit. Any commercial use requires purchase of a commercial license. It is a one-time fee and does not cover future major releases of the code. Minor releases with bug-fixes and small updates are included in the fee. Thank you for purchasing DSSR. Funds help to support further development of the DSSR software product.
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.
Pricing Information
Total Price $1,000.00
--- End quote ---
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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.
