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61
Only two chains? How about more than two chains? What do you mean by "the cross chain base_pair notation"?
62
I will use the new feature to predict the base level interaction of two chain, so i need to obtain the cross chain base_pair notation (not include the inter chain inter chain base interaction)
63
RNA structures (DSSR) / Re: base-pair in dot-bracket notation in dbn file
« Last post by xiangjun on July 09, 2021, 09:10:54 am »
Quote
why number of base-pair in dot-bracket notation file (dssr.dbn) is not complete?

DSSR derives all base pairs (including noncanonical ones) in a given coordinate file. The .dbn output is for 2D structure with canonical pairs only.

Please read the 2015 NAR paper "DSSR: an integrated software tool for dissecting the spatial structure of RNA" thoroughly, perhaps several times, to gain a better understanding of the fundamentals. See also the post "Reproducing results published in the DSSR-NAR paper" and links therein.

Best regards,

Xiang-Jun
64
I get what you're saying, but I'm having trouble imagining how the requested new feature would be used. Please give specific examples to demonstrate what you're trying to accomplish.

Best regards,

Xiang-Jun
65
hi,
 I want to get the interaction base pair across the chain, but the dssr default output is the  base-pair of the whole the sequence ,can i use a optation to get the cross-chain interaction of two chain?
 thanks!
66
RNA structures (DSSR) / base-pair in dot-bracket notation in dbn file
« Last post by langmei on July 09, 2021, 04:47:56 am »
hi,
   why number of base-pair in dot-bracket notation file (dssr.dbn) is not complete? for example:
 in RNA with id "2YIE", dot-bracket notation file consists of 32 base-pairs as shown below:
>2YIE nts=112 [2YIE] -- secondary structure derived by DSSR
gGAUCUUCGGGGCAGGGUGAAAUUCCCGACCGGUGGUAUAGUCCACGAAUCCAU&gGAUUGAUUUGGUGAAAUUCCAAAACCGACAGUAGAGUCUGGAUGAGAGAAGAUUCG&?
((((((((......(((.......))).[[((((((....[[))))...(((..&)))....(((((.......)))))]])).(((....]]))).......)))))))).&.
but if you extract base-pair from .json file, then there are 50 base-pairs in this RNA as shown below:
['X.GTP1', 'Z.C112']
['X.G2', 'Z.U111']
['X.A3', 'Z.U110']
['X.U4', 'Z.A109']
['X.C5', 'Z.G108']
['X.U6', 'Z.A107']
['X.U7', 'Z.A106']
['X.C8', 'Z.G105']
['X.G9', 'Z.A104']
['X.G10', 'X.G47']
['X.G12', 'X.C31']
['X.G12', 'Z.G93']
['X.C13', 'X.G28']
['X.A14', 'X.G28']
['X.G15', 'X.C27']
['X.G16', 'X.C26']
['X.G17', 'X.C25']
['X.U18', 'X.A22']
['X.G19', 'Z.A90']
['X.A29', 'Z.U94']
['X.C30', 'Z.G93']
['X.C31', 'Z.G84']
['X.G32', 'Z.C83']
['X.G33', 'X.C46']
['X.G33', 'Z.A104']
['X.U34', 'X.A45']
['X.G35', 'X.C44']
['X.G36', 'X.C43']
['X.U37', 'X.A40']
['X.A38', 'Z.G70']
['X.G41', 'Z.A63']
['X.G41', 'Z.C82']
['X.U42', 'Z.A81']
['X.A49', 'Z.U60']
['X.U50', 'Z.A59']
['X.C51', 'Z.G58']
['X.C52', 'Z.GTP57']
['Z.G62', 'Z.C83']
['Z.G62', 'Z.G84']
['Z.U64', 'Z.A80']
['Z.U65', 'Z.A79']
['Z.U66', 'Z.A78']
['Z.G67', 'Z.C77']
['Z.G68', 'Z.C76']
['Z.U69', 'Z.A73']
['Z.A85', 'Z.G98']
['Z.C86', 'Z.G97']
['Z.A87', 'Z.U96']
['Z.G88', 'Z.C95']
['Z.U89', 'Z.A92']

why there are many base-pair in the dssr-2ndstrs.dbn file?
67
General discussions (Q&As) / Re: How to setup 3DNA
« Last post by HZW on July 08, 2021, 08:55:00 am »
Okay, Thank you very much.
68
General discussions (Q&As) / Re: How to setup 3DNA
« Last post by xiangjun on July 08, 2021, 07:43:24 am »
Hi Zw Han,

Quote
I have installed the 3DNA v2.4.4, but I can't use it. Could you please send me the manual of 3DNA. Thank you very much.

Please follow the instructions in $X3DNA/doc/README file.

Alternatively, you may find http://web.x3dna.org useful.

Best regards,

Xiang-Jun
69
General discussions (Q&As) / Re: How to setup 3DNA
« Last post by HZW on July 08, 2021, 02:52:10 am »
Dear xiangjun,
 I'm glad to send message to you. I have installed the 3DNA v2.4.4, but I can't use it. Could you please send me the manual of 3DNA. Thank you very much.


Best Regards
Zw Han
70
FAQs / Re: Where to download x3DNA
« Last post by xl23 on June 23, 2021, 01:09:46 pm »
Thanks, Xiangjun!

I have re-registered using my academic mailbox and now I can see the Download tab.

Best,
Xingcheng



Hi Xingcheng,

Quote
I have registered a long time ago and used to be able to see the Download page. However, when I tried to download it just now, the page does not show up. Could I be granted the access again?

As noted in the FAQ "How to make the best use of the Forum" (http://forum.x3dna.org/faqs/how-to-make-the-best-use-of-the-forum/), private emails (gmail.com, yahoo.com, qq.com etc.) are no longer accepted on the 3DNA Forum. New registrations using private emails will be simply deleted. While previous such registrations (with posts), as in your case, are still kept, they do not have access to the download page any more.

Re-register on the 3DNA Forum using an identifiable (.edu) email, after activation, you will see the download page. Unactivated registrations will also been removed. I strive to keep this Forum spam-free and clean.

Hope this clarifies the issue.

Best regards,

Xiang-Jun
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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.