3DNA Forum

Questions and answers => RNA structures (DSSR) => Topic started by: langmei on July 09, 2021, 04:54:18 am

Netiquette · Download · News · Gallery · Homepage · DSSR Manual · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · DSSR Download/Licensing · {Video Overview of DSSR}

Title: can i get the cross_chain base-pair as a dot-bracket notation just use dssr
Post by: langmei on July 09, 2021, 04:54:18 am
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!
Title: Re: can i get the cross_chain base-pair as a dot-bracket notation just use dssr
Post by: xiangjun on July 09, 2021, 09:10:12 am
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
Title: Re: can i get the cross_chain base-pair as a dot-bracket notation just use dssr
Post by: langmei on July 09, 2021, 09:50:43 am
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)
Title: Re: can i get the cross_chain base-pair as a dot-bracket notation just use dssr
Post by: xiangjun on July 09, 2021, 10:18:24 am
Only two chains? How about more than two chains? What do you mean by "the cross chain base_pair notation"?
Title: Re: can i get the cross_chain base-pair as a dot-bracket notation just use dssr
Post by: langmei on July 11, 2021, 09:16:55 pm
all the chain interaction in one pdb file, i want to get the dot-bracket of cross chain interaction. thank you!
Title: Re: can i get the cross_chain base-pair as a dot-bracket notation just use dssr
Post by: xiangjun on July 11, 2021, 10:52:36 pm
Please give specific examples of what you want to accomplish so that others can assist you. It's also a good way to get your thoughts straight.
Title: Re: can i get the cross_chain base-pair as a dot-bracket notation just use dssr
Post by: langmei on July 11, 2021, 11:15:51 pm
OK, for example RNA 2YIE there are two chain as fellow:
>strand_X
gGAUCUUCGGGGCAGGGUGAAAUUCCCGACCGGUGGUAUAGUCCACGAAUCCAU
(((((((((<..(.(((({..)..))))[[((((((({.)[[))))>.((((..
>strand_Z
gGAUUGAUUUGGUGAAAUUCCAAAACCGACAGUAGAGUCUGGAUGAGAGAAGAUUCG
))))...((((((}..)..)))))]]))(((((}.)]])))).....))))))))).
the dot-bracket contain cross chain base-pair and inner chain base-chain. but i just need the base-pair that cross X and Z.(X and Z interaction)
Title: Re: can i get the cross_chain base-pair as a dot-bracket notation just use dssr
Post by: xiangjun on July 11, 2021, 11:24:55 pm
What the .dbn should be in this case (2YIE, between chains X and Z)?
Title: Re: can i get the cross_chain base-pair as a dot-bracket notation just use dssr
Post by: langmei on July 12, 2021, 02:16:06 am
just contain the base pair x-z like fellow,not contain x-x or z-z。 it is clear? maybe i can use the .json reproduce the result, but i do not know how to do.
X.g1 - 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.G12 - Z.G93;
X.G19 - Z.A90;
X.A29 - Z.U94;
X.C30 - Z.G93;
X.C31 - Z.G84;
X.G32 - Z.C83;
X.G33 - Z.A104;
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.g57;
X.G11 - Z.G84;
X.A29 - Z.G93;
X.C31 - Z.C83;
X.U42 - Z.C82;


Title: Re: can i get the cross_chain base-pair as a dot-bracket notation just use dssr
Post by: xiangjun on July 12, 2021, 06:56:59 am
Code: [Select]
X.g1 - Z.C112;
X.G2 - Z.U111;
X.G41 - Z.A63;
X.G41 - Z.C82;
X.U42 - Z.A81;
X.U42 - Z.C82;

Are you sure this is the dot-bracket notation, with desired base-pairs you want???
Title: Re: can i get the cross_chain base-pair as a dot-bracket notation just use dssr
Post by: langmei on July 12, 2021, 07:59:07 am
this not dot-bracket notation , i want to get the dot-bracket notation just contain the above cross chain pairs.
Title: Re: can i get the cross_chain base-pair as a dot-bracket notation just use dssr
Post by: xiangjun on July 12, 2021, 08:12:37 am
Please pay close attention to my requests for clarification.
Title: Re: can i get the cross_chain base-pair as a dot-bracket notation just use dssr
Post by: xiangjun on August 26, 2021, 12:04:19 pm
As a followup, DSSR Pro now has the option to derive only pairs across chains.

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.