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51
this not dot-bracket notation , i want to get the dot-bracket notation just contain the above cross chain pairs.
52
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???
53
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;


54
What the .dbn should be in this case (2YIE, between chains X and Z)?
55
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)
56
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.
57
all the chain interaction in one pdb file, i want to get the dot-bracket of cross chain interaction. thank you!
58
RNA structures (DSSR) / Re: Color each block nucleotide at each locations
« Last post by xiangjun on July 09, 2021, 03:49:05 pm »
OK. Let's forget about coloring DSSR blocks for the moment, focusing exclusively on PyMOL coloring of residues.

Could you color each nucleotide at each locations in PyMOL?

Now let G4 be G at position 4, the following will color its DSSR block yellow:

Code: Bash
  1. select G4, resi 4
  2. dssr_block G4, block_color='G:yellow'
  3. # OR combined the above two steps as below:
  4. # dssr_block resi 4, block_color='N:yellow'

Let Gs be selection of Gs at postions 5, 10, 11, do the following to color their blocks blue:

Code: Bash
  1. select Gs, resi 5+10+11
  2. dssr_block Gs, block_color='G:blue'
  3. # OR combined as below:
  4. # dssr_block resi 5+10+11, block_color='N:blue'

HTH,

Xiang-Jun
59
RNA structures (DSSR) / Re: Color each block nucleotide at each locations
« Last post by spark159 on July 09, 2021, 03:33:40 pm »
And manual selection of a particular nucleotide in particular position didn't help as I post i the earlier thread:
It only change the color of real nucleotide in the block not the block itself....
60
RNA structures (DSSR) / Re: Color each block nucleotide at each locations
« Last post by spark159 on July 09, 2021, 03:30:09 pm »
Thank you for your kind answer!

Yes, I understood the color-option in the article but this setting will color "all" nucleotide of same kinds into a single color.
For example, color all Guanine by yellow.

But I want to do this:
color G at position 4 by yellow but Gs at position 5, 10, 11 by blue, etc

Do you have any idea to do that?
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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.