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General discussions (Q&As) / Re: Can the v2.4 x3DNA(mut_base)mutate more than one base at multiple sites of RNA
« on: July 28, 2021, 08:56:59 am »
DSSR Pro can do it and more.
Xiang-Jun
Xiang-Jun
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Yes, I tried and finally manage to color differently at each nucleotide blocks.
But it is quite slow since it make all individual block object for every nucleotide.
And also it print lots of warning messages during the run.
I can't locate the origin of this warning.
PyMOL>dssr_block (chain J and resi 56), block_color='N:[1.0 0.393 0.0]'
x3dna-dssr --more --loop=with-stems --json -i=6jwe.pdb -o=6jwe.json
Processing file '6jwe.pdb'
total number of nucleotides: 20
total number of base pairs: 18
total number of helices: 2
total number of multiplets: 4
total number of atom-base capping interactions: 2
total number of splayed-apart dinucleotides: 2
total number of non-loop single-stranded segments: 1
total number of G-tetrads: 3
total number of G4-helices: 1
total number of G4-stems: 1
As I understand correctly, for the moment there is no program (or database) that annotates (or stores) classical RNA loop motifs explicitly.
By the classical RNA loop motifs I mean sarcin/ricin loop, E-loop, tandem sheared G-A, GA/AAG internal loop, UAA/GAN internal loop, kink-turn, etc.
As I know it:
1) only kink-turns are annotated by DSSR.
2) for sarcin/ricin loop, E-loop, and tandem sheared G-A the best way of annotation is to use manually curated annotation from RNAMotifContrast and merge it with the RNA Motif Atlas clusters' identifiers.
3) for GA/AAG internal loop and UAA/GAN internal loop annotation there are no existing ways at all.
If I'm wrong, could you please let me know if I missed anything?
If I'm right, are there any plans to add the mentioned motifs to DSSR functionality in the future?
X.g1 - Z.C112;
X.G2 - Z.U111;
X.G41 - Z.A63;
X.G41 - Z.C82;
X.U42 - Z.A81;
X.U42 - Z.C82;
why number of base-pair in dot-bracket notation file (dssr.dbn) is not complete?
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.
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?
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
I suggest you summarize the content of the [CTV] page in a forum post, to provide a reliable source of information about DSSR licensing, maybe?
Ok, I'll check these structures,
but it looks like our discussion goes beyond the canonical G-quadruplex structures (think in Webb da Silva's convention), hence the problems.
I look forward to the update if everything will be clearly explain in the publication. However, I hope that the "new convention" will be consistent with eg interpretations of CD spectra.
Unfortunately I am using the basic version of DSSR, I have to think about buying the PRO version.
dssr_block [ selection [, state [, block_file [, block_depth [, block_color [, name [, exe ]]]]]]]
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).
List of 1 G4-stem
Note: a G4-stem is defined as a G4-helix with backbone connectivity.
Bulges are also allowed along each of the four strands.
stem#1[#1] layers=3 INTRA-molecular loops=3 descriptor=3(-P-P-P) note=parallel(4+0) UUUU parallel
1 glyco-bond=s--- sugar=.--- groove=w--n Major-->WC nts=4 GGGG A.DG2,A.DG18,A.DG14,A.DG6
2 glyco-bond=---- sugar=---. groove=---- Major-->WC nts=4 GGGG A.DG3,A.DG19,A.DG15,A.DG7
3 glyco-bond=---- sugar=---3 groove=---- Major-->WC nts=4 GGGG A.DG4,A.DG20,A.DG16,A.DG8
step#1 pm(>>,forward) area=19.15 rise=3.41 twist=21.0
step#2 pm(>>,forward) area=12.05 rise=3.47 twist=28.2
strand#1 U DNA glyco-bond=s-- sugar=.-- nts=3 GGG A.DG2,A.DG3,A.DG4
strand#2 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG18,A.DG19,A.DG20
strand#3 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG14,A.DG15,A.DG16
strand#4 U DNA glyco-bond=--- sugar=-.3 nts=3 GGG A.DG6,A.DG7,A.DG8
loop#1 type=propeller strands=[#1,#4] nts=1 C A.DC5
loop#2 type=propeller strands=[#4,#3] nts=5 CACGA A.DC9,A.DA10,A.DC11,A.DG12,A.DA13
loop#3 type=propeller strands=[#3,#2] nts=1 A A.DA17
148d 186d 1bub 1c34 1c35 1c38 1hao 1hap 1hut 1i34 1qdf 1qdh 1rde 201d
230d 2e4i 2f8u 2gku 2hy9 2jpz 2jsk 2jsl 2jsm 2jsq 2kf7 2kf8 2kka 2km3
2kow 2kpr 2kqg 2kzd 2l88 2lod 2lyg 2m6v 2m6w 2m8z 2m91 2may 2mb3 2mbj
2mft 2mfu 2ms9 2mwz 2n2d 4dih 4dii 4lz1 4lz4 4ni7 4ni9 4u5m 5cmx 5ew1
5ew2 5j05 5j4p 5j4w 5j6u 5lqg 5lqh 5mjx 5mta 5mtg 5mvb 5o4d 5oph 5yey
5zev 6ac7 6ccw 6eo6 6eo7 6erl 6evv 6f4z 6fc9 6ftu 6gh0 6gn7 6gzn 6h1k
6ia4 6jkn 6jwd 6jwe 6kfj 6l8m 6l92 6r9k 6r9l 6rs3 6tc8 6tcg 6ycv 6yep
6z8v 6z8w 6z8x 6zx6 7atz 7cv3 7cv4 7ntu
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