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91
RNA structures (DSSR) / Re: Incorrect topology assignment
« Last post by xiangjun on May 26, 2021, 11:26:18 pm »
Quote
It is possible that there are more mistakes. I am curious what they come
from and I am looking forward to the revised version of the database.

As another concrete example, what do you think the descriptor for PDB entry 6r9k should be?

Xiang-Jun
92
RNA structures (DSSR) / Re: Color each block nucleotide at each locations
« Last post by xiangjun on May 26, 2021, 06:06:18 pm »
Please provide reproducible examples, illustrated with screenshots if necessary. Otherwise, I (maybe many other viewers of the thread) cannot understand exactly what you are talking about.
93
RNA structures (DSSR) / Re: Color each block nucleotide at each locations
« Last post by spark159 on May 26, 2021, 04:23:47 pm »
I tried it in pymol, but only the color of real nucleotide was changed, not the color of "block".
94
RNA structures (DSSR) / Re: Color each block nucleotide at each locations
« Last post by spark159 on May 26, 2021, 04:19:42 pm »
Thanks for reply!

Could I know how to do in pymol-plugin ?
95
RNA structures (DSSR) / Re: Color each block nucleotide at each locations
« Last post by xiangjun on May 26, 2021, 04:18:58 pm »
No, at least not automatically. That said, you could manually select each nucleotide and then color it whatever way you want.
97
RNA structures (DSSR) / Color each block nucleotide at each locations
« Last post by spark159 on May 26, 2021, 03:43:15 pm »
I know I can color according to nucleotide type (like A, T, C, G).
But is it possible to color each block nucleotide at different location with different user-defined color?

For example,
nucleotide at residue 1 -> yellow
nucleotide at residue 2 -> purple, etc
98
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
99
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
100
RNA structures (DSSR) / Bug or feature (?) : residue numbering not understood
« Last post by persalteas on May 26, 2021, 12:33:10 pm »
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: [Select]
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

Thanks,

Louis
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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.