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Topics - persalteas

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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



RNA structures (DSSR) / Do you provide DSSR 1.* downloads ?
« on: September 15, 2020, 08:38:20 am »
Hi xiangjun,

Do you provide downloads of old versions ? I published using v1.9.9 and need to ensure reproductibility.
If not, do you allow us to embed the executable in a larger software container (e.g. Docker) ? The DSSR functionalities will not be available from outside the container.

I also could ensure my work gives the same results with DSSR 2.0, which is probably the case, but the CTV licensing page is empty (issue ? maintenance ?).
EDIT: (for people reading this in the future): Disable your ad blocker so that the page's content loads correctly.

What is the best thing to do ?


RNA structures (DSSR) / Documentation of the Json output fields ?
« on: March 03, 2020, 05:25:07 am »

I noticed DSSR's json output of a structure analysis gives a lot of information (about individual nucleotides in particular), and i do not know (yet) all their meanings.
I searched a bit for a documentation, but the manual does not provide the fields descriptions.

The list of fields i am talking about:

summary (and there are several fields inside)
alpha, beta, gamma, delta, epsilon, zeta
ssZp, Dp
splay_angle, splay_distance, splay_ratio
eta, theta, eta', theta', eta_base, theta_base
v0, v1, v2, v3, v4
frame (several descriptors)

In particular, i am interested in the following points:
  • Why are we interested in the C5' XYZ position ?
  • What are the "splay" descriptors ?
  • What are the v0-v4 descriptors ?
  • What is the difference between sugar_class and puckering ?
  • What is the frame, and the RMSD value provided ?

I am mostly trying to learn more, if such documentation does not exist (yet), i welcome some bibliography references if you have some...

Thanks a lot for your time,


Hi there,

First, thank you a lot to each and everyone of you developing DSSR, this is an awesome piece of software that perfectly suits my needs. I already use it for some time without any problems. Today, i have a technical question to enhance my productivity.

I am trying to "analyze -t" a few thousands of RNA chains to get their eta' and theta' pseudotorsions, which works very well. So, i use several threads which run analyze in parallel, on a multicore CPU.

The fact is "analyze -t" creates a file named Borg_P_C1_C4.dat with the cartesian coordinates of the atoms used. As we cannot control this file's name, i am afraid of conflicts between my threads, each of them trying to read/write different content into the same file.

Therefore, two questions:
  • Is the .dat file necessary to compute the .tor file, or the opposite ?
  • Is there a way to control that file's name ?

Example command i run:
Code: [Select]
analyze -t=/path/to/pseudotorsions/folder/4v8p[1]-B3.tor /path/to/chains/folder/4v8p[1]-B3.pdb
Thanks a lot for your help,

Louis Becquey
PhD Student @Univ Evry, Université Paris-Saclay

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.