Messages

26

General discussions (Q&As) / Re: Generation of ssDNA PDB with m3C modification using 3DNA webserver

« on: January 30, 2025, 11:10:45 am »

Hi,

Thanks for your interesting in using 3DNA and for posting your questions on the Forum.

The http://web.x3dna.org has features to build regular fiber models or customized structures (including single-stranded structure as detailed in the supplemental PDF). However, the web-server does not allow you to generate  single-stranded DNA containing a 3-methylated cytosine. The web server simply does not have 'knowledge' of what a 3-methylated cytosine is. I know of no other tools that can do this automatically.

However, 3DNA/DSSR has features that would allow for such modeling from the command line. I need more details of exactly what you want to achieve to be of further help.

See the FAQ: How can I mutate cytosine to 5-methylcytosine?

Best regards,

Xiang-Jun

27

MD simulations / Re: overwritten output files

« on: January 13, 2025, 10:47:57 am »

Hi Mamta,

The output file name is derived from the input PDB filename, by deleting extension and add ".out". Since your PDB frame is named "output-filename.pdb.${i}", the output file will always be "output-filename.pdb.out" by replacing ".{i}" with ".out". You could name your PDB frame "output-${i}.pdb" and the corresponding output file will be "output-${i}.out".

Have a look of the C source code, and the x3dna_ensemble script (x3dna_ensemble analyze -h). Overall, the x3dna-v2.4 support for MD analysis is limited. There is also do_x3dna -- I'm not sure if it is still actively maintained.

I'm in the process of incorporating x3dna-v2.4 features into DSSR (Free academic license available from CTV). Further improvement for MD support will be implemented in DSSR.

Best regards,

Xiang-Jun

28

MD simulations / Re: overwritten output files

« on: January 13, 2025, 08:30:07 am »

Hi Mamta,

Thanks for using 3DNA/DSSR and for posting your question on the 3DNA Forum. Could you please be specific with the command you used? The x3dna-v2.4 suite comes with a Ruby script 'x3dna_ensemble' for analyzing MODEL/ENDMDL delineated ensemble of NMR or MD structures. The x3dna-dssr program has an --nmr (--md) option that streamline the analysis of such ensembles.

Best regards,

Xiang-Jun

29

RNA structures (DSSR) / Re: DNA bend angle

« on: December 30, 2024, 10:49:36 pm »

Hi Narendra,

Thanks for using DSSR and for posting your question on the 3DNA Forum. Regarding DNA bending angle in 3DNA/DSSR, please refer to the FAQ How to calculate DNA bending angle?. With DSSR, the helical axis info is available with the --more option. See the step-by-step procedures for reproducing Figure 2 -- analysis of the yeast phenylalanine tRNA (1ehz) of the 2015 DSSR paper in NAR.

For your specific example of 1fjl, DSSR readily identifies a helix (stem) with details on the helical axis. However, DSSR does not directly provide you a bending angle for reason given in the above mentioned FAQ.

Best regards,

Xiang-Jun

30

Site announcements / DSSR-PyMOL enabled schematics on the covers of the RNA Journal

« on: December 16, 2024, 04:11:24 pm »

Cover image provided by X3DNA-DSSR, an NIGMS National Resource for structural bioinformatics of nucleic acids (R24GM153869; skmatics.x3dna.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).

See the 2020 paper titled "DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL" in Nucleic Acids Research and the corresponding Supplemental PDF for details. Many thanks to Drs. Wilma Olson and Cathy Lawson for their help in the preparation of the illustrations.


May 2025 (link to the source)

Complex of terminal uridylyltransferase 7 (TUT7) with pre-miRNA and Lin28A (PDB id: 8OPT; Yi G, Ye M, Carrique L, El-Sagheer A, Brown T, Norbury CJ, Zhang P, Gilbert RJ. 2024. Structural basis for activity switching in polymerases determining the fate of let-7 pre-miRNAs. Nat Struct Mol Biol 31: 1426–1438). The RNA-binding pluripotency factor LIN28A invades and melts the RNA and affects the mechanism of action of the TUT7 enzyme. The RNA backbone is depicted by a red ribbon, with bases and Watson-Crick base pairs represented as color-coded blocks: A/A-U in red, C/C-G in yellow, G/G-C in green, U/U-A in cyan; TUT7 is represented by a gold ribbon and LIN28A by a white ribbon. Cover image provided by X3DNA-DSSR, an NIGMS National Resource for structural bioinformatics of nucleic acids (R24GM153869; skmatics.x3dna.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).

April 2025 (link to the source)

Cryo-EM structure of the pre-B complex (PDB id: 8QP8; Zhang Z, Kumar V, Dybkov O, Will CL, Zhong J, Ludwig SE, Urlaub H, Kastner B, Stark H, Lührmann R. 2024. Structural insights into the cross-exon to cross-intron spliceosome switch. Nature 630: 1012–1019). The pre-B complex is thought to be critical in the regulation of splicing reactions. Its structure suggests how the cross-exon and cross-intron spliceosome assembly pathways converge. The U4, U5, and U6 snRNA backbones are depicted respectively by blue, green, and red ribbons, with bases and Watson-Crick base pairs shown as color-coded blocks: A/A-U in red, C/C-G in yellow, G/G-C in green, U/U-A in cyan; the proteins are represented by gold ribbons. Cover image provided by X3DNA-DSSR, an NIGMS National Resource for structural bioinformatics of nucleic acids (R24GM153869; skmatics.x3dna.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).

February 2025 (link to the source)

Structure of the Hendra henipavirus (HeV) nucleoprotein (N) protein-RNA double-ring assembly (PDB id: 8C4H; Passchier TC, White JB, Maskell DP, Byrne MJ, Ranson NA, Edwards TA, Barr JN. 2024. The cryoEM structure of the Hendra henipavirus nucleoprotein reveals insights into paramyxoviral nucleocapsid architectures. Sci Rep 14: 14099). The HeV N protein adopts a bi-lobed fold, where the N- and C-terminal globular domains are bisected by an RNA binding cleft. Neighboring N proteins assemble laterally and completely encapsidate the viral genomic and antigenomic RNAs. The two RNAs are depicted by green and red ribbons. The U bases of the poly(U) model are shown as cyan blocks. Proteins are represented as semitransparent gold ribbons. Cover image provided by X3DNA-DSSR, an NIGMS National Resource for structural bioinformatics of nucleic acids (R24GM153869; skmatics.x3dna.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).

January 2025 (link to the source)

Structure of the helicase and C-terminal domains of Dicer-related helicase-1 (DRH-1) bound to dsRNA (PDB id: 8T5S; Consalvo CD, Aderounmu AM, Donelick HM, Aruscavage PJ, Eckert DM, Shen PS, Bass BL. 2024. Caenorhabditis elegans Dicer acts with the RIG-I-like helicase DRH-1 and RDE-4 to cleave dsRNA. eLife 13: RP93979). Cryo-EM structures of Dicer-1 in complex with DRH-1, RNAi deficient-4 (RDE-4), and dsRNA provide mechanistic insights into how these three proteins cooperate in antiviral defense. The dsRNA backbone is depicted by green and red ribbons. The U-A pairs of the poly(A)·poly(U) model are shown as long rectangular cyan blocks, with minor-groove edges colored white. The ADP ligand is represented by a red block and the protein by a gold ribbon. Cover image provided by X3DNA-DSSR, an NIGMS National Resource for structural bioinformatics of nucleic acids (R24GM153869; skmatics.x3dna.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).

How are the detailed steps used to generate the above cover image, using DSSR v2.4.6-2024nov15:

Code: Bash

1. # Download the PDB structure in cif format from RCSB
2. wget https://files.rcsb.org/download/8t5s-assembly1.cif -O 8t5s.cif
3.  
4. # Run DSSR with the following settings. See below for file "8t5s-specific.pml"
5. x3dna-dssr -i=8t5s.cif \
6.            --blocview=png-session-black \
7.            --block-file=wc-g4 \
8.            --block-depth=1.0 \
9.            --pymol-ray-size=5000 \
10.            --pymol-aa-color=gold \
11.            --block_color="minor:white" \
12.            --cartoon-cmd-file=8t5s-specific.pml \
13.            -o=8t5s.pml
14.  
15. # Run PyMOL to render the image. Here it is from the command line.
16. # You can also load the 8t5s.pml into PyMOL interactively.
17. # Generate file "8t5s-pymol.png"
18. pymol -Qkc 8t5s.pml
19.  
20. # Use ImageMagick to trim extra margins
21. magick 8t5s-pymol.png -trim +repage -bordercolor black -border 120 8t5s.png

Note the setting of black background, and coloring of minor-groove edge in white. By default, DSSR-PyMOL renders with a white background and black minor-groove edges, as in 8t5s. Whenever feasible, I've integrated features into DSSR to automate routine tasks as much as possible.

Here are the related files:

• 8t5s-specific.pml -- specific settings
• 8t5s.pse -- PyMOL session file
• 8t5s.pml -- PyMOL script file
• -- ray-traced image

Moreover, the following 30 [12(2021) + 12(2022) + 6(2023)] cover images of the RNA Journal were generated by the NAKB (nakb.org).

Cover image provided by the Nucleic Acid Database (NDB)/Nucleic Acid Knowledgebase (NAKB; nakb.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).

31

FAQs / Re: How to set up 3DNA on Windows with WSL2

« on: December 14, 2024, 08:41:59 am »

Hi Chian,

Thanks for using 3DNA. Working in native Windows command-line (cmd or PowerShell) has seen lots of troubles, as evidenced from this long thread. I've split the thread so it is easier to see the new posts.

Since you are on Windows 11, please install WSL2 (Window Subsystem for Windows). The default ubuntu system is good to get 3DNA up and running quickly. Please have a try and report back how it goes.

Xiang-Jun

32

FAQs / Re: Running DSSR on macOS

« on: November 08, 2024, 09:30:04 pm »

As a follow up, please note that:

The CTV distributes DSSR Basic and Pro versions in zip format for macOS, Linux, and Windows. Each zip file contains a DSSR binary executable as well as the associated user manual.

Assuming basic command-line knowledge, users should be able to follow the instructions in the manual and reproduce reported results.

33

FAQs / Re: Running DSSR on macOS

« on: November 08, 2024, 06:46:53 pm »

Thanks for your interest in using DSSR. Your screenshot provides information that explains why you're having problems using DSSR.

You're on a macOS, and you have double-clicked the x3dna-dssr executable to run it. I can reproduce your case by installing x3dna-dssr under the ~/Downloads folder and double-clicking it. The error message is quite informative, by showing that x3dna-dssr is run, and immediately exit. Running x3dna-dssr without any options gives the following message:

missing required option: must specify -i=PDBFile/mmCIF

type: 'x3dna-dssr -h (or --help)' for further help
      'x3dna-dssr --citation' for preferred citation(s)

Time used: 00:00:00:00

That means DSSR is already successfully installed on your macOS. It is just that DSSR is a command-line (CLI) program, and you need a terminal window to run it. There are many online tutorials on how to get started using terminal on macOS. Here is one: Absolute BEGINNER Guide to the Mac OS Terminal. Once you are familiar with the terminal, running DSSR should be straightforward, as detailed in the User Manual.

The DSSR executable (x3dna-dssr for macOS and Linux, and x3dna-dssr.exe for Windows) is self-contained and does not rely on any third-party libraries. There is no need for any setup or configurations: type x3dna-dssr -h to verify your installation. Note that DSSR is a command-line program: you need a terminal window to run it.

If you're GUI-driven and do not want to use CLI at all, then you may find the following two resources helpful:

• DSSR-enabled Innovative Schematics of 3D Nucleic Acid Structures with PyMOL
• Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures

Best regards,

Xiang-Jun

34

RNA structures (DSSR) / Re: plotting the helical axis along curved helices

« on: October 25, 2024, 08:46:14 pm »

Hi Di,

Do you have any idea of how to easily find the axis of each 2-bp segment of a helix?

The info is within DSSR, but not exposed. I'm considering to add this feature in DSSR JSON output for easy parsing. For WC-like pairs, things are not that complicated. However, with there are subtitles with non-Watson-Crick pairs, e.g., Hoogsteen and reverse Hoogsteen base pairs.

Also, I think an easier solution for A-form helix is to do a shift of the origin in the plane of the reference frame so that the shifted origin is where the axis passes through the plane.

See "Worked examples on base-pair parameters" in the DSSR Pro User Manual. especially Session "6 Local helical parameters". The vectors o1_h and o2_h are what you need. They are not simple shifts of the origin in the reference frame.

This thread actually prompt me to refine the detailed algorithmic descritpion and get the content published. They are the real meat of 3DNA!

Best regards,

Xiang-Jun

35

RNA structures (DSSR) / Re: plotting the helical axis along curved helices

« on: October 24, 2024, 10:53:08 pm »

Hi Di,

Thanks for posting on the Forum. Indeed the origins of base-pairs are centered within a pair, as defined in the standard base reference frame. For B-form DNA where the helical axis passes through and is perpendicular to base pairs, the line connecting bp origins appears as expected. For A-form DNA or RNA (which is in A-form), the helical axis passes through the central hole where the bps (and their origins) spiral around. See "Figure 4. Influence of non‐zero Slide and Roll at sequential dimer steps on overall DNA helical conformation" of the 2003 3DNA paper in NAR.

DSSR does output a linear helical axis when a helical segment is not too strongly curved. See the 2015 DSSR paper "Figure 2 -- analysis of the yeast phenylalanine tRNA (1ehz)" for an example. You could also run the following commands:

Code: [Select]

x3dna-dssr -i=1ehz.pdb --helical-axis
pymol 1ehz.pdb dssr-helicalAxes.pdb
# within PyMOL: as lines; png 1ehz-helices.png
You will see an image as attached below.

However, DSSR currently does not fit a smooth curvilinear helical axis around an arbitrary shape, e.g., a DNA circle. In principle, DSSR can fit a mini-helical axis for each base-pair step (i.e., a 2-bp segment) and then perform a b-spline interpolation. I'm open to suggestions and welcome collaborations to pursue this topic further.

Best regards,

Xiang-Jun

36

Site announcements / X3DNA-DSSR is funded and DSSR Basic is free for academic users

« on: September 25, 2024, 10:31:18 am »

Dear 3DNA/DSSR users,

It gives me great pleasure to announce that the 3DNA/DSSR project is now funded by the NIH R24GM153869 grant, "X3DNA-DSSR: a resource for structural bioinformatics of nucleic acids". I am deeply grateful for the opportunity to continue working on a project that has basically defined who I am. It was a tough time during the funding gap over the past few years. Nevertheless, I have experienced and learned a lot, and witnessed miracles enabled by enthusiastic users.

Since late 2020 when I lost my R01 grant, DSSR has been licensed by the Columbia Technology Ventures (CTV). I appreciate the numerous users (including big pharma) who purchased a DSSR Pro License or a DSSR Basic paid License. Thanks to the NIH R24GM153869 grant, we are pleased to provide DSSR Basic free of charge to the academic community. Academic Users may submit a license request for DSSR Basic or DSSR Pro by clicking "Express Licensing" on the CTV landing page. Commercial users may inquire about pricing and licensing terms by emailing techtransfer@columbia.edu, copying xiangjun@x3dna.org.

The current version of DSSR is v2.4.5-2024sep24 which contains miscellaneous bug fixes (e.g., chain id with > 4 chars) and minor improvements. This release synchronizes with the new R24 funding, which will bring the project to the next stage. All existing users are encouraged to upgrade their installation.

Lots of exciting things will happen for the project. The first important thing is to make DSSR freely accessible to the academic community. I'm now starting to monitor the Forum closely and answer users questions promptly.

I am committed to making DSSR a brand that stands for quality and value. By virtue of its unmatched functionality, usability, and support, DSSR saves users a substantial amount of time and effort when compared to other options. My track record throughout the years has unambiguously demonstrated my dedication to this solid software product.

Xiang-Jun

DSSR Basic contains all features described in the three DSSR-related papers, and include the originally separate SNAP program (still unpublished) for analyzing DNA/RNA-protein complexes. The Pro version integrates the classic 3DNA functionality, plus advanced modeling routines, with email/Zoom/phone support.

37

RNA structures (DSSR) / Re: A pair is absent in dot-bracket notation ?

« on: September 05, 2024, 11:10:22 pm »

Pay attention to the following section:

# x3dna-dssr -i=8SH5.pdb

  stem#3[#2, #3]* bps=2 parallel
      strand-1 5'-GG-3'
       bp-type    ||
      strand-2 5'-CC-3'
      helix-form  .
   1 R.G19          R.C49          G-C WC           19-XIX    cWW  cW-W
   2 R.G20          R.C50          G-C WC           19-XIX    cWW  cW-W

These two WC pairs form a parallel mini-duplex. Both pairs (not just G19-C49 but also G20-C50) are excluded from the DBN notation.

Best regards,

Xiang-Jun

38

RNA structures (DSSR) / Re: How the length of the sequence depends on _pdbx_unobs_or_zero_occ_atoms ???

« on: September 05, 2024, 10:58:42 pm »

Hi,

DSSR is based on 3D structures of DNA/RNA, deriving features of base-pairing and stacking interactions. It also takes abasic sites into consideration in later releases, requiring only P or at least 5 out of the 6 main-chain backbone atoms (P, O5', C5', C4', C3', and O3'). In PDB entry 4AL5, nucleotide C4 has only one backbone atom (O3'), and C21 has 4 backbone atoms (P, O1P, O2P, and O5') as shown below.

ATOM   2826 O "O3'"  . C   B 2 3   ? 14.682 -18.630 19.841  1.00 152.11 ? 4    C   B "O3'"  1
......
ATOM   3343 P P      . C   B 2 20  ? 2.515  -3.243  14.608  1.00 43.27  ? 21   C   B P      1
ATOM   3344 O OP1    . C   B 2 20  ? 1.257  -3.732  14.022  1.00 60.70  ? 21   C   B OP1    1
ATOM   3345 O OP2    . C   B 2 20  ? 2.599  -1.863  15.133  1.00 37.31  ? 21   C   B OP2    1
ATOM   3346 O "O5'"  . C   B 2 20  ? 2.975  -4.175  15.812  1.00 40.82  ? 21   C   B "O5'"  1

So in previous DSSR versions, both nucleotides are ignored.

Following your question, I've revised DSSR to v2.4.4-2024sep06 which can recognize these two nucleotides. See below:

# x3dna-dssr -i=4AL5.cif
Secondary structures in dot-bracket notation (dbn) as a whole and per chain
>4AL5 nts=18 [whole]
CACUGCCGUAUAGGCAGC
..(((((.....))))).
-.AAAA..A...AAAA--

****************************************************************************
Summary of structural features of 18 nucleotides
  Note: the first five columns are: (1) serial number, (2) one-letter
    shorthand name, (3) dbn, (4) id string, (5) rmsd (~zero) of base
    ring atoms fitted against those in a standard base reference
    frame. The sixth (last) column contains a comma-separated list of
    features whose meanings are mostly self-explanatory, except for:
      turn: angle C1'(i-1)--C1'(i)--C1'(i+1) < 90 degrees
      break: no backbone linkage between O3'(i-1) and P(i)
   1  C . B.C4      ---    non-stack,ss-non-loop
   2  A . B.A5      0.013  anti,~C2'-endo,non-pair-contact,ss-non-loop,splayed-apart
   3  C ( B.C6      0.007  anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,phosphate,splayed-apart
   4  U ( B.U7      0.009  anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate
   5  G ( B.G8      0.015  anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate
   6  C ( B.C9      0.011  anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate
   7  C ( B.C10     0.011  anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop,phosphate
   8  G . B.G11     0.043  u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor,phosphate
   9  U . B.U12     0.019  turn,u-turn,anti,~C3'-endo,non-pair-contact,hairpin-loop
  10  A . B.A13     0.022  u-turn,anti,~C3'-endo,non-pair-contact,hairpin-loop,cap-donor,phosphate
  11  U . B.U14     0.006  turn,u-turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,phosphate,splayed-apart
  12  A . B.A15     0.007  anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,splayed-apart
  13  G ) B.G16     0.017  anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop
  14  G ) B.G17     0.011  anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem
  15  C ) B.C18     0.011  anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem
  16  A ) B.A19     0.014  anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem
  17  G ) B.G20     0.018  anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end
  18  C . B.C21     ---    non-stack,ss-non-loop,phosphate

Best regards,

Xiang-Jun

39

General discussions (Q&As) / Re: All Possible Base Pairs

« on: August 08, 2024, 07:33:33 pm »

Hi Parivash,

DSSR (http://forum.x3dna.org/site-announcements/no-more-grant-funding-for-3dnadssr/) can find all base pairs and tertiary stacking interactions, among numerous other features. Using your RNA.pdb as an example, run the following commands:

Code: [Select]

x3dna-dssr -i=RNA.pdb -o=RNA.out
x3dna-dssr -i=RNA.pdb --non-pair | grep 'stacking:' | grep -v connected > long-stacks.txt
The output files RNA.out and long-stacks.txt are attached for your reference. The RNA.out contains a port of stacking interactions as listed below:

Code: [Select]

****************************************************************************
List of 63 base stacks
  Note: a stack is an ordered list of nucleotides assembled together via
        base-stacking interactions, regardless of backbone connectivity.
        Stacking interactions within a stem are *not* included.
   1 nts=2 AG A.A563,A.G567
   2 nts=2 GA A.G570,A.A873
   3 nts=2 AA A.A573,A.A574
   4 nts=2 GG A.G587,A.G755
   5 nts=2 GU A.G597,A.U598
   6 nts=2 GC A.G617,A.C618
   7 nts=2 AG A.A632,A.G633
   8 nts=2 AC A.A642,A.C643
   9 nts=2 GC A.G644,A.C645
  10 nts=2 GG A.G657,A.G658
  11 nts=2 GG A.G688,A.G700
  12 nts=2 CG A.C701,A.G703
  13 nts=2 GG A.G727,A.G731
  14 nts=2 CC A.C747,A.C748
  15 nts=2 AG A.A777,A.G778
  16 nts=2 UC A.U804,A.C805
  17 nts=2 CA A.C817,A.A819
  18 nts=2 GU A.G818,A.U820
  19 nts=2 UU A.U827,A.U870
  20 nts=2 GC A.G838,A.C840
  21 nts=2 CU A.C862,A.U863
  22 nts=2 CG A.C866,A.G867
  23 nts=2 AG A.A872,A.G874
  24 nts=2 CC A.C879,A.C880
  25 nts=2 GG A.G898,A.G902
  26 nts=2 CA A.C912,A.A913
  27 nts=3 CUC A.C562,A.U884,A.C883
  28 nts=3 CUG A.C564,A.U565,A.G566
  29 nts=3 AAA A.A572,A.A864,A.A865
  30 nts=3 GAU A.G577,A.A816,A.U813
  31 nts=3 GAG A.G662,A.A663,A.G664
  32 nts=3 AAG A.A728,A.A729,A.G730
  33 nts=3 CAA A.C732,A.A665,A.A733
  34 nts=3 GGG A.G774,A.G775,A.G776
  35 nts=3 GGG A.G821,A.G575,A.G881
  36 nts=3 GGU A.G890,A.G906,A.U905
  37 nts=3 CAA A.C899,A.A900,A.A901
  38 nts=4 UGGU A.U580,A.G581,A.G758,A.U757
  39 nts=4 GAGA A.G588,A.A753,A.G654,A.A655
  40 nts=4 GGUA A.G594,A.G595,A.U641,A.A640
  41 nts=4 CAAC A.C620,A.A621,A.A622,A.C623
  42 nts=4 CUGU A.C651,A.U652,A.G752,A.U751
  43 nts=4 GGGU A.G666,A.G741,A.G742,A.U743
  44 nts=4 GAGU A.G683,A.A684,A.G685,A.U686
  45 nts=4 CGGU A.C689,A.G690,A.G691,A.U692
  46 nts=4 CAGG A.C779,A.A780,A.G800,A.G799
  47 nts=4 GAUU A.G786,A.A787,A.U788,A.U789
  48 nts=4 CGGC A.C857,A.G858,A.G869,A.C868
  49 nts=4 GGAU A.G887,A.G888,A.A889,A.U891
  50 nts=5 GAUGG A.G584,A.A583,A.U582,A.G760,A.G761
  51 nts=5 AAUAC A.A687,A.A704,A.U705,A.A706,A.C707
  52 nts=5 CGCCC A.C764,A.G765,A.C812,A.C811,A.C810
  53 nts=5 GAAAA A.G769,A.A768,A.A767,A.A766,A.A814
  54 nts=5 CAUAG A.C783,A.A782,A.U801,A.A802,A.G803
  55 nts=5 GAAAG A.G829,A.A828,A.A859,A.A860,A.G861
  56 nts=6 UGGGGG A.U605,A.G606,A.G631,A.G630,A.G629,A.G628
  57 nts=6 AAAGAC A.A607,A.A608,A.A609,A.G610,A.A611,A.C612
  58 nts=6 GAAAUG A.G693,A.A694,A.A695,A.A696,A.U697,A.G698
  59 nts=6 AGGAAC A.A712,A.G713,A.G714,A.A715,A.A716,A.C717
  60 nts=6 AGAACC A.A790,A.G791,A.A792,A.A794,A.C795,A.C796
  61 nts=7 UUAAGGG A.U678,A.U677,A.A676,A.A675,A.G674,A.G673,A.G734
  62 nts=7 GCCGAGG A.G718,A.C719,A.C720,A.G721,A.A722,A.G724,A.G725
  63 nts=7 GCAAAAC A.G894,A.C893,A.A892,A.A907,A.A908,A.A909,A.C910

Best regards,

Xiang-Jun

40

General discussions (Q&As) / Re: All Possible Base Pairs

« on: June 09, 2024, 10:34:29 pm »

Hi Parivash,

Thanks for your interest in using 3DNA. The find_pair -p command should give you a list of all pairs, canonical or not. Please provide a concrete example to illustrate what base pairs are missing.

As for the availability of x3dna-dssr, please see the post "No more grant funding for 3DNA/DSSR" (http://forum.x3dna.org/site-announcements/no-more-grant-funding-for-3dnadssr/). You could use http://skmatics.x3dna.org to analyze/visualize a structure using x3dna-dssr.

Hope this helps.

Xiang-Jun

41

MD simulations / Re: Gromacs missing ' P ' atom

« on: May 27, 2024, 06:41:08 pm »

No, it is for information only: i.e., the first nucleotide (DG1) does not have the phosphate group.

42

RNA structures (DSSR) / Re: DSSR Basic Licence Application: Seeking Status Update and Assistance

« on: February 20, 2024, 06:02:31 pm »

Hi Junkai,

Thanks for the update. Getting DSSR-Basic, Academic license has been very straightforward from past experiences. As I heard from the CTV, your application has triggered a review of the license policy, and thus the delay. I am not sure of the exact details, but being patient seems to the best thing that can be done.

Let's stop this thread and put future communications via email.

Best regards,

Xiang-Jun

43

RNA structures (DSSR) / Re: DSSR Basic Licence Application: Seeking Status Update and Assistance

« on: February 16, 2024, 09:05:42 am »

Hi Junkai,

Thanks for your interest in purchasing a DSSR Basic Academic License. Sorry for the unexpected delay in response from the CTV. I've communicated with people in charge, and hopefully the issue will be resolved shortly.

Best regards,

Xiang-Jun

44

RNA structures (DSSR) / Re: How does 3dna-dssr convert the atomic coordinates from PDB files into its output

« on: February 04, 2024, 11:19:43 am »

Code: [Select]

what are the criteria for selecting the origin and XYZ axis vectors for the coordinate system?

It helps that you reads 3DNA/DSSR-related publications, and report back what you find.

45

RNA structures (DSSR) / Re: How does 3dna-dssr convert the atomic coordinates from PDB files into its output

« on: February 02, 2024, 09:35:33 pm »

Hi Junkai,

Thanks for your follow-up. Now your question can be answered, using C5' atom as an example:

ATOM    195  C5'  U A  10     -15.795  -3.890 -14.824  1.00  0.34           C  
C5' atom coordinate       C5prime_xyz: [-1.405, 8.313, 1.694]

C5prime_xyz is the original C5' atomic coordinates [-15.795  -3.890 -14.824] expressed in the local base reference frame,

Code: [Select]

{"rmsd":0.013,"origin":[-7.546,-2.079,-13.202],
              "x_axis":[-0.071,0.233,0.970],
              "y_axis":[-0.997,0.020,-0.078],
              "z_axis":[-0.037,-0.972,0.231],
"quaternion":[0.543,0.412,-0.464,0.566]}


dd = [-15.795  -3.890 -14.824] - [-7.546,-2.079,-13.202] = [-8.249  -1.811  -1.622]

dd * [ -0.071  -0.997  -0.037
        0.233   0.020  -0.972
        0.970  -0.078   0.231 ] = [-1.4096   8.3145   1.6908]

The slight difference between [-1.4096   8.3145   1.6908] and [-1.405, 8.313, 1.694] is due to round off errors.

Hope this helps.

Xiang-Jun

PS. Which version of DSSR are you using?

46

Feature requests / MOVED: 2D DNA structure

« on: February 02, 2024, 12:14:28 pm »

This topic has been moved to RNA structures (DSSR).

http://forum.x3dna.org/index.php?topic=1020.0

47

RNA structures (DSSR) / Re: 2D DNA structure

« on: February 02, 2024, 12:13:19 pm »

Hi Luka,

Thanks for attaching file AATAAA_dna.pdb (no need to copy-and-paste the content). DSSR does what you want, as shown below:

Code: [Select]

x3dna-dssr -i=AATAAA_dna.pdb -o=AATAAA_dna.out

# dssr-2ndstrs.dbn
>AATAAA_dna nts=16 [AATAAA_dna] -- secondary structure derived by DSSR
GCGCGAATAAACGCGC
(((((......)))))

# dssr-2ndstrs.ct
   16 ENERGY = 0.0 [AATAAA_dna] -- secondary structure derived by DSSR
    1 G     0     2    16     1
    2 C     1     3    15     2
    3 G     2     4    14     3
    4 C     3     5    13     4
    5 G     4     6    12     5
    6 A     5     7     0     6
    7 A     6     8     0     7
    8 T     7     9     0     8
    9 A     8    10     0     9
   10 A     9    11     0    10
   11 A    10    12     0    11
   12 C    11    13     5    12
   13 G    12    14     4    13
   14 C    13    15     3    14
   15 G    14    16     2    15
   16 C    15     0     1    16

It generates output file AATAAA_dna.out, and a few auxiliary files including dssr-2ndstrs.ct and dssr-2ndstrs.dbn which are all attached.

See the post [No more grant funding for 3DNA/DSSR](http://forum.x3dna.org/site-announcements/no-more-grant-funding-for-3dnadssr/).

Xiang-Jun

48

RNA structures (DSSR) / Re: 2D DNA structure

« on: February 01, 2024, 11:05:25 am »

Please attach the file: AATAAA_dna.pdb

49

RNA structures (DSSR) / Re: 2D DNA structure

« on: February 01, 2024, 10:07:44 am »

Hi Luka,

Please use a specific to illustrate unambiguously what you want to achieve. What you have tried and the results you got.

Xiang-Jun

50

RNA structures (DSSR) / Re: How does 3dna-dssr convert the atomic coordinates from PDB files into its output

« on: February 01, 2024, 08:57:36 am »

Hi,

Please be specific with your questions by providing a minimal, reproducible example. What commands did you use? What results did you get? What did you expect? ....

Best regards,

Xiang-Jun