Messages

1

General discussions (Q&As) / Re: Rebuilding Z-DNA

« on: March 17, 2025, 09:18:59 am »

But I am unable to properly download the pdb file.

What do you mean? Just click on the link and it should download automatically. I've never heard of any issues with downloading files as long as you have an active internet connection. Please clarify your issue so I can assist you better.

2

General discussions (Q&As) / Re: Rebuilding Z-DNA

« on: March 15, 2025, 12:18:44 am »

Does the attached PDB file (with base schematic image) fulfill your needs? The backbone connection between the two segments are a bit longer than normal O--P covalent bond distance, which you can regulated with energy minimizations (e.g., using Phenix, as shown in "Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures" (https://doi.org/10.1093/nar/gkz394).

3

General discussions (Q&As) / Re: Rebuilding Z-DNA

« on: March 14, 2025, 08:12:34 am »

Thanks for your follow-up questions and the details you provided. It is always helpful to to be specific when discussing research topics.

Yes, "rebuild -atomic" would have issues with backbone connectivity, since in Z-DNA, nucleotide G is in syn conformation instead of anti (for C). The building block must be adjusted accordingly. I'll look into this further to see what we can get.

Another approach is to take the whole Z-DNA structure as a unit, and perform some transformations to extend it. See the PyMOL thread a few years ago on "create a 26 bp RNA from a 13 bp system" (https://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg16190.html). The idea is applicable to Z-DNA as well. Note that the features are now available in the free DSSR Academic license (previously in DSSR Pro Academic only). Check if that method makes sense to you.

Best regards,

Xiang-Jun

4

General discussions (Q&As) / Re: Rebuilding Z-DNA

« on: March 13, 2025, 03:56:04 pm »

Thanks for your quick follow-up.

As noted in the x3dna_utils cp_std -h help message, the utility covers the most common use cases:

Select the standard data files to be used with "analyze" and "rebuild".
Available sets include BDNA, ADNA, NDB96 and RNA, which have exactly
the same base geometry and orientation (in the standard base reference
frame) but different backbone conformations.

Z-DNA is different from the standard right-handed DNA/RNA double helix in that it has not only a left-handed twist but also a base flip, and it has a di-nucleotide (most commonly CpG) as a the building block. So the x3dna_utils cp_std does not cover Z-DNA. However, you can run analyze, modify the output parameters (and extend as needed), and then rebuild a Z-DNA structure according to the modified parameters.

What specific Z-DNA structure you’d like to extend? If you do not want share details, please use a sample Z-DNA structure that helps illustrate your point. Reproducibility is important.

Best regards,

Xiang-Jun

5

General discussions (Q&As) / Re: Rebuilding Z-DNA

« on: March 13, 2025, 02:14:06 pm »

Hi,

Thanks for using 3DNA and for posting your questions on the Forum. 3DNA rebuild should be able to build Z-DNA structures given a set of parameters. Please be specific with what you are trying to achieve, and we can start from there.

Best regards,

Xiang-Jun

6

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

« on: February 28, 2025, 08:47:06 am »

Welcome back.

But I do not have a PDB structure with the m3C modification, I was hoping that we would be able to generate the PDB (and PSF) using 3DNA/DSSR by specifying the residues.

Are you expecting 3DNA/DSSR to "generate the PDB" by specifying the residues, including unknown ones?  3DNA/DSSR can build DNA/RNA structures with standard bases (A,C,G,T,U), or modified ones with *known* building block as illustrated in 5-methylcytosine in the FAQ. It does not generate structures for ligands like m3C. It is up to the user to provide such building blocks for 3DNA/DSSR to proceed. CCP4 and Phenix may have utilities to generate new ligands.

By the way, what does PSF stand for?

As a side question, what would be a good force field that can allow us to perform a phase separation simulation with the methylated ssDNA and IDR sequence?

Sorry, I'm not familiar with this field, and I cannot offer any valuable suggestions. Overall, this question is out of the scope of the Forum.

Best regards,

Xiang-Jun

7

MD simulations / Re: Update of do_x3dna package

« on: February 22, 2025, 11:23:27 pm »

Hi Rajendra,

Thanks for the update to do_x3dna for GROMACS-2025. It is great that the "binary package can be used with files generated by any version of GROMACS". Over the years, I've received emails about applying 3DNA to MD simulations, and I know that your do_x3dna package is well received by the community.

Best regards,

Xiang-Jun

8

General discussions (Q&As) / Re: Opening values and the definition for base-pair parameters

« on: February 07, 2025, 10:22:26 am »

Hi Jing,

Please follow what I suggested in the previous response. As for the 3DNA source code, did you notice the download link at the top and the Download instructions post?

Best regards,

Xiang-Jun

9

General discussions (Q&As) / Re: Opening values and the definition for base-pair parameters

« on: February 06, 2025, 11:14:10 am »

Hi Jing,

I have attached several pictures here. They are G and G pairs. The first two are with the opening \~180, the third picture is with \~-180, and the last two are with \~90.

Thanks for your follow up, and for providing images that illustrate G.G pairs with opening around 180 and 90 degrees. It would have been more helpful if you attached the corresponding PDB files. When posting questions in the future, thinks about providing (mininal) examples so others can *reproduce* the cases.

Now I understand the question you're asking. Let's use a G+G pair in G-tetrad of G-quadruplexes as an example, which has an opening around 90 degrees. Assuming you have downloaded the coordinates file `5ua3.pdb` for PDB entry 5ua3 on "Crystal structure of a DNA G-quadruplex with a cytosine bulge". Please try the following DSSR commands:

Code: [Select]

# This extract DG1 and DG6 from chain A into file 5ua3-GG.pdb
x3dna-dssr -i=5ua3.pdb --select-residue='A 1+6' -o=5ua3-GG.pdb

# Set the pair into the base reference frame of A.DG1
x3dna-dssr -i=5ua3-GG.pdb --frame='A.1' -o=5ua3-GG-frame1.pdb

# Generate the schematic with base blocks
x3dna-dssr -i=5ua3-GG-frame1.pdb --cartoon-block=sticks-label --block-file=slim-outline -o=5ua3-GG-frame1.pml
Load `5ua3-GG-frame1.pml` into PyMOL to see the attached image where the (`slim`) base blocks are nearly perpendicular, corresponding to an opening angle of ~90 degrees.

Analyze `5ua3-GG.pdb` (or `5ua3-GG-frame1.pdb`) with `--more` option to see the six base-pair parameters, including opening.

Code: [Select]

x3dna-dssr -i=5ua3-GG.pdb --more

# With the following detailed information:
List of 1 base pair
     nt1            nt2            bp  name        Saenger   LW   DSSR
   1 A.DG1          A.DG6          G+G --          06-VI     cWH  cW+M
       [-131.0(anti) ~C2'-endo lambda=62.6] [-128.4(anti) ~C2'-endo lambda=28.0]
       d(C1'-C1')=11.59 d(N1-N9)=9.65 d(C6-C8)=9.30 tor(C1'-N1-N9-C1')=10.9
       H-bonds[2]: "N1(imino)-O6(carbonyl)[2.95],N2(amino)-N7[2.91]"
       interBase-angle=1  Simple-bpParams: Shear=-2.67 Stretch=2.83 Buckle=-0.8 Propeller=0.5
       bp-pars: [1.61    3.54    -0.15   0.14    0.94    -89.63]
Note that the opening is reported as `-89.63` --- if you try to align A.DG6 to A.DG1, you need to rotate ~`-90` degrees as can be seen in the attached images. If you swap the pair, the opening would be ~`+90` degrees. See the [2003 3DNA paper in NAR](https://doi.org/10.1093/nar/gkg680), specifically the section "Base pair parameters".

With a clear understand of the above example, you should have little difficult in understanding opening ~180 degrees. You are suggested to follow the above example on one of such cases, and report back your findings.

Note that 3DNA/DSSR report angular parameters in the range of [0, +-180] instead of [0, 360]. So opening of `-175` is not that much a difference from `+175` (vs `+185`). Also notice the opposite sign of opening for M+N vs N+M pairs.

Please read the [DSSR manual](http://docs.x3dna.org/dssr-manual.pdf) and the [practical guide for the DSSR-PyMOL](http://skmatic.x3dna.org/dssr-schematic-guide.pdf) article.

Best regards,

Xiang-Jun

10

General discussions (Q&As) / Re: Opening values and the definition for base-pair parameters

« on: February 03, 2025, 06:05:26 pm »

Hi Jing,

Thanks for using 3DNA, and for posting your questions on the Forum. Your confusions about the details are understandable, and can be clarified most effectively using concrete examples. Do you have examples with opening ~90 and 180?

Since 3DNA source code is available, you can dig into it to see exactly how the base reference frames are defined and how the various parameters are calculated.

Best regards,

Xiang-Jun

11

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

« on: January 31, 2025, 08:51:31 am »

Hi Sunera,

Thanks for your follow up. Is the idea in FAQ "How can I mutate cytosine to 5-methylcytosine?" relevant? Do you have a PDB structure with m3C modification?

Best regards,

Xiang-Jun

12

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

13

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

14

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

15

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

16

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.


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).

17

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

18

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.

19

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

20

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

21

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

22

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.

23

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

24

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

25

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