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Topics - xiangjun

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1
Site announcements / Clarification on DSSR licensing
« on: May 31, 2021, 01:58:55 pm »
Once in a while I receive emails from prospective users, both commercial and academic, about DSSR licensing from the Columbia Technology Venture (CTV). Louis made the following explicit suggestion in a recent thread titled "Bug or feature (?) : residue numbering not understood":

Quote from: Louis
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?

The different DSSR license types are thus summarized below:
  • Commercial users may inquire about pricing and licensing terms by emailing techtransfer@columbia.edu.

  • Academic users can obtain the DSSR Pro license ($1000) by contacting techtransfer@columbia.edu. It is a one-time fee and does not cover future major releases of the software. Minor releases with bug-fixes and small updates are included in the fee. In reality, I do not expect another major release of DSSR in the next four years. As a result, the average annual cost is $250, which is about a tenth of the cost of a journal publication or a two-night hotel stay.

    DSSR Pro includes advanced capabilities for model building, additional features in structural analyses, annotations, and visualizations. It comes with a comprehensive user manual, as well as one year of technical support from me.

  • Academic users can also obtain the free DSSR Basic license from the CTV website. DSSR Basic includes features described in the three DSSR papers (2015 DSSR, 2017 DSSR-Jmol, and 2020 DSSR-PyMOL, all published in NAR) so that reported results can be reproduced. DSSR Basic is provided "as is" without any warranty of support.

Users of DSSR Pro, both commercial and academic, receive first-rate support directly from the developer. For the benefit of the community, the open 3DNA Forum is the preferred method of communication. On the other hand, I'm fine with email or virtual meetings if that's what the DSSR Pro users want. Please keep in mind that the CTV does not provide a free DSSR Pro evaluation license.

Free academic users of DSSR Basic are welcome to ask DSSR-related questions on the 3DNA Forum. I will fix any reported and verified bugs as soon as possible. I might also be available to answer general questions, especially about reproducing published results or document features. Requests for additional features, however, may necessitate an upgrade to DSSR Pro. I would only respond to questions from free academic users via the open 3DNA Forum; no email or virtual meetings.

Please contact CTV via email (techtransfer@columbia.edu) if you have any additional questions about DSSR licensing. If you are unable to contact CTV via its DSSR website or email, please report your problem here. I'll then do my best to assist.

Xiang-Jun


PS: Chrome is the best browser for accessing the DSSR website on the CTV. Safari (on macOS) and Opera have also been reported to work flawlessly. On the other hand, you may experience issues with these browsers: Firefox, Edge, or Vivaldi.

4
Site announcements / Video: an overview of DSSR
« on: May 01, 2021, 01:32:37 pm »
I've just released a video "An overview of DSSR" -- http://docs.x3dna.org/dssr-overview/.

DSSR already has a large user base. Based on my observation, however, DSSR is still heavily underused for what it has to offer. This DSSR overview video is for new DSSR users, as well as existing ones.

As always, I appreciate your feedback.

Best regards,

Xiang-Jun

5
FAQs / MOVED: X3DNA and cif
« on: April 30, 2021, 10:45:41 am »

8
General discussions (Q&As) / MOVED: Circular DNA parameters
« on: February 18, 2021, 11:07:07 am »

9
Recently, while visiting the NAR website on DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL, I noticed a big red circle near “View Metrics”. The symbol is very obvious and a bit 'alarming'. I was curious to see what it meant. After a few clicks, I was delighted to read the following recommendation in Faculty Opinions by Quentin Vicens:

Quote
I really enjoyed “playing” with the revised and expanded version of Dissecting the Spatial Structure of RNA (DSSR) described by Xiang-Jun Lu in this July issue of NAR. The software is known to generate ‘block view’ representations of nucleic acids that make many parameters more immediately visible, such as base composition, stacking, and groove depth. This new version includes Watson-Crick pairs shown as single rectangles, and G quadruplexes as large squares, making such regions more quickly distinguishable from other regions within an overall tertiary structure. I was amazed at how simple and effective the web interface was, and I liked the possibility to download a PyMOL session to look at molecules under different angles. If need be, blocks can be further edited in PyMOL using the provided plugin (see on page 35). I highly recommend it!

The DSSR-PyMOL schematics paper/website has been rated “Very Good”, and classified as “Good for Teaching”. See Vicens Q: Faculty Opinions Recommendation of [Lu XJ, Nucleic Acids Res 2020 48(13):e74]. In Faculty Opinions, 14 Aug 2020; 10.3410/f.738001682.793577327. A screenshot is attached below.


10
Site announcements / DSSR 2.0 is licensed by Columbia University
« on: August 24, 2020, 08:35:04 am »
DSSR 2.0 is out. It integrates an unprecedented set of features into one computational tool, including analysis/annotation, schematic visualization, and model building of 3D nucleic acid structures. DSSR 2.0 supersedes 3DNA 2.4, which is still maintained but no additional features other than bug fixes are scheduled. See the DSSR 2.0 overview PDF.

DSSR delivers a great user experience by solving problems and saving time. Considering its usability, interoperability, features, and support, DSSR easily stands out among 'competitors'. It exemplifies a 'solid software product'. I strive to make DSSR a pragmatic tool that the structural bioinformatics community can count on.

DSSR 2.0 is licensed by Columbia University. The software remains free for academic users, with the basic user manual. The professional user manual (over 230 pages, including 7 appendices) is available for paid academic users or commercial users only. Licensing revenue helps ensure the long-term sustainability of the DSSR project.

Additionally, the paper "DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL" has recently been published in Nucleic Acids Research, 48(13):e74. Check the web interface.

The DSSR-PyMOL paper/website has been rated "very good" and classified as "Good for Teaching". See Vicens Q: Faculty Opinions Recommendation of [Lu XJ, Nucleic Acids Res 2020 48(13):e74]. In Faculty Opinions, 14 Aug 2020; 10.3410/f.738001682.793577327.

11
General discussions (Q&As) / MOVED: RNA Journal Covers
« on: July 28, 2020, 03:38:07 pm »

13
Bug reports / MOVED: modified nucleotides incorrect.
« on: February 05, 2020, 08:54:25 am »

15
This website http://skmatic.x3dna.org/ (see screenshot below) aims to showcase DSSR-enabled cartoon-block schematics of nucleic acid structures using PyMOL. It presents a simple interface to browse pre-calculated PDB entries with a set of default settings: long rectangular blocks for Watson-Crick base-pairs, square blocks for G-tetrads in G-quadruplexes, with minor-groove edges in black. Users can also specify an URL to a PDB- or mmCIF-formatted file or upload such an atomic coordinates file directly, and set several common options to customerize to the rendered image.

Moreover, a web API to DSSR-PyMOL schematics is available to allow for its easy integration into third-party tools.


Input a PDB id
Pre-calculated cartoon-block images together with summary information are available for PDB entries of nucleic-acid-containing structures. Note that gigantic structures like ribosomes that are only represented in mmCIF format are excluded from the resource. The base block images are most effective for small to medium-sized structures.

Here are a few examples:
  • 1ehz, the crystal structure of yeast phenylalanine trna at 1.93-A resolution
  • 2lx1, the major conformation of the internal loop 5'GAGU/3'UGAG
  • 2grb, the crystal structure of an RNA quadruplex containing inosine-tetrad
  • 4da3, the crystal structure of an intramolecular human telomeric DNA G-quadruplex 21-mer bound by the naphthalene diimide compound MM41
  • 1oct, crystal structure of the Oct-1 POU domain bound to an octamer site
  • 2hoj, the crystal structure of an E. coli thi-box riboswitch bound to thiamine pyrophosphate, manganese ions

Each entry is shown with images in six orthogonal perspectives: front, back, right, left, top, bottom. The 'front' image (upper-left in the panel) is oriented into the most-extended view with the DSSR --blocview option. The corresponding PyMOL session file and PDB coordinate file are available for download. One can also visualize the structure interactively via 3Dmol.js.

Sample PDB entries
Users can browse random samples of pre-calculated PDB entries. The number should be between 3 and 99, with a default of 12 entries (see below for an example). Simply click the 'Submit' button or the link "Random samples (3 to 99)" to see random results of 12 entries each time.

Specify an coordinate file
The atomic coordinate file must be in PDB or mmCIF format, and can be optionally gzipped (.gz). One can either specify an URL to or select a coordinate file. Several common options are available to allow for user customizations.

Web API help message
Usage with 'http' (HTTPie):
    http -f http://skmatic.x3dna.org/api [options] url=|model@
    http http://skmatic.x3dna.org/api/pdb/pdb_id  -- for a pre-calculated PDB entry
    http http://skmatic.x3dna.org/api/help        -- display this help message
Options:
    block_file=styles-in-free-text-format [e.g., block_file=wc-minor]
    block_color=nt-selection-and-color    [e.g., block_color='A:pink']
    block_depth=thickness-of-base-block   [e.g., block_depth=1.2]
    r3d_file=true-or-FALSE(default)       [e.g., r3d_file=true]
    raw_xyz=true-or-FALSE(default)        [e.g., raw_xyz=true]
Required parameter
    url=URL-to-coordinate-file [e.g., url=https://files.rcsb.org/download/1ehz.pdb.gz]
    model@coordinate-file      [e.g., model@1ehz.cif]
    # Only one must be specified. 'url' precedes 'model' when both are specified.
    # The coordinate file must be in PDB or PDBx/mmCIF format, optionally gzipped.
Examples
    http -f http://skmatic.x3dna.org/api block_file='wc-minor' model@1ehz.cif r3d_file=t
    http -f http://skmatic.x3dna.org/api url=https://files.rcsb.org/download/1ehz.pdb.gz -d -o 1ehz.png
    http http://skmatic.x3dna.org/api/pdb/1ehz -d -o 1ehz.png
    # with 'curl'
    curl http://skmatic.x3dna.org/api -F 'model=@1msy.pdb' -F 'block_file=wc-minor' -F 'r3d_file=1'
    curl http://skmatic.x3dna.org/api -F 'url=https://files.rcsb.org/download/1ehz.pdb.gz' -o 1ehz.png
    curl http://skmatic.x3dna.org/api/pdb/1ehz -o 1ehz.png

Sample images
       

16
Feature requests / MOVED: building circular DNA
« on: July 16, 2019, 11:56:46 am »

17
It is a great pleasure to see that our article "Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures" has been highlighted in the cover page of the web server issue of NAR’19. According to the editor, This year, 331 proposals were submitted and 122, or 37%, were approved for manuscript submission. Of those approved, 94, or 77%, were ultimately accepted for publication. Overall, that corresponds to a ~28% acceptance rate.

The cover image and its caption are shown below. Moreover, details on how the cover image was created are available on the 3DNA Forum.

Caption: Examples of customized molecular models that can be generated with 3DNA: (top) a chromatin-like, nucleosome-decorated DNA with the structures of known histone-DNA assemblies placed at user-defined binding sites; (lower left) molecular schematic of a DNA trinucleotide diphosphate illustrating the base planes and reference frames used to construct and analyze 3D nucleic acid-containing structures; (lower right) customized single-stranded tRNA model built from a user-defined base sequence and a set of rigid-body parameters describing the desired placement of successive bases. Color code of base blocks: A, red; C, yellow; G, green; T, blue; U, cyan.

18
"Cover image featuring the web 3DNA 2.0 paper" title="Cover image featuring the web 3DNA 2.0 paper"

Caption: Examples of customized molecular models that can be generated with 3DNA: (top) a chromatin-like, nucleosome-decorated DNA with the structures of known histone-DNA assemblies placed at user-defined binding sites; (lower left) molecular schematic of a DNA trinucleotide diphosphate illustrating the base planes and reference frames used to construct and analyze 3D nucleic acid-containing structures; (lower right) customized single-stranded tRNA model built from a user-defined base sequence and a set of rigid-body parameters describing the desired placement of successive bases. Color code of base blocks: A, red; C, yellow; G, green; T, blue; U, cyan.



The top image is as Fig. 1E, and the lower-left image is as Fig. 2A. The lower-right image is sort of like Fig. 1D. However, it was actually generated using DSSR and PyMOL with (long) base-pair blocks for Watson-Crick pairs, with he commands used listed below:

Code: Bash
  1. x3dna-dssr -i=1fir-rebuild.pdb --blocview --block-opts=wc-minor -o=1fir-raw.pml
  2.  
  3. # Manually re-oriented the block image: "turn z, -155", and
  4. #     changed the chain color from "red" (default for chain A) to "marine"
  5. #     ray-traced and rendered to a PNG image, "1fir-dssr-pymol.png".
  6. # The revised PYMOL .pml file is named "1fir-dssr.pml"
  7. pymol -qkc 1fir-dssr.pml
  8. # The above PyMOL command generates "1fir-dssr-pymol.png", which is trimmed as below
  9. convert -trim +repage -transparent white 1fir-dssr-pymol.png 1fir-dssr.png

The following key related files are attached:
  • 1fir-rebuild.pdb -- a tRNA model generated with web 3DNA 2.0
  • 1fir-raw.pml -- the PyMOL script crated with DSSR (line #1 above)
  • 1fir-dssr.pml -- manually edited PyMOL script based on 1fir-raw.pml
  • 1fir-dssr.png -- the schematic block images used in the cover image

19
Our research article, "Effects of Noncanonical Base Pairing on RNA Folding: Structural Context and Spatial Arrangements of G·A Pairs", has recently been published in the ACS Biochemistry journal [2019, 58(20), pp.2474-2487]. It covers many aspects of RNA structural analysis and showcases some of the fundamental and unique features available from DSSR. This section is dedicated to topics directly related to the paper, including details for recreating the figures and tables reported therein. For general questions on DSSR, please use the section "RNA structures (DSSR)".

Quote
Noncanonical base pairs play important roles in assembling the three-dimensional structures critical to the diverse functions of RNA. These associations contribute to the looped segments that intersperse the canonical double-helical elements within folded, globular RNA molecules. They stitch together various structural elements, serve as recognition elements for other molecules, and act as sites of intrinsic stiffness or deformability. This work takes advantage of new software (DSSR) designed to streamline the analysis and annotation of RNA three-dimensional structures. The multiscale structural information gathered for individual molecules, combined with the growing number of unique, well-resolved RNA structures, makes it possible to examine the collective features deeply and to uncover previously unrecognized patterns of chain organization. Here we focus on a subset of noncanonical base pairs involving guanine and adenine and the links between their modes of association, secondary structural context, and contributions to tertiary folding. The rigorous descriptions of base-pair geometry that we employ facilitate characterization of recurrent geometric motifs and the structural settings in which these arrangements occur. Moreover, the numerical parameters hint at the natural motions of the interacting bases and the pathways likely to connect different spatial forms. We draw attention to higher-order multiplexes involving two or more G·A pairs and the roles these associations appear to play in bridging different secondary structural units. The collective data reveal pairing propensities in base organization, secondary structural context, and deformability and serve as a starting point for further multiscale investigations and/or simulations of RNA folding.



20
FAQs / Which one is the 3DNA homepage: x3dna.org or home.x3dna.org?
« on: June 07, 2019, 12:11:20 pm »
Content-wise, home.x3dna.org is a duplicate of x3dna.org, so both are the homepage of the 3DNA suite of programs, including DSSR and SNAP.

I registered the x3dna.org domain name and has hosted it on a popular shared web hosting service. Later on, I noticed that the 3DNA website is not acceptable from China, presumably due to the politically sensitive contents of other websites. To cater for the increasingly large number of 3DNA users from China, I created the home.x3dna.org sub-domain which is hosted at Columbia University. As a side note, the 3DNA Forum (forum.x3dna.org) is similarly hosted at Columbia, so it is generally accessible.

21
Site announcements / Web 3DNA 2.0 and G.A pairs in RNA folding
« on: June 07, 2019, 11:48:16 am »
Two papers closely related to 3DNA/DSSR have recently been published, as shown below:
  • "Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures" in Nucleic Acids Research (NAR). Here is the abstract, including a graphical illustration.
    Quote
    Web 3DNA (w3DNA) 2.0 is a significantly enhanced version of the widely used w3DNA server for the analysis, visualization, and modeling of 3D nucleic-acid-containing structures. Since its initial release in 2009, the w3DNA server has continuously served the community by making commonly-used features of the 3DNA suite of command-line programs readily accessible. However, due to the lack of updates, w3DNA has clearly shown its age in terms of modern web technologies and it has long lagged behind further developments of 3DNA per se. The w3DNA 2.0 server presented here overcomes all known shortcomings of w3DNA while maintaining its battle-tested characteristics. Technically, w3DNA 2.0 implements a simple and intuitive interface (with sensible defaults) for increased usability, and it complies with HTML5 web standards for broad accessibility. Featurewise, w3DNA 2.0 employs the most recent version of 3DNA, enhanced with many new functionalities, including: the automatic handling of modified nucleotides; a set of ‘simple’ base-pair and step parameters for qualitative characterization of non-Watson–Crick double- helical structures; new structural parameters that integrate the rigid base plane and the backbone phosphate group, the two nucleic acid components most reliably determined with X-ray crystallography; in silico base mutations that preserve the backbone geometry; and a notably improved module for building models of single-stranded RNA, double- helical DNA, Pauling triplex, G-quadruplex, or DNA structures ‘decorated’ with proteins. The w3DNA 2.0 server is freely available, without registration, at http://web.x3dna.org.



    Notably, details for reproducing our reported results (figures and tables) are available in a dedicated section "web 3DNA 2.0 (http://web.x3dna.org)" on the 3DNA Forum.


  • "Effects of Noncanonical Base Pairing on RNA Folding: Structural Context and Spatial Arrangements of G·A Pairs" in ACS Biochemistry. Here is the abstract with a graphical illustration.
    Quote
    Noncanonical base pairs play important roles in assembling the three-dimensional structures critical to the diverse functions of RNA. These associations contribute to the looped segments that intersperse the canonical double-helical elements within folded, globular RNA molecules. They stitch together various structural elements, serve as recognition elements for other molecules, and act as sites of intrinsic stiffness or deformability. This work takes advantage of new software (DSSR) designed to streamline the analysis and annotation of RNA three-dimensional structures. The multiscale structural information gathered for individual molecules, combined with the growing number of unique, well-resolved RNA structures, makes it possible to examine the collective features deeply and to uncover previously unrecognized patterns of chain organization. Here we focus on a subset of noncanonical base pairs involving guanine and adenine and the links between their modes of association, secondary structural context, and contributions to tertiary folding. The rigorous descriptions of base-pair geometry that we employ facilitate characterization of recurrent geometric motifs and the structural settings in which these arrangements occur. Moreover, the numerical parameters hint at the natural motions of the interacting bases and the pathways likely to connect different spatial forms. We draw attention to higher-order multiplexes involving two or more G·A pairs and the roles these associations appear to play in bridging different secondary structural units. The collective data reveal pairing propensities in base organization, secondary structural context, and deformability and serve as a starting point for further multiscale investigations and/or simulations of RNA folding.



    The paper includes a paragraph in the discussion section on differences between 3DNA/DSSR and the well-established LW (Leontis-Westhof) scheme:

    Quote
    Qualitative descriptions of noncanonical RNA base pairing, pioneered by Leontis and Westhof9,41 and linked in this work to the rigid-body parameters of interacting bases, have proven valuable in deciphering the connections between RNA primary, secondary, and tertiary structures. The present categorization is based on the positions of the hydrogen-bonded atoms with respect to a standard, embedded base reference frame30 defined in terms of an idealized Watson−Crick base pair. The major- and minor-groove base edges used here correspond in most cases to what are termed the Hoogsteen and sugar edges in the Leontis−Westhof scheme (one can compare the two classification schemes in Table S2). The + and − symbols introduced in 3DNA24 and DSSR27 unambiguously distinguish the relative orientations of the two bases. The trans and cis designations used in the earlier literature, however, are qualitative in nature and often uncertain. There are many “nc” (near cis, as in ncWW) and “nt” (near trans, as in ntSH) annotations listed in the RNA Structure Atlas; see, for example, the base-pair interactions in the sarcin−ricin domain of E. coli 23S rRNA found by entering PDB entry 1msy at http://rna.bgsu.edu/rna3dhub/pdb. The assignment of qualitative descriptors of RNA associations on the basis of atomic identity alone is generally not clear-cut. Numerical differences in the rigid-body parameters are critical to differentiating pairing schemes that share a common hydrogen bond, e.g., the G(N3)···A(N6) interaction found in m−WII and m−MI arrangements of G and A (Table 1 and Figures 4 and S3). The numerical data also provide a basis for following conformational transitions and may potentially be of value in making functional and other meaningful distinctions among RNA base pairs.

    See also a recent thread Noncanonical base pair standards on the 3DNA Forum and the section titled “3.2.2 Base pairs” in the DSSR User Manual.

22
Figure 3. Commonly-used fiber models and in silico base mutations. (A) Six commonly used models highlighted in the ‘Fiber’ module: single-stranded RNA, double-helical A-, B-, and C-form DNA, the Pauling triplex model (32), and the parallel polyI:polyI:polyI:polyI quadruplex. (B) Single-stranded RNA fiber model of base sequence AUCGAUCGAUCG. (C) Double-helical B-DNA fiber model with sequence ATCGATCGATCG on the leading strand. (D) Pauling triplex model with each strand of sequence AAAACCCCGGGG. (E) parallel polyI:polyI:polyI:polyI quadruplex model with 12 layers of hydrogen-bonded hypoxanthine tetrads. Models in (B-E) were generated using the default settings on the w3DNA 2.0 server, each taking just two mouse clicks. (F) All hypoxanthine bases along the poly I chains mutated to guanine via the ‘Mutation’ module, leading to a parallel G-quadruplex. Color code for base blocks: A, red; C, yellow; G, green; T, blue; U, cyan; I, dark green.

Reproducing the results reported in the figure is straightforward via the w3DNA 2.0 interface, by simply clicking a few buttons in each case. Please read tutorials on the 'Fiber' module and the 'Mutation' module online or in the corresponding sections of the supplemental PDF. See also the blogpost "Pauling's triplex model of nucleic acids is available in 3DNA" for details and background information about this model of historical significance. Note the schematic representation allows direct readout of base identity.

Fig. 3A is a screenshot of the header of the 'Fiber' module. The list includes the six commonly used fiber models: single-stranded RNA, double-helical A-, B-, and C-form DNA, the Pauling triplex model, and the parallel polyI:polyI:polyI:polyI quadruplex.

Fig. 3B-D are easily created by clicking two buttons each via the w3DNA 2.0 interface. Please read tutorial on the 'Fiber' module online or the section "S4.5 Modeling module: 56 fiber models" in the supplemental PDF.

Listed below are the 3DNA command-line scripts.
Code: Bash
  1.     # Fig. 3B, single-stranded RNA
  2. fiber -seq=AUCGAUCGAUCG -rna -single fiber-ssRNA.pdb
  3. blocview -x 180 -i fiber-ssRNA.png fiber-ssRNA.pdb
  4.     # Fig. 3C, double-stranded DNA
  5. fiber -seq=ATCGATCGATCG fiber-B-dsDNA.pdb
  6. blocview -i fiber-B-dsDNA.png fiber-B-dsDNA.pdb
  7.     # Fig. 3D, Pauling triplex
  8. fiber --pauling -seq=AAAACCCCGGGG Pauling-triplex.pdb
  9. blocview -x 180 -i Pauling-triplex.png Pauling-triplex.pdb


Fig. 3E is generated by selecting "poly(I) : poly(I) : poly(I) : poly(I)" ("use this model" button) and then clicking "Build" with default repeat number of 12. In the w3DNA 2.0 output, the image is rotated 90 degrees to be in a horizontal orientation.

Fig. 3F is produced by clicking the link "[Use this structure for mutation]", directly after Fig. 3E, to the "Mutation" module. At the top, select the "Mutate to All: G" radio button, and then "Continue".

For Fig. 3E and 3F, please read tutorial on the 'Mutation' module online or the section "S4.6 Modeling module: base mutations" (especially "Example 6-3: Construction of a G-quadruplex DNA model") in the supplemental PDF.

23
Figure 2. New structural parameters that connect base and backbone atoms. (A) A pair of virtual torsion angles (η􏰀′′ and 􏰁θ′′) that are based on the positions of the phosphorus atoms (P) and the origins of the intervening bases in their standard base reference frames (7). Two closely related forms of virtual backbone torsion angles are depicted for comparison: the classic version (η􏰀 and 􏰁θ) defined by the P and C4′ atoms (27), and a more recent variant (􏰀η′ and 􏰁θ′) based on the P and C1′ atoms (28). Here, an ApTpG trinucleotide from a B-DNA fiber model is used for illustration, with base reference frames attached. Note that the standard base frames of purines and pyrimidines are symmetrical with respect to the dyad of an idealized Watson–Crick base pair, and thus independent of base identity (21): the base origin is accordingly more displaced from the atoms of T (a pyrimidine) than those of A or G (purines). (B–D) Single-stranded phosphate displacement, ssZp, in representative helical structures showing: (B) a small, positive number for a GpG step from a B-DNA fiber model where a C2′-endo sugar attaches to a base in an anti conformation (ssZp = +1.84 Å); (C) a large, positive value for an ApA step from an RNA fiber model where a C3′-endo sugar attaches to a base in an anti conformation (ssZp = +4.38 Å); (D) a negative value for a GpC step from a Z-DNA fiber model where the G adopts a syn conformation (ssZp = −1.74 Å). Color code for base blocks: A, red; G, green; T, blue. The illustrations were generated with DSSR (21) and PyMOL (https://pymol.org).

Fig. 1A: virtual torsion angles

Code: Text
  1. fiber -seq=ATG --single pseudo-torsion-raw.pdb
  2.   # remove the leading phosphate group for clarity
  3. tail +6 pseudo-torsion-raw.pdb > pseudo-torsion.pdb
  4.   # load 'pseudo-torsion.pdb' into PyMOL, run the following command commands
  5. load pseudo-torsion.pdb, whole_str
  6. select C1_prime, name C1'
  7. select C4_prime, name C4'
  8. select P, name P
  9. dssr_block block_file=frame, name=frame  # via the DSSR-PyMOL plugin
  10. dssr_block block_depth=0.28, name=block
  • Line#1: The illustration employs a DNA fragment with base sequence ATG from the B-DNA fiber model, default of the 3DNA fiber program.
  • Line#3: Remove the 5'-phosphate group for clarity.
  • Lines#5-10: Load 'pseudo-torsion.pdb' into PyMOL, choose a preferred orientation, select P, C1' and C4' atoms, and run two dssr_block commands  via the DSSR-PyMOL plugin. In line#10, the thickness of base blocks is set to 0.28 Å from the default value of 0.5 Å.
  • Within PyMOL, ray-trace the scene and then output a PNG image as depicted below. The corresponding PyMOL screenshot is also added here for reference.




Associate files:
The molecular schematic of a DNA trinucleotide diphosphate is used here to illustrate definitions of pseudo torsions angles. It is worth noting that the concept of embedded base planes and attached reference frames is generally applicable to the analysis, construction, and visualization of any 3D nucleic acid-containing structures.


Fig. 2B-D: Single-stranded phosphate displacement, ssZp

The three cases depicted in Fig. 2B-D are similar in nature for illustration purpose. The procedure for creating Fig. 2C is detailed below. Note the selection of the 5' nucleotide (base_ref, line #16): the base block and reference frame are attached only to the leading base, not the following one.

Code: Bash
  1.     # single-stranded RNA, with base sequence AA
  2. fiber --rna --seq=AA --single C3-endo-raw.pdb
  3.     # with the minor-groove of A1 facing the viewer
  4. x3dna-dssr -i=C3-endo-raw.pdb --frame='1:minor' -o=C3-endo-view.pdb
  5. tail +6 C3-endo-view.pdb > C3-endo.pdb    # remove the 5' phosphate group
  6.  
  7.     # Within PyMOL,
  8. load C3-endo.pdb, whole_str
  9. bg_color white
  10. set orthoscopic, 1
  11. turn x, 8    # slightly change the view so the frame x-axis shows up
  12. turn y, -8
  13.  
  14.     # some settings
  15. select P, name P
  16. select base_ref, resi 1    # select the 5' nucleotide as reference
  17.  
  18. set stick_radius, 0.03
  19. show sticks
  20. set_bond stick_radius, 0.06, base_ref
  21. hide sticks, (name O6+N2+N6+O2+O4+C7+N3) and base_ref
  22.  
  23. set sphere_scale, 0.08
  24. show sphere, P
  25.  
  26.     # add the base block and reference frame
  27. dssr_block base_ref, block_file=frame, name=frame
  28. dssr_block base_ref, block_depth=0.28, name=block



Associated files:

Using a similar procedure as the one for Fig. 2C, one can generate the following images from Fig. 2B and 2D.

-- Fig. 2B

-- Fig. 2D

Here are the associated files for Fig. 2B:

And the associated files for Fig. 2D:


See also the following blogposts:

24
Quote
Figure 1. Summary of web 3DNA 2.0. (A) The homepage, highlighting the three major components of the server (boxed) and links to key resources. (B) Excerpt from the ‘Analysis’ of a drug–DNA complex (PDB entry 1xvk) (38), showing a base-block image and tabulations of the ‘simple’ base-pair and step parameters. (C) Schematic ‘Visualization’ of an ensemble of NMR structures of a protein–DNA complex (PDB entry 2moe) (31). The models are aligned locally in the reference frame of the fifth base pair, with its minor-groove edge (colored black) facing the viewer. The protein, colored purple, binds in the major groove of the DNA. (D) An example of ‘Rebuilding’ a model from the local base-pair and step parameters obtained from an ‘Analysis’ of a tRNA structure (PDB entry: 1fir) (33). (E) ‘Composite’ model of a DNA ‘decorated’ with proteins. Here a nucleosome (PDB entry: 4xzq) (34) is used as a template to construct a three-nucleosome, chromatin-like structure. Color code for base rectangular blocks: A, red; C, yellow; G, green; T, blue; U, cyan. (B–D) were generated automatically via the 3DNA ‘blocview’ program, which calls MolScript (24) and Raster3D (25); (E) was rendered using JSmol (22). The annotations were created using Inkscape (https://inkscape.org).




Fig. 1A is simply a screenshot of the homepage header, including the six modules on the left and three related links on the right.

Fig. 1B is about the 'Analysis' module using PDB entry 1xvk as an example. The block image corresponds to the left view and the two tables ("Simple base-pair parameters" and "Simple base-pair step parameters") are screenshots, all from the w3DNA 2.0 output. The new 'simple' parameters have been devised for a more intuitive, qualitative characterization of non-Watson-Crick base pairs. The PDB entry 1xvk was chosen because of the thread "zero or negative helical rise?" on the Forum started on March 25, 2013 (and "question on +/- signs of local bp parameters" on January 11, 2013).

See also:


Fig. 1C illustrates the 'Visualization' module using the NMR ensemble from PDB entry 2moe as an example. Among the 20 models in 2moe, the first 10 models are used here by default. The image can be generated directly using the default settings.

Fig. 1D showcases the 'Rebuilding' module with a customized base sequence and corresponding rigid-body parameters, using a tRNA structure based on PDB entry 1fir as an example. Simply click the buttons with default settings will lead to the image shown here. See also section "S2.2 Rebuilding a single-stranded RNA structure" in the supplemental PDF.

Fig. 1E exhibits the 'Composite' module to create a chromatin-like structure with three nucleosomes. The tutorial "Example 4-2: Construction of a chromatin-like model" on the website (and in the supplemental PDF) provides the detailed steps.

The image shown below was interactively rotated in JSmol from the direct output view of w3DNA 2.0, and then rendered via the console, using the following command (as the one used in the DSSR-Jmol paper):
write  PNGJ  3000  3000  w3DNA2.0-fig1E-jmol.png

It is worth noting that PNGJ option retains the atomic coordinates used to create the PNG image. As a result, the file w3DNA2.0-fig1E-jmol.png can be reloaded to Jmol/JSmol for interactive manipulation.

Fig. 1D and 1E use Phenix to perform a the base-restraint optimization of backbone geometry. See also the FAQ entry "How do I build nucleic acid structures with sugar-phosphate backbone?"

25
The article "Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures" has been published in the 2019 web server issue of Nucleic Acids Research (NAR), and highlighted in the cover page! Co-authored by Shuxiang Li, Wilma Olson and me, this w3DNA 2.0 paper is a significant contribution to the field of nucleic acids structures, and it will undoubtedly push the popularity of 3DNA to a new level.

At nine pages, the paper is not a typical NAR web-server publication but contains several new parameters introduced in 3DNA after the initial publication of w3DNA in 2009. The abstract is shown below:

Quote
Web 3DNA (w3DNA) 2.0 is a significantly enhanced version of the widely used w3DNA server for the analysis, visualization, and modeling of 3D nucleic-acid-containing structures. Since its initial release in 2009, the w3DNA server has continuously served the community by making commonly-used features of the 3DNA suite of command-line programs readily accessible. However, due to the lack of updates, w3DNA has clearly shown its age in terms of modern web technologies and it has long lagged behind further developments of 3DNA per se. The w3DNA 2.0 server presented here overcomes all known shortcomings of w3DNA while maintaining its battle-tested characteristics. Technically, w3DNA 2.0 implements a simple and intuitive interface (with sensible defaults) for increased usability, and it complies with HTML5 web standards for broad accessibility. Featurewise, w3DNA 2.0 employs the most recent version of 3DNA, enhanced with many new functionalities, including: the automatic handling of modified nucleotides; a set of ‘simple’ base-pair and step parameters for qualitative characterization of non-Watson–Crick double- helical structures; new structural parameters that integrate the rigid base plane and the backbone phosphate group, the two nucleic acid components most reliably determined with X-ray crystallography; in silico base mutations that preserve the backbone geometry; and a notably improved module for building models of single-stranded RNA, double- helical DNA, Pauling triplex, G-quadruplex, or DNA structures ‘decorated’ with proteins. The w3DNA 2.0 server is freely available, without registration, at http://web.x3dna.org.



This section is dedicated to topics on reproducing the results reported in the w3DNA 2.0 article, with scripts and related data files. We welcome any questions and comments you may have, here on the 3DNA Forum.

Cover image
"Cover image featuring the web 3DNA 2.0 paper" title="Cover image featuring the web 3DNA 2.0 paper"

Caption: Examples of customized molecular models that can be generated with 3DNA: (top) a chromatin-like, nucleosome-decorated DNA with the structures of known histone-DNA assemblies placed at user-defined binding sites; (lower left) molecular schematic of a DNA trinucleotide diphosphate illustrating the base planes and reference frames used to construct and analyze 3D nucleic acid-containing structures; (lower right) customized single-stranded tRNA model built from a user-defined base sequence and a set of rigid-body parameters describing the desired placement of successive bases. Color code of base blocks: A, red; C, yellow; G, green; T, blue; U, cyan.

Figure 1. Summary of web 3DNA 2.0

Figure 1. Summary of web 3DNA 2.0. (A) The homepage, highlighting the three major components of the server (boxed) and links to key resources. (B) Excerpt from the ‘Analysis’ of a drug–DNA complex (PDB entry 1xvk) (38), showing a base-block image and tabulations of the ‘simple’ base-pair and step parameters. (C) Schematic ‘Visualization’ of an ensemble of NMR structures of a protein–DNA complex (PDB entry 2moe) (31). The models are aligned locally in the reference frame of the fifth base pair, with its minor-groove edge (colored black) facing the viewer. The protein, colored purple, binds in the major groove of the DNA. (D) An example of ‘Rebuilding’ a model from the local base-pair and step parameters obtained from an ‘Analysis’ of a tRNA structure (PDB entry: 1fir) (33). (E) ‘Composite’ model of a DNA ‘decorated’ with proteins. Here a nucleosome (PDB entry: 4xzq) (34) is used as a template to construct a three-nucleosome, chromatin-like structure. Color code for base rectangular blocks: A, red; C, yellow; G, green; T, blue; U, cyan. (B–D) were generated automatically via the 3DNA ‘blocview’ program, which calls MolScript (24) and Raster3D (25); (E) was rendered using JSmol (22). The annotations were created using Inkscape (https://inkscape.org).

Figure 2. New structural parameters that connect base and backbone atoms

Figure 2. New structural parameters that connect base and backbone atoms. (A) A pair of virtual torsion angles (η􏰀′′ and 􏰁θ′′) that are based on the positions of the phosphorus atoms (P) and the origins of the intervening bases in their standard base reference frames (7). Two closely related forms of virtual backbone torsion angles are depicted for comparison: the classic version (η􏰀 and 􏰁θ) defined by the P and C4′ atoms (27), and a more recent variant (􏰀η′ and 􏰁θ′) based on the P and C1′ atoms (28). Here, an ApTpG trinucleotide from a B-DNA fiber model is used for illustration, with base reference frames attached. Note that the standard base frames of purines and pyrimidines are symmetrical with respect to the dyad of an idealized Watson–Crick base pair, and thus independent of base identity (21): the base origin is accordingly more displaced from the atoms of T (a pyrimidine) than those of A or G (purines). (B–D) Single-stranded phosphate displacement, ssZp, in representative helical structures showing: (B) a small, positive number for a GpG step from a B-DNA fiber model where a C2′-endo sugar attaches to a base in an anti conformation (ssZp = +1.84 Å); (C) a large, positive value for an ApA step from an RNA fiber model where a C3′-endo sugar attaches to a base in an anti conformation (ssZp = +4.38 Å); (D) a negative value for a GpC step from a Z-DNA fiber model where the G adopts a syn conformation (ssZp = −1.74 Å). Color code for base blocks: A, red; G, green; T, blue. The illustrations were generated with DSSR (21) and PyMOL (https://pymol.org).

Figure 3. Commonly-used fiber models and in silico base mutations

Figure 3. Commonly-used fiber models and in silico base mutations. (A) Six commonly used models highlighted in the ‘Fiber’ module: single-stranded RNA, double-helical A-, B-, and C-form DNA, the Pauling triplex model (32), and the parallel polyI:polyI:polyI:polyI quadruplex. (B) Single-stranded RNA fiber model of base sequence AUCGAUCGAUCG. (C) Double-helical B-DNA fiber model with sequence ATCGATC- GATCG on the leading strand. (D) Pauling triplex model with each strand of sequence AAAACCCCGGGG. (E) parallel polyI:polyI:polyI:polyI quadruplex model with 12 layers of hydrogen-bonded hypoxanthine tetrads. Models in (B-E) were generated using the default settings on the w3DNA 2.0 server, each taking just two mouse clicks. (F) All hypoxanthine bases along the poly I chains mutated to guanine via the ‘Mutation’ module, leading to a parallel G-quadruplex. Color code for base blocks: A, red; C, yellow; G, green; T, blue; U, cyan; I, dark green.

Supplementary Data (w3DNA2.0-supp.pdf), serving as a manual to w3DNA 2.0. Note that the supplementary PDF here contains DOI links to the w3DNA 2.0 publication.

Graphical abstract (taken from Fig. 1E):

Pages: [1] 2 3 ... 5

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.