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26

web 3DNA 2.0 (http://web.x3dna.org) / Figure 3. Commonly-used fiber models and base mutations

« on: May 30, 2019, 12:42:48 pm »

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.

27

web 3DNA 2.0 (http://web.x3dna.org) / Figure 2. New structural parameters

« on: May 30, 2019, 12:37:13 pm »

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 PDB-formatted coordinate file: pseudo-torsion.pdb
• The PyMOL session file: pseudo-torsion.pse

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:

• The PDB-formatted coordinate file: C3-endo.pdb
• The PyMOL session file: C3-endo.pse

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:

• The PDB-formatted coordinate file: C2-endo.pdb
• The PyMOL session file: C2-endo.pse

And the associated files for Fig. 2D:

• The PDB-formatted coordinate file: G-syn-ref.pdb
• The PyMOL session file: G-syn-ref.pse

See also the following blogposts:

• Pseudo-torsions to simplify the representation of DNA/RNA backbone conformation
• Single- and double-stranded Zp

28

web 3DNA 2.0 (http://web.x3dna.org) / Figure 1. Summary of web 3DNA 2.0

« on: May 28, 2019, 02:33:34 pm »

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:

• "S1 ‘Simple’ base-pair and step parameters for non-Watson-Crick pairs" in the supplemental PDF for more information.
• Details on the simple base-pair parameters (blogpost on 2016-01-10)
• 'Simple' parameters for non-Watson-Crick base pairs (blogpost on 2016-01-01)
• Simple base-pair parameters (blogpost on 2015-09-04)
• Characterization of base pair geometry (short article in Computational Crystallography Newsletter, 2016, Volume 7, Part 1)

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?"

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web 3DNA 2.0 (http://web.x3dna.org) / Reproducing results in the web 3DNA 2.0 article (NAR'19 webserver issue)

« on: May 28, 2019, 11:39:47 am »

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:

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.

• Cover image
• Figure 1. Summary of web 3DNA 2.0
• Figure 2. New structural parameters
• Figure 3. Fiber models and mutations
• Supplemental PDF
• Graphical abstract (taken from Fig. 1E)

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

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):

30

FAQs / How to draw a helical axis

« on: November 29, 2018, 12:45:17 pm »

While experimentally-determined DNA/RNA double helices (as deposited in the PDB) are never strictly linear, oligonucleotides or fragments of large nucleic acid molecules may be approximately straight. In such cases, it is informative to draw a helical axis to visualize them in a 3D molecular viewer (such as PyMOL or Jmol). Moreover, helical axes from two different fragments can be used to determine the "bending angle" between them. 3DNA and DSSR provide this info, as illustrated below using PDB id 355d as an example.

• Running 3DNA (v2.3) find_pair 355d.pdb | analyze, the output file 355d.out contains the following segment:
  

  Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs
  Deviation from regular linear helix: 3.30(0.52)
  Helix:    -0.1269   -0.2753   -0.9530
  HETATM 9998  XS    X X 999      17.536  25.713  25.665
  HETATM 9999  XE    X X 999      12.911  15.677  -9.080
  Average and standard deviation of helix radius:
        P: 9.42(0.82), O4': 6.37(0.85),  C1': 5.85(0.86)

  The two HETATM records can be copy-and-pasted into the original PDB file. The line can be easily drawn between them, which is the helical axis.
  
  
• Running DSSR: x3dna-dssr -i=355d.pdb --more, the output contains the following segment:
  

    helix#1[1] bps=12
        strand-1 5'-CGCGAATTCGCG-3'
         bp-type    ||||||||||||
        strand-2 3'-GCGCTTAAGCGC-5'
        helix-form  BBBBBBBBBBB
      helical-rise:   3.30(0.52)
      helical-radius: 9.42(0.82)
      helical-axis:   -0.127    -0.275    -0.953
         point-one:   17.536    25.713    25.665
         point-two:   12.911    15.677    -9.080

  With the --helical-axis option, as in x3dna-dssr -i=355d.pdb --more --helical-axis, DSSR also generates a file named dssr-helicalAxes.pdb with the following content:
  

  REMARK-DSSR: helix#1
  ATOM      1  P1   DC A   1      17.536  25.713  25.665  1.00 10.97      H1   P
  REMARK-DSSR: helix#1
  ATOM      2  P2   DG A  12      12.911  15.677  -9.080  1.00 18.40      H1   P
  CONECT    1    2
  CONECT    2    1

  Loading both 355d.pdb and dssr-helicalAxes.pdb into PyMOL, one can get an image as attached.

31

w3DNA -- web interface to 3DNA / Notes on w3DNA v2

« on: November 18, 2018, 09:02:06 pm »

Hi Shuxiang,

Impressive progress with the new version (v2) of web 3DNA -- it is now fully functional! Here are some ideas that may further improve the website. The list is likely to be continuously updated as we work on the project.
 
Please update 3DNA on the server from v2.3-2016sept06 to the latest version (currently v2.3.4-2018nov06). In particular, the fiber program should contain 56 models (fiber -m), including the historically significant DNA triplex model by Pauling and Corey.

Under the "Fiber" tab, please make it stand out to build A-, B-, RNA-fiber models with generic sequence at the very top. They are the most frequently use-cases for typical 3DNA users. You may also include the Pauling triplex model which should be of general interest, especially for educational purposes. In the 3DNA fiber program command-line, they have corresponding sensible options for quick access. Here are some examples:

Code: Bash

1. # A B-DNA duplex model (default)
2. fiber -seq=ACCCCGGG b-model.pdb
3. # An A-DNA duplex model
4. fiber -A -seq=CGGGGAAAA fiber-ADNA.pdb
5. # a single-stranded RNA
6. fiber -seq=AAAGGUUU -rna -single fiber-ssRNA.pdb
7. # Pauling & Corey triplex model, with A4, C4, and G4 on the three strands
8. fiber -pauling -seq=AAAA:CCCC:GGGG Pauling-triplex-A4C4G4.pdb

A new tab with "Links" to the 3DNA home page, the 3DNA Forum, and the Curves+ web server etc. would also be helpful.

Note added on 2018-12-02:

The web 3DNA v2.0 is getting better! Following our Skype last night, I've listed below the major items to be considered for the next iteration.

• The blocview images are better created with higher resolution. This is controlled by settings in file $X3DNA/config/my_header.r3d. An example of high resolution settings is at $X3DNA/config/my_header_hres.r3d. We could choose medium settings.
• The stacking diagrams, derived from stack2img in EPS format, can be converted to PNG in much higher resolution. Since a dinucleotide-step stacking diagram contains only 4 nucleotides, the larger PNG file size is not an issue. The 3DNA-generated EPS file can also be converted to SVG, the standard scalable vector graphics format for the web.
• In the 'Analysis' section, please also include the following new features in 3DNA v2.3:
  
  • The 'simple' base-pair and step parameters in default output.
  • Also run "analyze --torsion" to generate a full list of torsion angles. In particular, the section of pseudo (virtual) torsion angles contains eta"/theta" that are defined based on the base origin and the backbone P atoms. The section on sugar conformational parameters contains ssZp (single-stranded Zp).

Note added on 2018-12-07:
Following our Skype last night, I've listed below a couple of items to polish for the next iteration.

• For the visualization of an NMR ensemble, please merge the 'middle frame' to the full list of frames of base-pair steps. Put the 'middle frame' on the very top and use it as the default. In the transformation step (x3dna_ensemble reorient), add 'm' (for the minor-groove side, see frame_mol -h) to the --frame option. This will make the reference step stands out with its minor-groove facing the viewer. This is a feature unique to 3DNA. While you're at it, also add an option that respects the alignment as in the original NMR ensemble.
• Add an option to directly transfer 3D models derived from "Rebuilding", "Composite", and "Fiber" to "Mutation". This would be helpful for building a customized initial structure for MD simulations, among other possible applications.

Note added on 2019-02-16:
Based on the feedback we received and my own tests, we need to do the following:

• On the header, change "Links | Q&As" to "Tutorial | Q&As | Links" so the "Tutorial" link stands out. Accordingly, in the "Links" page, remove the now redundant "Tutorial & Help" links at the top.
• Update 3DNA to v2.4.1. Re-run all PDB entries to account for revisions of simply step parameters in special cases.
• Reproduce block images with the minor-groove edge highlighted in black (the -m option).
• In the Fiber tab, fix the bug with repeats in generating Pauling triplex models. Currently, the "Repeating #:" option has no effects. With 3DNA v2.4.1, one can try for example, fiber -pauling-dna -seq=ACTT -repeat=6 DNA-triplex.pdb. For the convenience of users, it makes sense to turn each 'Short description' into a link, with the same functionality as the 'use this model' button.

Best regards,

Xiang-Jun
 

32

Bug reports / MOVED: x3dna-v2.3 no backbone ribbon

« on: July 31, 2018, 12:54:39 pm »

This topic has been moved to General discussions (Q&As).

http://forum.x3dna.org/index.php?topic=789.0

33

DNA/RNA-protein interactions (SNAP) / SNAP revision history

« on: February 14, 2018, 11:54:44 pm »

As the list is becoming quite long, for easy reference, I have split up the DSSR release notes from the main post "SNAP: software for characterizing DNA-protein interactions".

SNAP has been integrated into DSSR, and is available from the Columbia Technology Ventures (CTV) website.

Release history (in reverse chronological order):

• v1.0.7-2020sep09 -- miscellaneous code refinements.
• v1.0.6-2019sep30 -- Added the --methyl-C option dedicated to the characterization of interactions between DNA 5-methyl cytosine (5CM) and amino acids in DNA-protein complexes.
• v1.0.5-2019sep16 -- Documented variations on the --get-hbond option.
• v1.0.4-2019aug26 -- Added the --json option for easy parsing of SNAP output; Expanded base-pair/amino-acid interactions to include all base pairs listed in the helices section; plus miscellaneous code refactoring and refinements.
• v1.0.3-2019aug03 -- Added a list of modified nucleotides (such as 5CM) to the main output as in DSSR; Fixed a bug in rare cases, plus miscellaneous code refinements.
• v1.0.2-2019mar28 -- Revised the algorithm for the identification of stacking interactions between planar side-chains of amino acids with bases of DNA/RNA.
• v1.0.1-2019feb11 -- Along with DSSR, refined code and fixed a couple of bugs in rare occasions.
• v1.0.0-2019feb03 -- After four years of continuous developments based on my own research and users' feedback, SNAP is mature and robust enough to merit the version 1.0 release. SNAP shares the codebase and follows the same style as DSSR, and it aims to become a preferred software tool for the analyses of DNA-protein or RNA-protein 3D structures.

• beta-r16-2018sep06 -- added the --citation option; numerous code refinements along with DSSR.
• beta-r15-2018feb15 -- added a new section that lists interface stack(s) with 3+ planar moieties. An interface stack is an ordered list of three and more nucleobases and planar moieties of amino acids, assembled together via stacking interactions (nucleobases within to a stem are excluded by default).
• beta-r14-2018jan05 -- added the --nmr option; classified H-bonds into six categories: phosphate/sugar/base moieties for nucleotides vs backbone/sidechain for amino acids.
• beta-r13-2017dec31 -- simplified output of H-bonds into mutually exclusive sections (phosphate group, sugar, or base with amino acid); added option --auxfile for producing additional auxiliary files (the default is now only the main output file); miscellaneous bug fixed and code refinements.
• beta-r12-2017dec26 -- added a summary section of nucleotides with interacting amino acids; revised code to avoid warning messages with GCC v7.
• beta-r11-2017dec11 -- revised output wording/formatting; added a list of additional files for pairwise H-bonding, base-amino acid pairing/stacking interactions; plus numerous code refinements.
• beta-r10-2017apr10 -- documented the --type=string where string can be "base" (the default), "backbone", "either", or "both". The "base" argument reports protein interactions with only DNA/RNA base atoms, "backbone" with only DNA/RNA backbone atoms, "either" with base or backbone atoms, and "both" with base plus backbone atoms.
• beta-r09-2016sept28 -- fixed a bug with the --cleanup option (thanks to jms89).
• beta-r08-2016jun02 -- added the --tshape (or --t-shape) option to fix issues reported in the Supplemental Table S1 of the Wilson et al. paper "Topology of RNA–protein nucleobase–amino acid π–π interactions and comparison to analogous DNA–protein π–π contacts". Specifically, the authors said:
  
  "Furthermore, although the recently released beta-r06-2015oct23 version of 3DNA-SNAP (Lu and Olson 2008) is able to distinguish between such errors, and accurately detects stacking interactions between nucleobases and amino acids, it unfortunately is currently unable to identify T-shaped interactions (see, for example, Supplemental Table S1)."
  
  
• beta-r07-2016may21 -- fixed the "Segmentation fault" bug (due to undefined reference frames for certain amino acids with missing side-chain atoms); miscellaneous internal code refinements.
• beta-r06-2015oct23 -- detected aromatic stacking interactions between bases and amino acids; numerous refinements along with DSSR.
• beta-r05-2015may03 -- added option --get-hbond to output a list of H-bonds between protein and nucleic acid; numerous internal code refinements.
• beta-r04-2014sep30 -- removed the (undocumented) --rna option so that RNA-protein complexes are handled the same way as DNA-protein complexes; relaxed default settings so SNAP now runs on pure nucleic acid or protein structures in addition to their complexes; added DSSP output for the protein component in file snap-dssp.txt.
• beta-r03-2014sep16 -- listed base-AA pseudo-pairs and output an associated PDB ensemble file (snap-pseudoPairs.pdb); significant code speed-up.
• beta-r02-2014may31 -- detailed listing of H-bonding interactions between a component of nucleotide (base/phosphate/sugar) and an amino acid.
• beta-r01-2014may05 -- initial release to kick the ball rolling. SNAP identifies base-AA or BP-AA interactions based on a distance cutoff (default to 4.5 angstrom), calculates six parameters to uniquely quantify the spatial relationships, and sets the coordinates in the standard base or BP reference frame for easy visualization and for deriving knowledge-based potentials.

34

General discussions (Q&As) / MOVED: Quantifying base stacking interactions

« on: August 17, 2017, 03:30:32 pm »

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

http://forum.x3dna.org/index.php?topic=728.0

35

FAQs / How to set up 3DNA on Windows

« on: July 14, 2017, 12:44:23 pm »

3DNA v2.3 and previous versions contain a suite of programs, and associated data files. Setting up 3DNA is intended to be a simple process for those with command-line experience: it entails creating an environment variable named X3DNA to point to where 3DNA is stored, and an updated PATH that includes the $X3DNA/bin directory. The whole process is facilitated by a Ruby script, x3dna_setup, and should take no more than a few minutes.

With Linux and Mac OS, setting up 3DNA has normally not been an issue. For Windows, however, the situation is more complicated than desired. Cygwin or MinGW/MSYS is the preferred way to run 3DNA on Windows, but each requires the installation of a big package and the ending environment is not familiar to Windows users. By far, the most frequent and longest threads on the Forum are on how to properly set up 3DNA on Windows, initiated by new users who have no experience in command-line interface.

As of 3DNA v2.3.1-2017jun24, the compiled .exe files in the tarball x3dna-v2.3-mingw-win.tar.gz should run in native Windows (i.e. without Cygwin or MinGW/MSYS) via the command prompt. However, the default Windows command prompt (cmd.exe) is a dinosaur and awkward to use. I played with Windows PowerShell a bit, but it gave some surprises with processing of command-line options. The win-bash shell may be a choice, or one can install Bash on Windows 10.

In the long run, when the 'Bash on Windows' becomes a default, the whole issue of setting 3DNA will on longer exist any more. In the meantime, this FAQ entry provides detailed instruction on how to set up 3DNA v2.3 on native Windows (tested on Windows 7).

• Install ConEmu (Stable, Installer) -- it is far superior to Windows cmd.exe
  

  ConEmu-Maximus5 is a Windows console emulator with tabs, which presents multiple consoles and simple GUI applications as one customizable GUI window with various features...file and archive management, command history and completion, powerful editor.
• Download the Windows version of 3DNA v2.3, the x3dna-v2.3.zip file (Note that you need to register and log in to see the download link). The zip file normally ends up in the Downloads/ folder under your home folder (e.g., C:\Users\xiangjun\Downloads.)
• Right-click the x3dna-v2.3.zip file, in the context menu select "Extract All...". In the setting window, you can select the folder under which 3DNA will be installed. Please do not specify x3dna-v2.3 explicitly in setting the folder, since x3dna-v2.3 will always be appended to it.
  
  In principle, you can install 3DNA anywhere. It is a good choice to put it directly under your home folder (e.g., C:\Users\xiangjun). See the screenshot below.
  
  
  
  Click the "Extract" button at the bottom right. You'll see lots of files being extracted. Take a note of the 3DNA folder (i.e., C:\Users\xiangjun\x3dna-v2.3\ as shown above) as this information is needed next.
  
  Navigate to the designated 3DNA folder and make sure it has the content shown below. Right-click on file license.txt and select "Properties". The Location: field should report its parent folder (no ending slash) that agrees with the one shown above.
  
  
  
  
• Set the X3DNA environment variable and update the PATH. See "How to set the path and environment variables in Windows" for details. Here I am using Windows 7 as an example.
  
  
  • From the "Desktop", right-click the "Computer" icon and select "Properties". If you don't have a Computer icon on your desktop, click the "Start" button, right-click the "Computer" option in the Start Menu, and select "Properties".
  • Click the "Advanced System Settings" link in the left column.
  • In the System Properties window, click on the "Advanced" tab, then click the "Environment Variables..." button near the bottom of that tab.
  • In the Environment Variables window, the top part is for User variables (for xiangjun in the example). Click the "New..." button, and you will see the New User Variable window. For the Variable name text field, type X3DNA, and for Variable value, type C:\Users\xiangjun\x3dna-v2.3\ (with ending slash). Note that this value must match what is specified in the extraction step, i.e., pointing to where 3DNA is actually installed. See the following screenshot.
    
    
    
    Click the "OK" button, and the result is as shown below:
    
    
  • In the Environment Variables window, the bottom part is for System variables. Scroll to find the Path variable, which contains a long list of values separated by semicolon (e.g. C:\Windows\system32;...). Highlight (select) the Path entry and click the "Edit..." button. The Edit System Variable window will appear. The Variable name text field will be Path. Scroll to the end of Variable value, add ;C:\Users\xiangjun\x3dna-v2.3\bin. Note that each different directory is separated with a semicolon. See screenshot below.
    
    
• Now double-click the ConEmu icon on the desktop to open a new terminal window. Type find_pair -h in the command prompt, you should see a result screen as shown below.
  
  
• Optionally, install Ruby on Windows. You may skip this step when you just get started with 3DNA on Windows. The Ruby scripts distributed with 3DNA v2.3 are mostly for generating schematic block images, and analyzing NMR ensembles.
  
  Do not forget to click the check box "Add Ruby executables to your PATH". See the first entry in Troubleshooting.
  
  
  
  Note that at the end of the installation, you do not need to click the checkbox to install "MSYS2 and development toolchain". 3DNA v2.3 runs just fine as is, even though getting them installed does not hurt.
  

If you notice any problem, please post below with details.

36

Site announcements / DSSR-Jmol featured in cover image of NAR'17 web-server issue

« on: June 30, 2017, 08:10:43 pm »

The DSSR-Jmol paper, titled "DSSR-enhanced visualization of nucleic acid structures in Jmol", has been officially published in the 2017 web-server issue of Nucleic Acids Research (NAR). Notably, the work has been featured in the cover image, as shown below:

Caption: 3D interactive visualization of selected RNA structural features enabled by the DSSR-Jmol integration (http://jmol.x3dna.org). Clockwise from upper left: Structure of the xpt-pbuX guanine riboswitch in complex with hypoxanthine (PDB id: 4fe5) in ‘base blocks’ representation. The three-way junction loop encompassing the metabolite (in space-filling representation) is color-coded by base identity: A, red; C, yellow; G, green; U, cyan. The loop-loop interaction (a kissing-loop motif) at the top is highlighted in red (upper left corner). Structure of the Thermus thermophilus 30S ribosomal subunit in complex with antibiotics (PDB id: 1fjg) in step diagram. The 16S ribosomal RNA is color-coded in spectrum with the 5′-end in blue and the 3′-end in red (upper middle). Structure of the classic L-shaped yeast phenylalanine tRNA (PDB id: 1ehz) in step diagram, with the three hairpin loops highlighted in red and the [2,1,5,0] four-way junction loop in blue (upper right corner). Structure of the Pistol self-cleaving ribozyme (PDB id: 5ktj), showcasing (in red) the horizontal helix in space-filling representation. The helix is composed of six short stems stabilized via coaxial stacking interactions (bottom).

The DSSR-Jmol integration bridges the DSSR command-line analyzing tool and the Jmol molecular viewer seamlessly together via the standard JSON interface. Now users can select DSSR-derived RNA structural features (such as base pairs, double helices, various loops, etc.) and visualize them in novel representations in Jmol interactively. Moreover, fine-grained characteristics of these features can be queried via the Jmol SQL for DSSR. The DSSR-Jmol integration fills a gap in RNA structural bioinformatics, and brings RNA visualization to an entirely new level. The web interface (http://jmol.x3dna.org) is fully functional and easy to use, serving a huge user base of researchers, educators, and students alike.

Featured as the cover image of the 2017 NAR web-server issue, DSSR's publicity would surely increase through the DSSR-Jmol integration. Additionally, I've written a new post (on the 3DNA Forum) that provides the scripts and datafiles used to create the cover image.

37

DSSR-Jmol integration / cover image

« on: June 30, 2017, 01:56:36 pm »

Caption: 3D interactive visualization of selected RNA structural features enabled by the DSSR-Jmol integration (http://jmol.x3dna.org). Clockwise from upper left: Structure of the xpt-pbuX guanine riboswitch in complex with hypoxanthine (PDB id: 4fe5) in ‘base blocks’ representation. The three-way junction loop encompassing the metabolite (in space-filling representation) is color-coded by base identity: A, red; C, yellow; G, green; U, cyan. The loop-loop interaction (a kissing-loop motif) at the top is highlighted in red (upper left corner). Structure of the Thermus thermophilus 30S ribosomal subunit in complex with antibiotics (PDB id: 1fjg) in step diagram. The 16S ribosomal RNA is color-coded in spectrum with the 5′-end in blue and the 3′-end in red (upper middle). Structure of the classic L-shaped yeast phenylalanine tRNA (PDB id: 1ehz) in step diagram, with the three hairpin loops highlighted in red and the [2,1,5,0] four-way junction loop in blue (upper right corner). Structure of the Pistol self-cleaving ribozyme (PDB id: 5ktj), showcasing (in red) the horizontal helix in space-filling representation. The helix is composed of six short stems stabilized via coaxial stacking interactions (bottom).

Upper left corner (Jmol script: 4fe5.scr; image: 4fe5.png):

Code: [Select]

# Jmol 14.17.1 (2017-05-27)
load =4fe5/dssr
select nts; display nts
rotate best; rotate z 90; rotate y 50
cartoon only
set cartoonsteps off
set cartoonblocks on
set antialiasdisplay on
background white; color grey
select within(dssr, "junctions..1"); color nucleic
select within(dssr, "junctions..2"); color red
select HPA; cpk; color cpk
frank off
write PNGJ 3000 3000 4fe5-raw.png
Upper middle (Jmol script: 1fjg.scr; image: 1fjg.png):

Code: [Select]

# Jmol 14.17.1 (2017-05-27)
load =1fjg/dssr
select nts; display nts
rotate best; rotate z 90
cartoon only
set cartoonsteps on
set cartoonblocks off
set antialiasdisplay on
background white; color monomer
frank off
write PNGJ 3000 3000 1fjg-raw.png
Upper right corner (Jmol script: 1ehz.scr; image: 1ehz.png):

Code: [Select]

# Jmol 14.17.1 (2017-05-27)
load =1ehz/dssr
select nts; display nts
rotate best; rotate z 90
cartoon only
set cartoonsteps on
set cartoonblocks off
set antialiasdisplay on
background white; color grey
select hairpins; color red
select junctions; color blue
frank off
write PNGJ 3000 3000 1ehz-raw.png
Bottom (Jmol script: 5ktj.scr; image: 5ktj.png):

Code: [Select]

# Jmol 14.17.1 (2017-05-27)
load =5ktj/dssr
select nts; display nts
rotate best
cartoon only
set cartoonsteps off
set cartoonblocks off
set antialiasdisplay on
background white; color grey
select within(dssr, "helices..2"); color red; cpk
frank off
write PNGJ 3000 3000 5ktj-raw.png
The 'raw' images were automatically generated from the corresponding script files via command line using the Jmol application with options -ions. The ImageMagick convert program was used to remove empty boundaries. Using 4fe5 as an example, the procedure is as follows:

Code: [Select]

jmol -ions 4fe5.scr   # generate 4fe5-raw.png
convert -trim +repage -border 10 -bordercolor white 4fe5-raw.png 4fe5.png
The four images were then combined using InkScape, and exported to one big composite PNG file (DSSR-Jmol-for-NAR17-web-cover.png, 18MB).

Finally, the tarball file, reproduce-dssr-jmol.tar.gz, contains all the scripts and data files for reproducing the cover image.

38

FAQs / How to make the best use of the Forum

« on: May 19, 2017, 11:35:45 am »

Please be aware that I do not provide private email/personal message assistance, for the benefit of the 3DNA/DSSR-user community as a whole; the Forum was created specifically for open discussions of all 3DNA/DSSR-related issues. In other words, all questions concerning 3DNA and DSSR should be posted here.

Registration on the 3DNA Forum allows you to download 3DNA v2.4 and SCHNAaP/SCHNArP, as well as ask questions about them. Please keep in mind that DSSR licenses and downloads may only be obtained through the the Columbia Technology Venture (CTV). If you have any DSSR-related queries, please post them here as well.

• Register with a valid, work-related email address. I strive to make the Forum spam free. Private emails (gmail.com, yahoo.com, qq.com etc.) are not accepted; such registrations will be removed. Approved registrations that are not activated via email will be deleted. Activated accounts that are not accessed (logins) will be erased. The first post from a registered account is moderated. Posts that are not 3DNA/DSSR related in the broad sense are taken as spams and are strictly forbidden.
  
  Please notify me if you do not receive an email confirmation of your registration within two days. I've recently heard of instances where notification emails have failed to deliver.
• Download 3DNA by clicking the corresponding links within the legitimate member-only 'Downloads' section.
• Post on the Forum any 3DNA-related questions, or share your experience/use case with the community. After registration, you must post your questions yourself on the Forum to get them answered. I do not post questions asked privately via email on the Forum on your behalf.
  
  To post (after logging in), first select a proper section (e.g., General discussions (Q&As), RNA structures (DSSR)). If you need to create a new thread, click the "NEW TOPIC" button on the top-right, and pick up a concise Subject. If you are following an existing thread, click "REPLY" at the bottom. You will then be presented with a familiar, Word-like form to compose and format your post.
  
  Be specific with your questions; provide a minimal, reproducible example if possible; use attachments where appropriate.
  
  Respond to requests for clarification. Failure to do so may result in delay or no answer to your questions.
  
  Summarize the solution to your problem from a user's perspective by providing step-by-step details, for the community's benefit.
  
  Contribute back to the 3DNA project: (1) Report bugs — including typos; (2) Make constructive suggestions — anything that can make 3DNA better; (3) Answer other users' questions; and (4) Share your use cases in the "Users' contributions" section.
  
  By posting your questions on the 3DNA Forum, you are asking for help from others, for free. Be appreciative if you receive responses. Be open-minded, since your questions may not be answered in a way you expect, or receive any reply at all.
  
  Your posts on the 3DNA Forum are in the public domain. Search engines like Google index and cache the website. The 3DNA Forum is automatically backed up every day.
• Click the Notify button (in the upper right corner) to receive email alerts for new posts in the threads or sections you are interested in. You can also change your settings for notifications and newsletters via "Profile" • "Modify Profile" • "Notifications" (login required).
• Share what you know that could be of interest to the general 3DNA user community. Be helpful.
• Behave yourself. No spam or trolling allowed. Violators are removed immediately without any further notice.

39

Site announcements / DSSR-Jmol paper in NAR

« on: May 05, 2017, 05:20:04 pm »

I am pleased to announce the (advance online, May 3, 2017) publication of a new paper titled ["DSSR-enhanced visualization of nucleic acid structures in Jmol"](https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkx365) in *Nucleic Acids Research* (NAR). Co-authored by Robert Hanson (Jmol) and me (DSSR), the article will appear in the July 2017 web-server issue of NAR. Here are the key links related to the paper:

* [DSSR-Jmol website](http://jmol.x3dna.org/)
* [PDF version (DSSR-Jmol paper)](https://academic.oup.com/nar/article-pdf/doi/10.1093/nar/gkx365/14134996/gkx365.pdf)
* [Online HTML (DSSR-Jmol paper)](https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkx365)
* [DSSR-Jmol manual](http://jmol.x3dna.org/dssr-jmol-manual.pdf)
* [Materials to reproduce reported results](http://forum.x3dna.org/dssr-jmol-integration/)

The DSSR-Jmol integration project was initiated in October 2013 when I approached Bob at a meeting organized by RCSB PDB at Rutgers. Thereafter, we met only once in July 2014 in Paris. Over the years, we have mostly communicated via email, occasionally facilitated by Skype. Our work bridges the DSSR command-line analyzing tool and the Jmol molecular viewer together via a simple JSON interface and a powerful query language. Users can now select DSSR-derived RNA structural features (such as base pairs, double helices, and various loops) as easily as they can select protein alpha-helices and beta-strands. Moreover, fine-grained characteristics of these features can be queried via Jmol SQL for DSSR (see examples below). Notably, the novel representation styles (step diagram and base blocks) and coloring schemes bring RNA visualization to an entirely new level (see [Figure 3 of the paper](http://forum.x3dna.org/dssr-jmol-integration/figure-3)).

Code: Bash

1.     load =1ehz/dssr   # load yeast phenylalanine tRNA to Jmol with DSSR annotation
2.     SELECT hairpins   # select the three hairpin loops
3.     SELECT junctions  # select the four-way junction loop
4.     select within(dssr, "nts WHERE is_modified")  # select modified nucleotides (14 total)
5.     SELECT within(dssr, "pairs WHERE name != 'WC'")  # select non-Watson-Crick pairs
6.     SELECT within(dssr, "pairs WHERE name = 'WC' OR name = 'Wobble'")  # select canonical pairs
7.     Select within(dssr, "pairs WHERE name != 'WC' AND name != 'Wobble'")  # select non-canonical pairs
8.     SELECT within(dssr, "pairs WHERE LW = 'tSW'")  # select pairs of type tSW per Leontis-Westhof

The DSSR-Jmol integration fills a gap in RNA structural bioinformatics, serving a huge user base of researchers, educators, and students alike. Its functionality is freely accessible either via the **Jmol application**, or the **JSmol-based website** (http://jmol.x3dna.org). By adhering to web standards, the website is fully functional in all modern browsers on various computer/operating systems (including handheld devices, such as tablets and smart phones). The web interface is simple and intuitive, and new users can get started easily. It also allows power users to take full advantage of Jmol scripting via a command-line console.

This work also provides an example for integrating DSSR-derived features into other molecular graphics programs or bioinformatics pipelines involving nucleic acid structures. By design, DSSR is a stand-alone, command-line program written in ANSI C. The binary executables are only ~1MB in size, and *self-contained*. With zero dependencies, no setup or configuration, it is trivial to get DSSR up and running. DSSR uncovers a wide range of RNA/DNA structural features in a consistent, easily accessible framework. It possesses a much richer set of functionalities for nucleic acid structural analysis (see the [DSSR User Manual](http://x3dna.bio.columbia.edu/docs/dssr-manual.pdf)) than any other existing tools I am aware of. Moreover, the program is efficient and robust, making it an ideal component to be integrated into other pipelines, especially via the standard and structured **JSON** interface.

Collaborating with Bob has been a truly exciting experience. The NAR-web publication represents a gratifying intermediate result along an on-going journey. Hopefully, others (may be some of you) can join us in pushing forward the field of RNA structural bioinformatics.

Best regards,

Xiang-Jun

40

DSSR-Jmol integration / Figure 3

« on: May 04, 2017, 02:06:12 pm »

Figure 3. Sample molecular images illustrating selected RNA structural features enabled by the DSSR-Jmol integration. (A) Structure of yeast phenylalanine tRNA (PDB id: 1ehz) in step diagram with bases labeled, highlighting (in red) the [2,1,5,0] four-way junction loop in 3D. (B) Structure of the Pistol self-cleaving ribozyme (PDB id: 5ktj), showcasing (in red) the vertical helix in space-filling representation. The helix is composed of six short stems stabilized via coaxial stacking interactions. (C) Structure of the xpt-pbuX guanine riboswitch in complex with hypoxanthine (PDB id: 4fe5) in ‘base blocks’ representation. The three-way junction loop encompassing the metabolite (in space-filling representation) is color-coded by base identity: A, red; C, yellow; G, green; U, cyan. The loop-loop interaction (a kissing-loop motif) at the top is highlighted in red. (D) Structure of the yeast GAL4 protein-DNA complex (PDB id: 1d66) in Jmol cartoon representation. DNA is color-coded by DSSR stems, and protein is in translucent brown. The DNA helix is broken into two stems due to a non-Watson-Crick pair (G11 with C28 in gray) in the middle. (E) Structure of the Thermus thermophilus 30S ribosomal subunit in complex with the antibiotics (PDB id: 1fjg) using a step diagram. The 16S ribosomal RNA is color-coded in spectrum with the 5'-end in blue and the 3'-end in red.

Figure 3A (Jmol script: 1ehz.scr):

Code: [Select]

load =1ehz/dssr
select nucleic; display nucleic
rotate best; rotate z 90
cartoon only
set cartoonsteps on
set cartoonblocks off
set antialiasdisplay on
set fontSize 4
background white; color grey
select nucleic and leadAtom; spacefill 1.5
label %[group1]; set labeloffset 0 0; color labels yellow
select junctions; color red
select selected and *.P; label %n%r; color label black; set labeloffset 0 0; set labelfront;
select @{_M.dssr.nts.select("where is_modified")} and *.P; color label blue
Figure 3B (Jmol script: 5ktj.scr):

Code: [Select]

load =5ktj/dssr
cartoon only
select nts; display nts
set cartoonsteps off
set cartoonblocks off
set antialiasdisplay on
background white; color grey
select within(dssr, "helices..2"); color red; cpk
rotate best; rotate z -90; rotate y 90
Figure 3C (Jmol script: 4ef5.scr):

Code: [Select]

load =4fe5/dssr
select nts; display nts
rotate best; rotate z 90; rotate y 50
cartoon only
set cartoonsteps off
set cartoonblocks on
set antialiasdisplay on
background white; color grey
select within(dssr, "junctions..1"); color nucleic
select within(dssr, "junctions..2"); color red
select HPA; cpk; color cpk
Figure 3D (Jmol script: 1d66.scr):

Code: [Select]

load =1d66/dssr
cartoon only
set cartoonsteps off
set cartoonblocks off
set antialiasdisplay on
background white; color grey
color property DSSR stems
select protein; color TRANSLUCENT 0.9 brown
Figure 3E (Jmol script: 1fjg.scr):

Code: [Select]

load 1fjg.pdb
calculate structure dssr
cartoon only
select nts; display nts
rotate best
set cartoonsteps on
set cartoonblocks off
set antialiasdisplay on
background white; color monomer

41

DSSR-Jmol integration / Table 1

« on: May 04, 2017, 01:45:06 pm »

Here is Table 1 and the corresponding DSSR/jq command for each example item on the right column [other than "Jmol (SQL) selections"].

Table 1. DSSR-derived features and DSSR-specific selections in Jmol, using yeast phenylalanine tRNA (1ehz) as an example

Code: Javascript

1. Accessible features (16 keys)  ["pairs","multiplets","helices","stems","isoCanonPairs","coaxStacks","hairpins","bulges","iloops","junctions","kissingLoops","ssSegments","stacks","nonStack","hbonds","nts"]
2.                                // x3dna-dssr --json=ebi -i=1ehz.cif | jq -c '.paths | keys_unsorted'
3.  
4. Actual counts (1ehz)           {"pairs":34,"multiplets":4,"helices":2,"stems":4,"isoCanonPairs":1,"coaxStacks":2,"hairpins":3,"junctions":1,"kissingLoops":1,"ssSegments":1,"stacks":11,"nonStack":4,"hbonds":118,"nts":76}
5.                                // x3dna-dssr --json=ebi -i=1ehz.cif | jq -c .counts
6.                                
7. Base pair (G1–C72)             {"index":1,"nt1":"|1|A|G|1||||","nt2":"|1|A|C|72||||","bp":"G-C","name":"WC","Saenger":"19-XIX","LW":"cWW","DSSR":"cW-W"}
8.                                // x3dna-dssr --json=ebi -i=1ehz.cif | jq -c .pairs[0]
9.                                
10. Nucleotide (2MG10)             {"nt_name":"2MG","nt_id":"|1|A|2MG|10||||","is_modified":true,"chi":169.599,"puckering":"C3'-endo"}
11.                                // x3dna-dssr --json=ebi -i=1ehz.cif | jq -c '.nts[9] | {nt_name, nt_id, is_modified, chi, puckering}'
12.  
13. Jmol (SQL) selections          SELECT hairpins
14.                                SELECT within(dssr, "nts WHERE is_modified")
15.                                SELECT within(dssr, "pairs WHERE name !='WC'")
16.  

42

DSSR-Jmol integration / The graphical abstract

« on: May 04, 2017, 01:35:32 pm »

3D interactive visualization of the classic L-shaped tRNA (PDB id: 1ehz) with the three hairpin loops highlighted in red and the four-way junction loop in blue. The image was created using the DSSR-Jmol integration.

The Jmol script (abstract-graphics.scr) used to create the original image is shown below. The image was annotated using Inkscape.

Code: [Select]

# Jmol 14.13.1 (2017-04-09)
load =1ehz/dssr
select nucleic; display nucleic
rotate best; rotate z 90
cartoon only
set cartoonsteps on
set cartoonblocks off
set antialiasdisplay on
background white; color grey
select hairpins; color red
select junctions; color blue

The raw image from the above script is as below:

43

DSSR-Jmol integration / DSSR-enhanced visualization of nucleic acid structures in Jmol

« on: May 04, 2017, 01:23:35 pm »

I am excited to announce that a paper titled "DSSR-enhanced visualization of nucleic acid structures in Jmol" has just been published online for the 2017 web-server issue of Nucleic Acids Research (NAR). Co-authored by Robert Hanson and me, this paper represents an idealized result I could expect from a scientific collaboration. I first approached Bob in October 2013 at a meeting organized by RCSB PDB at Rutgers, and we then met again in July 2014 in Paris. Over the years, we have communicated extensively via email, facilitated by Skype. Collaborating with Bob has been a truly exciting experience, and it is gratifying to see a joint publication coming out of our efforts.

The DSSR-Jmol integration bridges the DSSR command-line analyzing tool and the Jmol molecular viewer seamlessly together via a simple JSON interface and a powerful query language. This work fills a gap in RNA structural bioinformatics, and brings the 3D interactive visualization of nucleic acid structures to an entirely new level. The website (http://jmol.x3dna.org) is fully functional, useful to researchers, educators, and students alike. Furthermore, it can serve as a starting point for anyone who wishes to develop additional interactive web-based resources involving nucleic acid structures.

The DSSR-Jmol paper has been featured in the cover image of the NAR'17 web-server issue. Undoubtedly, this recognition would further increase this publicity of this solid piece of work. (note added on June 30, 2017)

The abstract of the paper is quoted below:

Sophisticated and interactive visualizations are essential for making sense of the intricate 3D structures of macromolecules. For proteins, secondary structural components are routinely featured in molecular graphics visualizations. However, the field of RNA structural bioinformatics is still lagging behind; for example, current molecular graphics tools lack built-in support even for base pairs, double helices, or hairpin loops. DSSR (Dissecting the Spatial Structure of RNA) is an integrated and automated command-line tool for the analysis and annotation of RNA tertiary structures. It calculates a comprehensive and unique set of features for characterizing RNA, as well as DNA structures. Jmol is a widely used, open-source Java viewer for 3D structures, with a powerful scripting language. JSmol, its reincarnation based on native JavaScript, has a predominant position in the post Java-applet era for web-based visualization of molecular structures. The DSSR-Jmol integration presented here makes salient features of DSSR readily accessible, either via the Java-based Jmol application itself, or its HTML5-based equivalent, JSmol. The DSSR web service accepts 3D coordinate files (in mmCIF or PDB format) initiated from a Jmol or JSmol session and returns DSSR-derived structural features in JSON format. This seamless combination of DSSR and Jmol/JSmol brings the molecular graphics of 3D RNA structures to a similar level as that for proteins, and enables a much deeper analysis of structural characteristics. It fills a gap in RNA structural bioinformatics, and is freely accessible (via the Jmol application or the JSmol-based website http://jmol.x3dna.org).

This section on the 3DNA Forum is dedicated to topics on reproducing the results reported in the DSSR-Jmol article, and the cover image. Scripts and related data files where necessary are provided so interested parties can rigorously reproduce our results. We welcome any questions and comments you may have. Please post them here instead of (or in addition to) sending me emails.

• Supplementary data (DSSR-Jmol manual) -- it serves as the manual for the DSSR-Jmol integration.
• Graphical abstract
• Table 1
• Figure 3
• reproduce-dssr-jmol.tar.gz -- the tarball file

• Cover image
• reproduce-cover-image.tar.gz

Note that the reported results in the paper were based on DSSR version 1.6.8 (released on 2017-03-28) and Jmol version 14.13.1 (released on 2017-04-09). During the proof stage, Jmol was updated to version 14.15.1 (released on 2017-04-27), which was the one reported in the manuscript and the supplementary data.

Best regards,

Xiang-Jun


For completeness, here are Figure 1 (brief description of DSSR algorithms) and Figure 2 (screenshot of the DSSR-Jmol website).

Definitions of key nucleic acid structural components in DSSR [reproduced from Figure 1 of reference (9)]. (A) Nucleotides are recognized using standard atom names and base planarity. This method works for both the standard bases (A, C, G, T and U), and those of modified nucleotides, regardless of their tautomeric or protonation states. (B) Bases are assigned a standard reference frame (25) that is independent of sequence identity: purines and pyrimidines are symmetrically placed with respect to the sugar. (C) The standard base frame is derived from an idealized Watson-Crick base pair, and defines three base edges (Watson-Crick, minor groove, and Major groove) that are used to classify pairing interactions. (D) Base pairs are identified from the co-planarity of base rings and the occurrence of hydrogen bonds. This geometric algorithm can find canonical (Watson-Crick and G–U wobble) as well as non-canonical pairs. Higher-order (three or more) co-planar base associations, termed multiplets, are also detected. (E) Helices are defined by stacking interactions of base pairs, regardless of pairing type (canonical or otherwise) or backbone connectivity (covalently connected or broken). A helix consists of at least two base pairs. The same algorithm is applied to identify continuous base stacks that are outside of helical regions, by using bases instead of pairs as the assembly unit. Nucleotides not involved in base-stacking interactions are collected into one separate group. A stem is defined as a special type of helix, made up of canonical pairs and with a continuous backbone along each strand. Coaxial stacking is defined by the presence of two or more stems within one helix. An isolated canonical pair is one that is not contained within a stem. (F) ‘Closed’ loops of various types (hairpin, bulge, internal, and junction loops) are delineated by stems or isolated pairs, and specified by the lengths of the intervening, consecutive nucleotide segments. A kissing-loop motif entails formation of one or more canonical pairs between the bases in different hairpin loops. Single-stranded segments that lie outside loops are separately listed.

A screenshot of the DSSR-JSmol web interface, highlighting the two reverse Hoogsteen pairs (U8–A14 and 5MU54–1MA58) of yeast phenylalanine tRNA (PDB id: 1ehz). (A) DSSR-derived structural features integrated into Jmol. (B) The main JSmol viewer canvas for visualization and interactive manipulations. (C) Common representation styles for selected structural features. (D) A simple text input field for advanced users to enter (short) Jmol script commands. (E) Structure input by PDB id, file upload (drag-and-drop), or selecting one from the twelve sample RNA structures. (F) Utilities to toggle between two states for six common cases. (G) Export of coordinate file or PNG image. (H) Links to online resources for DSSR and Jmol.

44

Site announcements / Highlights of recent developments of 3DNA/DSSR

« on: November 20, 2016, 07:13:58 pm »

Dear 3DNA Forum subscribers,

Here are some highlights of recent developments of 3DNA/DSSR:
Note: If you've difficulty in accessing the 3DNA homepage, possibly the case from mainland China (as I know it), please visit its duplicate at http://home.x3dna.org. This newsletter is written in Markdown, with a translated HTML version posted on the 3DNA homepage.

3DNA v2.3

• The C source code is now available. Since the programs are written in strict ANSI C, 3DNA can be compiled (as is) on any computers/operating systems with a C (or C++) compiler. For user convenience, three binary distributions (with source code under the src/ subdirectory) are provided for Windows, Linux, and Mac OS X. The distributed Windows version works in native Windows (7 and up, via the cmd command-line interface, or ConEMU), MinGW/Msys (Msys2), and Cygwin, in either 32 or 64-bit.
• A new set of 'simple' base-pair and step parameters was introduced to give 'intuitive' numerical values for non-Watson-Crick base pairs and associated steps. See the short communication titled Characterization of base pair geometry in the January 2016 issue of Computational Crystallography Newsletter (CCN).
• The fiber program includes a new option, --pauling, for easy generation of Pauling & Corey triplex models of DNA/RNA with arbitrary base sequence. See my blogpost titled Pauling's triplex model of nucleic acids is available in 3DNA.
• Thomas Holder (PyMOL Principal Developer at Schrödinger, Inc.) has built a PyMOL wrapper to 3DNA fiber models. Now generating standard, regular DNA/RNA models in PyMOL is straightforward -- thanks, Thomas!

DSSR (Dissecting the Spatial Structure of RNA)

• Selected features of DSSR have been incorporated into Jmol (in collaboration with Robert Hanson, Jmol Principal Developer), and PyMOL (in collaboration with Thomas Holder). In Jmol application (via the Console window), one can now, for example, load =1ehz/dssr and then select hairpins; color red to see where the three hairpin loops are in 3D. The Jmol-DSSR web interface makes DSSR-enhanced visualization of nucleic acid structures in Jmol readily accessible to a broad user base, and has been employed in classes for educational purpose. A sample image of DSSR-derived cartoon-block representation via PyMOL is available for PDB entry 5dww, which has a G-quadruplex-duplex interface.
• Since the publication of the Nucleic Acids Research paper in 2015, DSSR has been continuously refined and expanded, with a total of 36 new releases (from v1.2.8 to v1.6.4) as of this writing. Notably, the --json option provides DSSR-derived parameters in the simple, structured, and standard JSON format that can be easily parsed. This JSON output format is the (preferred) way for the outside world to interface with DSSR, and the Jmol-DSSR integration is built upon it. The --nmr option allows for batch processing of MODEL/ENDMDL-delineated NMR ensembles or trajectories of molecular dynamics (MD) simulations. Did you know that scripts and data files for reproducing the reported results are available in the DSSR-NAR paper section on the 3DNA Forum?
• The User Manual is now 88-page long, covering nevertheless only the most common use cases of what DSSR has to offer. Miss a feature that you would like to have? Maybe it is already there or can be easily implemented in DSSR. Simply ask (on the 3DNA Forum), and I'll try my best to help.

SNAP (Structures of Nucleic Acid-Protein complexes)

• SNAP aims to consolidate, refine, and significantly extend commonly used functionalities for DNA/RNA-protein structural analysis in one easy-to-use program. Currently in beta testing, SNAP is already fully functional, with features for characterizing the protein-nucleic acid interface and identifying amino acid-base pairing and stacking interactions.

A note for 3DNA/DSSR users in mainland China: It's a pleasure to see the ~100 registrations on the 3DNA Forum with emails ending in .cn, 163.com, or qq.com etc., mostly from recent years. I'm planning a trip to China in 2017, and I'd be happy to meet some of you for academic exchanges and possible collaborations (学术交流、合作). If you're interested, let's get in touch!

Best regards,

Xiang-Jun

45

Site announcements / Pauling's triplex model of DNA and RNA

« on: November 17, 2016, 11:26:31 am »

As of v2.3-2016nov16, the 3DNA fiber program has added the --pauling option. This new feature is intended for easy generation of DNA/RNA triplex models based on the historical paper of Pauling and Corey in 1953, titled "A proposed structure for the nucleic acids". Combined with the existing --sequence option, 3DNA users can now construct a Pauling triplex model with arbitrary base sequence.

The basic usage is very straightforward, as illustrated in the following list of examples. There are also other variants as well, which may be useful for advanced users.

Code: [Select]

fiber -pauling triplex-C10C10C10.pdb        # default: 10 Cs per strand
fiber -pauling -seq=AAA triplex-A3A3A3.pdb  # 3 As per strand
fiber -pauling -seq=AAAA:CCCC:GGGG Pauling-triplex-A4C4G4.pdb
fiber -pauling -seq=ACGGUU,UUGGAC,GGAACC  Pauling-triplex-mixed.pdb
fiber --pauling-dna -seq=ACGGTT,TTGGAC,GGAACC  Pauling-triplex-DNA.pdb
A sample 3D image for the mixed sequence (last one in the above list, Pauling-triplex-DNA.pdb) is shown below:



See my blogpost titled "Pauling's triplex model of nucleic acids is available in 3DNA" for further information.

46

Site announcements / The number registrations has reached 3000

« on: October 15, 2016, 11:51:55 am »

As of October 15, 2016, the number of registrations on the 3DNA Forum has reached over 3,000! It takes slightly longer (15 days) than I predicted in my previous post "Summary of registrations" dated April 26, 2016, where I said:

If the current trend continues, the number of 3DNA Forum registered users will reach 3,000 by the end of September 2016.

In the past fews months, the number of new registrations has been in the 40s, slightly lower than the 50s averaged over previous years/months.

With 3,000 registrations from users all overall the world, yet no spams, the Forum is certainly functioning better than I could originally imagine. It serves well as a virtual platform that I can interact effectively with the ever-increasing 3DNA/DSSR user community. It is worth noting that the Forum has recently received contributions from Dr. Steve Harvey, a well-known computational structural biologist.

I'll write another announcement post when the number of registration reaches 5,000.

47

MD simulations / MOVED: Concatenated Helices

« on: August 29, 2016, 12:19:08 pm »

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

http://forum.x3dna.org/index.php?topic=641.0

48

General discussions (Q&As) / MOVED: How to change the criteria of base pair

« on: July 27, 2016, 06:55:00 pm »

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

http://forum.x3dna.org/index.php?topic=632.0

49

General discussions (Q&As) / MOVED: global bending of a single stranded DNA

« on: July 18, 2016, 04:46:34 pm »

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

http://forum.x3dna.org/index.php?topic=630.0

50

General discussions (Q&As) / How to setup 3DNA

« on: May 05, 2016, 02:24:00 pm »

Follow the instructions on "How to install 3DNA on Linux (Mac OS X) and Windows?" and post back any questions you may have.

Enjoy using 3DNA!

Xiang-Jun