Notes on w3DNA v2

[xiangjun]

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
 

[shuxiang]

Hi Xiang-Jun,

Thank you so much for above wonderful suggestions. I have finished some of them and will update the public server as soon as I finish all.

One thing I want to mention is about the high resolution image in the Visualization part. I compared the high resolution png file (converted from eps file with high resolution option)  with the default svg file (convert eps to pdf then to svg) in our web sever.  It looks like the high resolution png file is better than the default svg file (see the attached image, the top one is png file and the bottom is svg file). I will use the png file currently.

Best regards,
Shuxiang

[xiangjun]

Hi Shuxiang,

Thanks for the update. Using high-resolution PNG files for the stacking diagrams is fine with me.

Best regards,

Xiang-Jun

[shuxiang]

Hi Xiang-Jun,

I found an interesting base (TNT) when calculating the torsion angles of a structure (pdbid: 102D). I found this because my code was killed to extract the base name and cannot import the data into a local database.
the command I used:  analyze -t=test.tor 102D.pdb
the result:
              base      chi A/S     alpha    beta   gamma   delta  epsilon   zeta     e-z BI/BII
   1 A:...1_:[.DC]C  -110.9 anti     ---     ---    162.9   155.9  -177.3  -105.1   -72.2  BI
   2 A:...2_:[.DG]G   -96.2 anti    -48.5  -172.5    22.9   149.7  -176.0  -111.9   -64.1  BI
   3 A:...3_:[.DC]C  -113.1 anti    -68.6   172.1    55.5   132.3  -168.4  -105.4   -63.0  BI
   4 A:...4_:[.DA]A   -89.3 anti    -57.8  -159.4    40.9   144.7   171.5  -105.3   -83.3  BI
   5 A:...5_:[.DA]A   -97.6 anti    -61.0   178.3    54.8   152.7  -169.7  -114.6   -55.1  BI
   6 A:...6_:[.DA]A  -102.2 anti    -66.1  -176.1    48.1   142.8   178.2   -92.7   -89.1  BI
   7 A:...7_:[.DT]T  -101.7 anti    -80.5   177.5    55.4   148.6   -91.5   175.7    92.7  BII
   8 A:...8_:[.DT]T   -99.5 anti    -45.3   168.6    -4.0   150.3  -168.8  -102.8   -66.0  BI
   9 A:...9_:[.DT]T   -94.3 anti    -76.5  -165.2    41.7   136.8  -176.4  -109.3   -67.1  BI
  10 A:..10_:[.DG]G   -87.6 anti    -51.9   170.2    42.6   152.9  -134.3  -169.8    35.5  BII
  11 A:..11_:[.DC]C  -105.4 anti    -66.5   169.1    47.4   143.7  -169.3   -95.4   -73.9  BI
  12 A:..12_:[.DG]G   -77.2 anti    -74.8  -176.4    46.8   148.5    ---     ---     ---   ---
  13 B:..13_:[.DC]C   -98.7 anti     ---     ---    -63.7   161.9  -125.0  -178.8    53.8  BII
  14 B:..14_:[.DG]G  -110.4 anti    -50.4   154.6    25.0   146.5  -170.5  -108.0   -62.5  BI
  15 B:..15_:[.DC]C  -118.7 anti    -59.8   170.6    52.8   140.4  -155.7  -134.9   -20.8  BI
  16 B:..16_:[.DA]A   -98.2 anti    -57.8   158.8    61.9   152.0  -168.7  -114.0   -54.7  BI
  17 B:..17_:[.DA]A  -103.2 anti    -63.8   175.0    52.4   143.3  -166.0  -105.7   -60.2  BI
  18 B:..18_:[.DA]A  -104.3 anti    -55.4   177.7    40.6   145.7  -177.8   -98.8   -79.0  BI
  19 B:..19_:[.DT]T  -103.1 anti    -73.4   175.6    58.0   147.4  -141.7  -160.8    19.1  BI
  20 B:..20_:[.DT]T   -99.1 anti     10.2   173.1   -35.0   157.6   178.5   -98.2   -83.3  BI
  21 B:..21_:[.DT]T  -106.8 anti    -69.9   177.9    55.3   139.2  -155.6  -118.1   -37.5  BI
  22 B:..22_:[.DG]G   -80.4 anti    -41.0   155.2    33.8   148.7  -104.0   174.8    81.2  BII
  23 B:..23_:[.DC]C  -109.9 anti    -62.5   156.8    15.6   150.0  -160.2  -123.2   -37.0  BI
  24 B:..24_:[.DG]G  -116.0 anti    -62.7   162.5    57.1   138.2    ---     ---     ---   ---
  25 -:..25_:[TNT]     ---  ---      ---     ---     ---     ---     ---     ---     ---   ---

I'm not sure this base should be in the torsion angle file. I cannot find it in any other 3dna output files including .inp, .out.

Thank you.

Best regards,
Shuxiang

[xiangjun]

Hi Shuxiang,

Good catch. The issue you noticed is due to a bug that shows up only in special cases like TNT, and with the analyze -t option. It has been fixed. I'll release an update of 3DNA v2.3 next week, along with several other minor revisions, after we finish (mostly) the web 3DNA v2.0.

Best regards,

Xiang-Jun