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Questions and answers => w3DNA -- web interface to 3DNA => Topic started by: xiangjun on November 18, 2018, 09:02:06 pm

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Title: Notes on w3DNA v2
Post by: xiangjun on November 18, 2018, 09:02:06 pm
Hi Shuxiang,

Impressive progress with the new version (v2) of web 3DNA (http://web.x3dna.org) -- 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 (http://x3dna.org/highlights/pauling-triplex-model-of-nucleic-acids-is-available-in-3dna).

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 (http://curvesplus.bsc.es) 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.


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.


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

Best regards,

Xiang-Jun
 
Title: Re: Notes on w3DNA v2
Post by: shuxiang on December 03, 2018, 02:43:55 pm
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

Title: Re: Notes on w3DNA v2
Post by: xiangjun on December 03, 2018, 02:53:08 pm
Hi Shuxiang,

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

Best regards,

Xiang-Jun
Title: Re: Notes on w3DNA v2
Post by: shuxiang on December 06, 2018, 03:30:49 pm
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
Title: Re: Notes on w3DNA v2
Post by: xiangjun on December 07, 2018, 10:47:08 am
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

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.