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Questions and answers => w3DNA -- web interface to 3DNA => Topic started by: ghzheng on November 29, 2008, 12:18:52 pm

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Title: What kind of services we will provide?
Post by: ghzheng on November 29, 2008, 12:18:52 pm

Hi Xiangjun,

I created a framework for the web interface, setting up the overall php framework (CodeIgniter framework), Flexigrid grid (Gridview of data), and mysql tables. Currently, as a test, I have a starting page
http://dnaserver.rutgers.edu/~ghzheng/w3dnadev/ (http://dnaserver.rutgers.edu/~ghzheng/w3dnadev/)
There, please just try typing in 1KX3 (no others, others might not work due to the 3dna web access problem, which I am still working with the computer supporters).

Basically, I am asking for your advice. What kinds of services do you think we can provide on either of the three sub pages: Analyzing, Rebuilding, and Visualizing.

1) Analyzing: I am thinking to show results of nucleic acid sequence, base pairing, base-pair parameters, base-pair step parameters.
2) Rebuilding: I am thinking to allow build i) ideal fibers and base-pair steps; ii) DNA/protein complexes with DNA/protein complex templates, i.e. protein coordinates will be integrated into the structure; iii) is it possible to visualize the pdb files in an embedded visualization tool, such as vmd?
3) Visualizing: I am thinking to provide blocview...

There are lots of beautiful functions of 3DNA that I am just not very familiar. Please advise me what kind of services we can provide and attract users.
Thanks.

Guohui

Title: Re: What kind of services we will provide?
Post by: xiangjun on November 30, 2008, 01:32:06 pm

Hi Guohui,

Good start!

Overall, I would like to make w3DNA simple, accurate and robust, at least at the very beginning: take, for example, the 'google' home page. Do not put too many stuffs; whatever is there should be useful.


• Analyzing: list the various 3DNA output files files for download first, followed by any extracted info. A nice, simple add-on would be to mark non-Watson-Crick pairs (or G.U wobble pair).
• Rebuilding: put fiber model-building part first since this is the most-useful part to the general community; add sequence-specific building funcationality next: do not forget with sugar-phosphate backbone in various conformation, and the simplified Calladine-Drew style in Alchemy format. The download page should also be linked to Jmol/RasMol for online view.
• Visualizing: blocview is certainly the first choice, followed by stacking diagram, and base-pairing diagram (see the 3DNA NP paper). This is linked directly to the analyzing part.

You might want to put fiber-model building first in the list, following by visualization. In the home-page, you might also want to put some nice images to illustrate 3DNA major functionality to attract visitors.

Best regards,

Xiang-Jun

Title: Re: What kind of services we will provide?
Post by: ghzheng on December 01, 2008, 11:50:41 am

Thanks - Xiangjun. I will move on with your advice and let you know any progress.

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.