1. Create DNA molecular structure file using w3DNA

This tutorial is part of a detailed guide on making an abstract scientific illustration. You can get all the files associated with the guide here.

1. First the DNA molecule is defined using base-pair step parameters describing each dinucleotide step in the structure and set up in an input file for 3DNA or w3DNA (the file called 'DNA.txt').

2. Then a pdb file of the structural parameters is constructed using w3DNA. Go to http://w3dna.rutgers.edu and click on the Reconstruction-tab.

3. On the next page, click 'Customized model' and scroll down to 'Customized base-pair-step/nucleotide parameters'. Then press Continue.

4. Then, under 'Base-pair parameter file' choose the created structural input file (DNA.txt). Press Build.

5. Download the constructed pdb file from the results page.

Note that since this structure design strategy is done base-by-base by hand it may require a large number of iterations before the desired three-dimensional structure is obtained (if you know of an easier way of creating 100% user-defined nucleic acid molecular structure files, let me know).

Next: 2. Position the dyes within the DNA molecule using Avogadro

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