2. Position the dyes within the DNA molecule using Avogadro
Avogadro is a freeware that can be downloaded here.
1. The individual dye molecular structures are created manually in your favorite molecular editing program such as ChemBio3D, HyperChem, GaussView, etc.. In this case they are called 'Cy3_DNA.pdb', 'conedye_DNA.pdb', etc.
2. Use Avogadro to position the individual dye molecules within the DNA molecule file. Open the dye molecule in Avogadro and select all atoms using the Selection tool. Press Ctrl+C to copy the molecule to the clipboard.
3. Open the DNA molecule DNA.pdb in a new Avogadro window and press Ctrl+V to insert the dye molecule. Position the dye at the desired position and orientation using the Manipulation tool.
4. When the dye has been positioned correctly go to Select -> Invert selection and press delete. This will delete the DNA structure and leave the naked dye molecule at the new coordinates.
5. Save this new dye molecule file.
6. Redo step 7-10 for all dye structures.
7. The accessible volume (AV), plotted in the top of the final figure, is a pdb file consisting of many atoms defined in a grid. This AV file was courtesly provided by S. Sindbert from their 2011 JACS paper. The AV is positioned in an similar manner as for the dyes described above.