How do I build a nucleic acid structure with a sugar-phosphate backbone?
The easiest way to build a nucleic acid structure with the sugar-phosphate backbone, other than predefined fiber models, is to use the rebuild program. The backbone building scheme uses exactly the same protocol as the default base-only model building scheme. The user needs to add the -atomic option to rebuild, and to choose the desired rigid sugar-phosphate backbone to be attached to the standard base geometry. The four currently available backbones are listed in the directory X3DNA/config/atomic. To use any of these backbones, it is necessary to copy the five standard nucleotide files associated with each backbone to X3DNA/config or your current working directory, and to name each nucleotide as follows: Atomic_X.pdb (X = A, C, T, G, U etc). The default Atomic_X.pdb files contains only the C1′ backbone atom. The base geometry is independent of the backbone conformation. To build a DNA structure with B-DNA backbone conformation, for example, one uses the BDNA_stdX.pdb set to replace At
