Hi,

I am trying to characterize DNA nucleotides from PDB files into buried and accessible regions based on their accessible surface area. For definitions, i need relative accessibility.

I am using NACCESS and I do get relative accessibilities for the protein residues but for the DNA, it is always -99.9. Is there a way I can calculate it myself? Or use a tool/method that does it for me? I looked into literature but didn't find anything. Conceptually, how wrong would it be to use the absolute accessibilities?

I am attaching an example here.

RES  DA X   1   120.78 -99.9 120.78 -99.9   0.00 -99.9  40.06 -99.9  80.72 -99.9
RES  DC X   2    87.76 -99.9  79.83 -99.9   7.93 -99.9  20.90 -99.9  66.86 -99.9
RES  DC X   3    71.04 -99.9  70.60 -99.9   0.45 -99.9  32.26 -99.9  38.79 -99.9
RES  DG X   4   120.87 -99.9 120.87 -99.9   0.00 -99.9  57.37 -99.9  63.50 -99.9
RES  DG X   5    73.91 -99.9  71.78 -99.9   2.14 -99.9  29.52 -99.9  44.39 -99.9
RES  DG X   6    84.86 -99.9  81.24 -99.9   3.62 -99.9  29.76 -99.9  55.10 -99.9
RES  DC X   7    73.78 -99.9  69.07 -99.9   4.71 -99.9  22.78 -99.9  51.00 -99.9
RES  DC X   8    94.58 -99.9  94.45 -99.9   0.14 -99.9  59.21 -99.9  35.37 -99.9
RES  DC X   9   107.53 -99.9 104.66 -99.9   2.87 -99.9  36.91 -99.9  70.62 -99.9
RES  DT X  10   108.41 -99.9 105.72 -99.9   2.70 -99.9  54.78 -99.9  53.63 -99.9