Accounting for N1 and N3 CSA differences in RNA

[Alexandar Hansen]

As I was running the full_analysis.py for an RNA data set of U and G data, I realized that it's trying to use the same CSA for each residue.  Looking into the script, it would seem to be relatively easy to code the "set the bond length and CSA values" section in such a way that it chooses a different CSA value for the given residue types. Currently it's simply:

            value.set(name, 1.02 * 1e-10, 'bond_length')
            value.set(name, -170 * 1e-6, 'csa')

to modify this for RNA, could one edit it to say:

            value.set(name, 1.01 * 1e-10, 'bond_length')
            if residuename = G
                value.set(name, -130 * 1e-6, 'csa')
            else if residuename = U
                value.set(name, -100 * 1e-6, 'csa')

Am I overtrivializing this, or should it be pretty straight forward?


Alex Hansen

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