Hi Justin,
> I'm working with an RNA which has many nonstandard nucleotides. The
> 2' position of the pyrimidines is fluorinated, the 2' position of (all
> but two of the) purines is methylated and the 3' termini has Thymine
> linked backwards (via its 3' O).
>
> I have a pdb for this molecule, which I can post if it would help.
Do you have the three letter codes used in the PDB for these
residues? If not, you can try to search for them on:
http://www.ebi.ac.uk/msd-srv/msdchem/cgi-bin/cgi.pl
The 'ccpCode' used in CCPN matches the code used in the PDB (at least
for this kind of residue). You can then create a molecule with the
correct nonstandard nucleotides - the molecular type won't be 'RNA',
but 'other', and the residues won't be linked in the 'standard'
fashion (where you have start, middle and end residues), but this
should not matter for assignment purposes - it just means the
molecule is not as well described inside the CCPN framework.
It'll be a while before I'll get around to writing it, but in the 2.0
version there will eventually be a way to create modified 'standard'
residues yourself... .
Bye,
Wim
|