Hi Wim,
Thanks for the help. I have found four of my five non-standard
residues in EBI website. Unfortunately, I cannot find two of them
(code A2M and CFL) in Analysis in the Select Small Molecule popup.
(Molecule->Molecular Templates -> Add Other Compound). I've recently
update Analysis, so I'm sure the problem isn't that I'm out-of-date.
Is there a convenient way to get new molecules into Analysis? If I
click on the retrieve button on the EBI website, it gives me an XML
file, but this doesn't seem like the same type of XML file as in
ccpnmr1.0/data/ccp/chemComp/other. However, when I selected one of
the two residues which was in the Select Small Molecule popup (UMF or
OMG), analysis downloaded the appropriate molecules.
That brings me to a related question. One residue is not in the
databank. If I were to be so intrepid as to try to add it manually by
editing the XML file how could I get analysis to recognize the new xml
files.
Thanks,
Justin
On Mon, Mar 3, 2008 at 6:07 AM, Wim Vranken <[log in to unmask]> wrote:
> 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
>
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