Hi Justin,
> 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 update Analysis, so I'm sure the problem isn't that I'm out-of-date.
XML files for A2M and CFL attached - the first one slipped through
the net somewhere, the second one is quite recent and didn't end up
in the search dictionaries.
> 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.
Make your molecule in a 'chemical editor', save it as a .mol2 file,
then read it in with the formatConverter (Import->Single Files-
>Chemical compounds->mol2). You'll be able to give it a ccpCode of
your own (provided it doesn't exist yet), then you can name the atoms
(they get default names which won't make sense for RNA).
Bye,
Wim
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