Hi Wim,
Thank you very much for the files.
However I'm still unclear on how to get these xml files into analysis.
By that I mean, I'm unclear on how to get these new molecules in the
Select Small Molecule popup (Molecule-> Molecular Template-> Add Other
Compound) which I use to make the polymer chain.
Thanks,
Justin
On Wed, Mar 5, 2008 at 6:29 AM, Wim Vranken <[log in to unmask]> wrote:
> 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 update Analysis, so I'm sure the problem isn't that I'm out-of-date.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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