Hello,
That list is hard-wired (because they are not all distributed with the
release). The only way to do what you want is to edit the file:
ccpnmr1.0/python/ccp/general/ChemCompOverview.py
and search for chemCompOtherOverview and add the data in there. This is a
dictionary. The key is the ccpCode. The value is a list of length 4.
The first element of the list is the code1Letter which you can take to be
None. The second element is the code3Letter, which you might as well take
to be the same as the ccpCode. The third element is the name of the
chemComp. The fourth element is the molecularFormula.
I would just copy an existing line and edit that. The order of the
entries in the dictionary does not matter so you might as well put yours
at the top.
Wayne
On Wed, 5 Mar 2008, Justin Douglas wrote:
> 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 update Analysis, so I'm sure the problem isn't that I'm out-of-date.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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