Dear All,
It would indeed be desirable to be able to edit molecules. The problem is
how to do it without making existing information inconsistent. Molecules
are pretty much defined by their sequence - we should only have one
hexaAlanine (AAAAAA) stored, for instance. If you describe a sample of
hexaAlanine, you would not like it if someone went in and changed
hexaAlanine to hexaGlycine behind your back. It would make the description
of your sample incorrect.
We can think about this, but we would have to make absolutely sure that
this kind of unintended effect can not occur.
Currently the data model allows you to add residues and to set up links to
a molecule under certain conditions, but not to remove or change them.
This will need some thought before we can make changes.
Yours,
Rasmus
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Dr. Rasmus H. Fogh Email: [log in to unmask]
Dept. of Biochemistry, University of Cambridge,
80 Tennis Court Road, Cambridge CB2 1GA, UK. FAX (01223)766002
On Wed, 16 May 2007, Tim Stevens wrote:
> > This can be done, in a way. In proteins we have an unknown amino acid. Of
> > course all amino acids have the same 'linkage positions', so that is
> > easier. You could add one or more unknown sugars. There are problems,
> > though.
> >
> > We can not change the composition of an existing molecule.
>
> I am hoping that the data model can evolve so that molecules can be edited
> in the API. This might be tricky to achieve though. It seems to be a
> reasonably common occurrence that Analysis users don't know their exact
> sequence (e.g. from inaccuracies in DNA seq or unexpected constructs)
> until part way through the assignment procedure.
>
> I guess this would also be an issue for sample management where molecules
> become better resolved, and generally it might be nice to record
> intermediate molecular information, just as we can record intermeditate
> NMR assignment information. NMR can be used to determine what a molecule
> is.
>
> Hopefully it would be less work to substitute or add the occasional
> molResidue, rather than repace an entire molecule and all of its links,
> especially considering that they could span lots of parts of the model.
>
> T.
>
> -------------------------------------------------------------------------------
> Dr Tim Stevens Email: [log in to unmask]
> Department of Biochemistry [log in to unmask]
> University of Cambridge Phone: +44 1223 766018 (office)
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