Dear Magnus,
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. So if you
create a molecule with unknowns in it, you will have to make a different
molecule when you find the right structure, and then copy all the links
across from the old to the new molecule.
We could have only one set of linkages, so you would have to find a set of
linkages that would do for all alternatives. Hopefully that should work?
If you wanted to add substituents latere (without changing the ChemComp)
you would have to have separate residues for the substituents - which is
the alternative we agreed not to use. In theory you could have a single
hexose ChemComp and treat teh different stereochemistries as variants, but
I doubt anybody would want that.
Anyway, Wim is the right person to talk to about getting a suitable
ChemComp.
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, Magnus Lundborg wrote:
> Hello,
>
> I wonder if it's possible to build molecule templates containing unknown
> (in my case carbohydrate) residues (if the user is not yet sure what
> residue it is) and unknown linkage positions. It would be very handy for
> me if it's possible, but I'm not sure if the data model allows this and
> I can't seem to manage to do it in analysis. An easy way could be to
> make a chemcomp that is just an unspecified hexose, pentose or whatever.
>
> Thanks
> /Magnus
>
> --
> Magnus Lundborg, ph.D. Student
> Stockholm University
> Department of Organic Chemistry
> Arrhenius Laboratory
> S-106 91 Stockholm
> Sweden
> E-mail address: [log in to unmask]
>
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