> Right, I think we need to go back one step first. Does the molecule with
> the two-residue gap have the two residues at either side of the gap as
> "middle" residues (so are covalently connected or not covalently connected
> but for some reason you want to pretend they are) or is the "top" part of
> the gap really a C-terminus and the "bottom" part an N-terminus?
>
> In the first case, the data model says that you should create one standard
> molecule, so you should *not* create those two sections the way Tim wrote
> in a previous email. That should only be done in the second case.
Aside from a few additions that need to be made to Analysis (e.g. to link
the fragments correctly and make alignmets) I don't see that it is
particularly bad to use two chain fragments. At least in this case I have
a quick way of knowning for sure about a possible discontinuity in
sequence numbering when I'm trying to derive offsets...
T.
-------------------------------------------------------------------------------
Dr Tim Stevens Email: [log in to unmask]
Department of Biochemistry [log in to unmask]
University of Cambridge Phone: +44 1223 766018 (office)
80 Tennis Court Road +44 7816 338275 (mobile)
Old Addenbrooke's Site +44 1223 364613 (home)
Cambridge CB2 1GA WWWeb: http://www.bio.cam.ac.uk/~tjs23
United Kingdom http://www.pantonia.co.uk
-------------------------------------------------------------------------------
------ +NH3CH(CH(CH3)OH)C(O)NHCH(CH(CH3)CH2CH3)C(O)NHCH(CH2CH2SCH3)CO2- -------
-------------------------------------------------------------------------------
|