But what connectivity would be implied by descending numbers: the order
in the file or the order of the numbering? I assume the former,
otherwise what would be the point of having descending numbering? And I
wonder how many programs would baulk at it (or even at ascending
negative numbers?).
-- Ian
> -----Original Message-----
> From: [log in to unmask] [mailto:[log in to unmask]]
On
> Behalf Of Frances C. Bernstein
> Sent: 19 September 2008 16:44
> To: Todd Geders
> Cc: [log in to unmask]
> Subject: Re: [ccp4bb] Non-sequential residue numbering?
>
> As long as each residue within a chain has a unique identifier
> (residue number plus insertion code), there is no restriction
> on numbering. The numbers can be in ascending or descending
> order, non-sequential, and even negative.
>
> Frances
>
> =====================================================
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> =====================================================
>
> On Fri, 19 Sep 2008, Todd Geders wrote:
>
> > Hello all,
> >
> > I have a structure from a non-natural fusion of the truncated
C-terminus
> of
> > one protein with the truncated N-terminus of another. For the
> deposition, we
> > want to keep the numbering as found in the separate proteins. It
looks
> > something like this:
> >
> > 1 12
> > | |
> > ....HWVCKDIALLMCFFLEEMSEEP....
> > | |
> > 754 763
> >
> > At no point is there an overlap in numbering (i.e. the N-terminal
> residue
> > number is higher than the C-terminal residue number).
> >
> > Is this numbering scheme supported by the PDB standard? Thus far,
all
> of the
> > software seems to handle it (refmac, Coot, PyMOL, pdb_extract, PDB
> precheck &
> > validation, etc).
> >
> > Can anyone see a reason to not deposit with this non-sequential
residue
> > numbering?
> >
> > ~Todd
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