I can't quote any percentages, but what I can say through direct experience
is that the PDB is no longer allowing non-standard, non-sequential numbering
of entries to the PDB. That's the good news; the bad news is that they will
not be going back and altering the old entries that exist with residue
numberings like 26, 26A, 26B, 26C, 27 et cetera. Gaps are still very much
allowed (and necessary due to disorder), so there will always be cases like
25, 26, ... 32, 33....
-Tom
On Fri, Apr 18, 2008 at 9:26 AM, Eric Martz <[EMAIL PROTECTED]>
wrote:
> Dear Rolf,
>
> Your point about sequence numbering irregularities is well taken.
> Regarding your proposed solution, I'm not sure how enthusiastic Bob
> is about checking for such irregularities within Jmol.
>
> If he is not enthusiastic, and if it has to be one or the other for
> all cases (having "select 100-200" be equivalent to "select
> resno>=100 and resno <= 200", or not), I am still in favor of having
> "select 100-200" be equivalent to "select resno>=100 and resno <= 200".
>
> My reasoning is that, in my experience, sequence numbering
> irregularites occur in a very small percentage of PDB entries. (Does
> anyone know the percentage?) On the other hand, residues without
> coordinates occur, I think, in the majority. So I prefer to handle
> the majority case correctly, and leave the struggle to the minority of
> cases.
>
> Otherwise, in the majority of cases, the user has to struggle to
> examine the SEQRES to coordinate mapping and carefully pick sequence
> numbers that have coordinates to succeed in selecting ranges.
>
> -Eric
>
> At 4/17/08, Rolf Huehne wrote:
> >Eric Martz wrote:
> > > Dear Bob,
> > >
> > > I'd like to suggest that "select 525-696:a" should select any
> > > residues with coordinates in the specified sequence range, regardless
> > > of whether residue 525 or 696 happens to have coordinates. For 2rd0,
> > > where 525-696:a is a domain of interest in Figure 1 of the primary
> > > reference, zero atoms are selected by Jmol because residue 525 lacks
> > > coordinates. The same command works in Chime (all residues with
> > > coordinates in the specified range are selected).
> > >
> > > Thus, I suggest that the above command should be equivalent to
> > >
> > > select :a and resno >= 525 and resno <= 696
> > >
> > > which does work in Jmol.
> > >
> >
> >This would be ok if all residues were always numbered sequentially. But
> >unfortunately there are a lot of entries with numbering irregularities
> >within the PDB. Take for example entry '1A4K' (the numbering
> >irregularities can be seen easily from the alignment view in our JenaLib
> >atlas page for this entry:
> >http://www.fli-leibniz.de/cgi-bin/ImgLib.pl?CODE=1a4k&EXPAND=alignment)
> >and issue the following 2 commands in Jmol
> >(http://www.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=1a4k):
> >
> >1) select 27-28:A
> >2) select :A and resno>=27 and resno<=28
> >
> >With command 1) 7 residues will be selected
> >(27,1027,2027,3027,4027,5027,28).
> >
> >With command 2) only 2 residues will be selected (27,28).
> >
> >Since residues 1027,2027,3027,4027,5027 are structurally between residue
> >27 and residue 28 the result of command 1) is clearly what would be
> >expected from a range selection command.
> >
> >Therefore I would argue strongly against simply replacing command 1) by
> >command 2) in Jmol.
> >
> >But maybe it would help to reduce the problem Eric has described by
> >restricting the replacement of command 1) by command 2) to cases without
> >numbering irregularities. This would mean that Jmol would look for
> >numbering irregularities while loading the file and set a flag if it has
> > found any.
> >
> >Regards,
> >Rolf
> >
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