I had always assumed that ASCII sort order was the standard so ' 128A'
comes after ' 128 ' in the collating sequence, and indeed the PDB
documentation seems to make it clear that it comes after, e.g. in the
section describing the ATOM record:
REFERENCE PROTEIN NUMBERING HOMOLOGOUS PROTEIN NUMBERING
---------------------------------------------------------------------------------------------------------------------
59
59
60
60
61
62
62
REFERENCE PROTEIN NUMBERING HOMOLOGOUS PROTEIN NUMBERING
----------------------------------------------------------------------------------------------------------------------
85
85
86
86
86A
86B
87
87
But does it actually matter if the insertion comes before? Surely the
sequence is completely defined by the file order, regardless of the residue
numbering, not by the alphanumeric sorting order? So if 86A comes
immediately before 86 in the file then you must assume that 86A C is linked
to 86 N (assuming of course that the bond length is sensible), if after
then it's 86 C to 86A N.
Cheers
-- Ian
On 5 December 2012 16:02, Robbie Joosten <[email protected]> wrote:
> Hi Ian,
>
> It's easy to forget about LINK records and such when dealing with the
> coordinates (I recently had to fix a bug in my own code for that).
> The problem with insertion codes is that they are very poorly defined in
> the
> PDB standard. Does 128A come before or after 128? There is no strict rule
> for that, instead they are used in order of appearance. This makes it hard
> for programmers to stick to agreed standards. Instead people rather ignore
> insertion codes altogether. They are really poorly soppurted by many
> programs. Perhaps switching to mmCIF gets rid of the problem.
>
> Cheers,
> Robbie
>
> > -----Original Message-----
> > From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of
> > Ian Tickle
> > Sent: Wednesday, December 05, 2012 16:39
> > To: [email protected]
> > Subject: Re: [ccp4bb] thanks god for pdbset
> >
> > The last time I tried the pdbset renumber command because of issues with
> > insertion codes in certain programs, it failed to also renumber the LINK,
> > SSBOND & CISPEP records. Needless to say, thanking god (or even God) was
> > not my first thought! (more along the lines of "why can't software
> > developers stick to the agreed standards?").
> >
> > I haven't tried it with the latest version, maybe it's fixed now.
> >
> > -- Ian
> >
> >
> >
> > On 5 December 2012 07:58, Francois Berenger <[email protected]> wrote:
> >
> >
> > Especially the renumber command that changes
> > residue insertion codes into an increment of
> > the impacted residue numbers.
> >
> > Regards,
> > F.
> >
> >
>
