[Biopython] PDB bfactor

[Eric Talevich]

Hi Fabian,

Since it's a limitation of the wwPDB format, you could try a different
format, e.g. mmCIF or PDBML.
http://pdbml.pdb.org/

Or, if the extra accuracy is only needed internally in your program, you
could store the B factors, or even the whole structure's data, in a Python
pickle or some other non-PDB serialization. Or a database.

-Eric

On Tue, Oct 26, 2010 at 1:43 AM, Fabian Glaser <fglaser at technion.ac.il>wrote:

> Hi Joao,
>
> Yes I know that there are only 5 characters alloted, I was hoping to
> find a way to bypass that... I need more accuracy.
>
> Thanks a lot,
>
> Fabian
>
> On Mon, Oct 25, 2010 at 5:14 PM, João Rodrigues <anaryin at gmail.com> wrote:
> > Hello Fabian,
> >
> > Please have a look here:
> > http://www.wwpdb.org/documentation/format32/sect9.html#ATOM
> >
> > The PDB format is quite annoying because it's basically space-based. So,
> for
> > the B factor, you have 5 characters alloted meaning it is usually YY.XX
> >
> > Therefore, although some programs might accept longer B factors, the
> Parser
> > will reject it.
> >
> > Best!
> >
> > João Rodrigues
> >
>
>
>
> --
> ------------------------------------------------------
> Fabian Glaser, PhD
> Bioinformatics Knowledge Unit,
> The Lorry I. Lokey Interdisciplinary
> Center for Life Sciences and Engineering
> Technion - Israel Institute of Technology
> Haifa 32000, ISRAEL
>
> E-mail: fglaser at technion.ac.il
> Tel:    +972-4-8293701
> Fax:   +972-4-8225153
>
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