[Biopython] Bio.PDB question - from PQR to an "extended" PDB

[Peter Cock]

On Thu, Oct 13, 2011 at 11:26 AM,  <paul at tonair.de> wrote:
>
> dear biopython users,
>
> i'm trying to read in a pqr file with the
> Bio.PDB module. In a PQR file, the atom charge and atom radius are
> stored instead of the occupancy & B-factor.
> Apparently, the negative
> charge values make trouble while reading in.
>
> (1) Is there a way to
> tweak Bio.PDB module to read in a PQR file?

If a negative B-factor was the only issue, probably yes.

> More to the background of
> this task: I would like to keep the charge and the radius in order to
> output a PDB file with more than 80 lines.

You mean more than 80 columns? i.e. Longer than PDB norms?

> The pdb-like output looks
> like this:
> ATOM 1 C1 UNL _0001_000 9.643 1.777 18.433 1.700 0.000
> BK____M000
> The text "BK____M000" refers to a conformer of a side chain
> and is needed by a PoissonBoltzmann named mcce (multi-conformation
> continuum electrostatics).
>
> (2) Can Bio.PDB generate such an output
> file?

Not yet ;)

> Cheers & Thanks,
> Paul

It would help if you could share some sample data (URLs) and links
to this PDB-like PQR file format's specification (assuming it has one).

Regards,

Peter