[Biopython] Bio.PDB question - from PQR to an "extended" PDB
paul at tonair.de
paul at tonair.de
Thu Oct 13 10:26:54 UTC 2011
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?
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. 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?
Cheers & Thanks,
Paul
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