[Biopython] PDB Construction Error

[Peter]

Please try and keep discussions on the list,

On Thu, May 6, 2010 at 11:17 AM, Bhima Auro van der Molen wrote:
>
> Hi Peter,
>
> Thanks for the response.. I thought it might be a typo somewhere however I don't
> know enough about the BioPython code to fix it myself yet..
>
> I am a bit curious that the is being raised is a PDB Construction error...
>
> As I said, I am storing DSSP data in the b-factor column, as is done using the
> hsexpo.py script, but in order to be thorough in a statistical analysis I need to
> randomise that data and assign it randomly to residues in the PDB file.. I am
> not making any changes to the atomic co-ordinates of any of the residues.. the
> only data that gets re-written in this process is the b-factor column. What would
> cause a PDBConstruction Error to be raised?
>
> Thanks
>
> Bhima

Hi Bhima,

The PDB Construction error (or rather PDBConstructionException) is being
raised in  the _parse_coordinates method, and indicated one or more of the
three atomic coordinates could not be turned into floats. Perhaps they are
badly aligned (in the wrong column)? Could you send me the problem PDB
file (off list - sending attachments to mailing lists is a bad idea)?

If you are creating the problem PDB file with the Biopython hsexpo script
this may indicate a problem elsewhere in Biopython (perhaps in the PDB
output code).

Peter