[Biopython] Reading in chimera generated files

[Patrick McGrath]

Thanks... the fix worked for my purposes though i don't use any of those
elements so i can't determine whether there were any potential downstream
issues with the change.

On Tue, May 5, 2015 at 7:31 AM, Peter Cock <p.j.a.cock at googlemail.com>
wrote:

> Hi Patrick,
>
> Assuming Biopython is interpreting the PDB specification correctly,
> you should file a bug with Chimera.
>
> Separately, you could look into replacing this assert statement with
> either an error or warning (as used elsewhere in Bio.PDB in order
> to tollerate somewhat improper files in strict or permissive mode).
>
> As a quick hack, do bad things happen if you replace the assert
> line with this?:
>
> element = element.upper()  # Hack for tools like Chimera
>
> Peter
>
> On Tue, May 5, 2015 at 11:57 AM, Patrick McGrath <ptmcgrat at gmail.com>
> wrote:
> > Hello,
> >
> > I am trying to use Bio.PDB to read in a PDB file generated from
> matchmaker
> > in chimera. It seems that Chimera changes the HG to Hg and ZN to Zn in
> the
> > last column of the pdb file which causes an error:
> >
> > assert not element or element == element.upper(), element
> > AssertionError: Hg
> >
> > Is there any solution to this besides creating a script to manually edit
> the
> > pdb file generated by chimera?
> >
> > _______________________________________________
> > Biopython mailing list  -  Biopython at mailman.open-bio.org
> > http://mailman.open-bio.org/mailman/listinfo/biopython
>
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