[Biopython] PDBParser Class --> Output

[Peter Cock]

On Sun, Feb 13, 2011 at 1:52 AM, Willis, Jordan R
<jordan.r.willis at vanderbilt.edu> wrote:
> Hello,
>
> I am loving the PDB tools that are available with Biopython. I am
> getting a weird output I can't figure out when I parse a PDB. My
> code looks something like this.
>
> .....Thousands of lines
> G --> ?
> CD --> ?
> CE --> ?
> .......More lines
>
> I wouldn't mind so much except i have to parse thousands of pdbs and
> the unnecessary printing adds to the computation time.
> Any ideas how to turn this off?

That looks like it is failing to assign the element to those atoms. Do
your PDB files have the element column filled in? Which version of
Biopython do you have as there have been a few changes to this
bit of code recently... could you try the latest code from github?
http://www.biopython.org/wiki/SourceCode

Peter