[Biopython-dev] Features of the GSOC branch ready to be merged

[Eric Talevich]

On Wed, Dec 1, 2010 at 12:15 PM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> On Wed, Dec 1, 2010 at 5:01 PM, João Rodrigues <anaryin at gmail.com> wrote:
> > I also noticed one thing: metal ions like CA and CL have their names
> > starting one character before regular C and N atoms. That allows some
> > discrimination between CA (alpha carbon) and CA (calcium) for example.
> I'd
> > never noticed this before, ...
>
> Is this documented in the PDB format definition? More importantly,
> do third party tools follow this rule? They are the only reason we
> need the code to guess the element in the first place, right? (Since
> the PDB provided files should all have the element column).
>
>
I think can rely on this convention. I'd read this somewhere else (maybe on
one of Andrew Dalke's pages) but didn't think to apply it to João's problem.


Here's a reference:
http://bmerc-www.bu.edu/needle-doc/latest/atom-format.html#pdb-atom-name-anomalies

-Eric