[Bioperl-l] PDB ATOM records: name, segid, etc.

[Kris Boulez]

Quoting Andrew Dalke (adalke@mindspring.com):
> Kris Boulez:
> 
> > I'll give a lightning talk about Bio::Structure at BOSC 02. We might
> > also discus this in more depth there.
> 
> How about a BoF on the topic?
> 
Yes, as long as it's not concurrent with another bioperl BOF.

> Me:
> >> It includes a 1.x and 2.x format description, as well as commentary
> >> about the XPLOR differences.
> >>
> >> ftp://ftp.ks.uiuc.edu/pub/group/dalke/UPDB-0.5.tar.gz
> 
> Kris:
> > Downloaded it. Found the 1.x format description and will have a look at
> > it.
> 
> As I recall, I typed that in based on my hardcopy from about 10 years
> ago.  I can bring a copy of that with me to Canada if you want to see
> some history.  :)
> 
Let's do that.

> 
> Not meaning any sort of disrespect.  I bring it up because even
> in chemistry things like SSSR (Smallest Set of Smallest Rings) isn't
> usually discussed.  That is what Daylight uses to compute which
> rings are aromatic.  The appropriate reference for this algorithm
> is Balducci and Pearlman, from JCICS in 1994.  I have a copy if
> you want me to bring that as well.
> 
> There is also trickiness for things like "chirality unknown but
> opposite to *that* chirality."  And I've heard several different
> chemists argue about if a given nitrogen is *really* an aromatic
> or not.
> 

Stop, please :)

When I worked at university I had an office opposite of someone who was
an expert in IUPAC nomenclature for organic molecules. 

Kris,