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

[Kris Boulez]

Quoting Andrew Dalke (adalke@mindspring.com):
> 
> > Does someone know where I could find descriptions of 'older' PDB
> > formats. The current parser is written based on a document titled
> > 'Protein Data Bank Contents Guide: version 2.1 (october 25, 1996)' .
> > 
> > If so I would certainly add other versions.
> 
> I have an old project called "UPDB" which is a parser generator for
> PDB files -- given a format description it produces a parser in Python,
> Perl, Tcl, and maybe a couple other languages.  Never went anywhere (yet).
> 
> 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
> 
Downloaded it. Found the 1.x format description and will have a look at
it.

> 
> > At the moment the Atom object is purely a container for info in the PDB
> > file. It only knows it's id ('CZ2'), it does not know that it is a
> > carbon.
> > 
> > Problem with these spaces is that people want to be able to say
> > 
> >   if ( $atom->id eq "CZ2" ) {
> > 
> > without bothering about the spaces and/or rearrangement of the name in
> > the PDB files
> > 
> > A ->display_id() method, which would give the name as it was in the PDB
> > file, might help
> 
> You need that to distinguish between " CA " and "CA  " (carbon alpha and
> calcium).  Better is to add the proper logic because everyone else will
> be confused as well.  And still make the original string accessible in
> case you got it wrong. 
> 
Yup, will do something along these lines.

> 
> > Which other format would people be intrested in ?
> 
> In large molecule chemistry, no one I know of has switched to mmCIF.

Other people in the X-ray field I had contact with said exactly the same
thing.

> 
> In small molecule chemistry there are a few other important formats:
[ .. ]
> 
> The problem with these is that they require good support for:
>    - bond types/orders
>    - aromaticity
>    - chirality
> 
> and if you are only used to dealing with PDB files you likely
> won't know how these should be handled. 

I did a major in chemistry, so these concepts are known to me.
> 
> Another place to look for details on these formats is Babel/OpenBabel
>   http://openbabel.sourceforge.net/
> 
The idea is not to add as much formats as possible, just to add the
formats that people really use.

Kris,
-- 
Kris Boulez 				Tel: +32-9-241.11.00
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