[BiO BB] Re: [BioPython] Automated ligand extraction from PDB

[Kalidas Yeturu]

Hi
 I would like to add to what Mr.Shameer has said.
 When DNA is a ligand, in many PDB files, it goes with ATOM instead of
HETATM -token; in such cases
 you can "grep" on "A or T or C or G" for residue-name field.

Regards
Kalidas. Y

On 10/20/06, Shameer Khadar <skhadar at gmail.com> wrote:
>
> I strongly beleive this can be done using a 'grep' and 'substitution'
> commands in linux.
> Since the ligand data starts with HETATM, they can  be easily grepable.
>
> No need any 'parser' - a simple perl script can do this !
> Cheers,
> Shameer Khadar
> NCBS-TIFR
> B'lore
>
> On 10/20/06, Tomek Jarzynka <tomee at genesilico.pl> wrote:
> >
> > Hi,
> >
> > I would like to create a script that would take a PDB file as input,
> > try and identify the ligand structures and delete them from the PDB
> > file. I figured this would be possible with Biopython by looking at
> > the atom id (whether it contains 'H_') and subclassing Select to
> > not allow those items to be written to a file.
> > Is there any more elegant way of doing this, perhaps another PDB parser
> > framework, or maybe someone has already done similar work?
> >
> > Thanks in advance,
> > --
> > Tomasz K. Jarzynka  /  +48 601 706 601  /  tomee(a-t)genesilico(d-o-t)pl
> > Laboratory of Bioinformatics and Protein Engineering | www.genesilico.pl
> > International Institute of Molecular and Cell Biology | www.iimcb.gov.pl
> >
> > "You can have either freedom of speech or quality of communication.
> >         -- Orson Scott Card"
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> >
>
>
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-- 
Kalidas Y
http://ssl.serc.iisc.ernet.in/~kalidas
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