[BiO BB] PDB files on Cn3D

[Shameer Khadar]

Is this MMDB format avaialable through openbabel for format conversion ?

On Mon, Nov 17, 2008 at 11:54 PM, Javier Forment Millet <
jforment at ibmcp.upv.es> wrote:

> AFAIK, Cn3D is not able to open .pdb files. It uses a specific format.
>
> >From the Cn3D FAQ
> (http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3dfaq.shtml#NOPDB):
>
> Cn3D reads only data files from the MMDB database, not PDB formatted
> records.
> MMDB is derived from the PDB database, but is corrected for
> naming-problems,
> performs domain-splitting, assigns consistent secondary structures, adds
> complete bonding information, and finally makes protein sequences
> corresponding
> exactly to the residues that appear in the structure. This work is done by
> a
> series of programs not possible to include in Cn3D.
>
> So...
>
>
>
>
> Quoting Shameer Khadar <skhadar at gmail.com>:
>
> > Hi,
> >
> > I trust you can download a standalone version of Cn3D from NCBI and use
> it
> > for visualization of custom .pdb files.
> > http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml
> >
> >
> > On Thu, Nov 13, 2008 at 5:30 AM, Javier Forment Millet <
> > jforment at ibmcp.upv.es> wrote:
> >
> > > Hi, all... Does anyone know any way to open custom .pdb files with the
> Cn3D
> > > tool?
> > >
> > > --
> > > Javier Forment Millet
> > > Instituto de Biología Celular y Molecular de Plantas (IBMCP) CSIC-UPV
> > >  Ciudad Politécnica de la Innovación (CPI) Edificio 8 E, Escalera 7
> Puerta
> > > E
> > >  Calle Ing. Fausto Elio s/n. 46022 Valencia, Spain
> > > Tlf.:+34-96-3877858
> > > FAX: +34-96-3877859
> > > jforment at ibmcp.upv.es
> > >
> > >
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> > >
> >
> >
> >
> > --
> > K.  Shameer
> > NCBS - TIFR
> >
> > =========================================
> > | Indulge | Innovate | Inspire |
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> >
>
>
> --
> Javier Forment Millet
> Instituto de Biología Celular y Molecular de Plantas (IBMCP) CSIC-UPV
>  Ciudad Politécnica de la Innovación (CPI) Edificio 8 E, Escalera 7 Puerta
> E
>  Calle Ing. Fausto Elio s/n. 46022 Valencia, Spain
> Tlf.:+34-96-3877858
> FAX: +34-96-3877859
> jforment at ibmcp.upv.es
>
>
>
> _______________________________________________
> BBB mailing list
> BBB at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/bbb
>
>


-- 
K. Shameer
------------------------------------------------------------
Computational Biology Lab, NCBS - TIFR
Molecular Biophysics Unit, IISc