[BiO BB] PDB files on Cn3D

Javier Forment Millet jforment at ibmcp.upv.es
Mon Nov 17 13:24:22 EST 2008


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





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