[BiO BB] PDB files on Cn3D

[Javier Forment Millet]

Yes, but I understand that it does not use directly the .pdb file from PDB. It
uses a MMDB-formatted file from MMDB. Maybe I'm wrong, but I understand from
this link that Cn3D just uses the PDB ID to identify the MMDB record
corresponding to that structure.



Quoting Shameer Khadar <skhadar at gmail.com>:

> http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3dtutP2.shtml#PDB_data
> This link says Structures in PDB can be visualised using Cn3D.
>
>
> 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
> > >
> > > =========================================
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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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> >
> >
>
>
> --
> K. Shameer
> ------------------------------------------------------------
> Computational Biology Lab, NCBS - TIFR
> Molecular Biophysics Unit, IISc
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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