It seems that MMDB format is not available through openbabel: see all the formats available through openbabel at:
http://openbabel.org/wiki/Category:Formats Quoting Shameer Khadar <[EMAIL PROTECTED]>: > Is this MMDB format avaialable through openbabel for format conversion ? > > On Mon, Nov 17, 2008 at 11:54 PM, Javier Forment Millet < > [EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]>: > > > > > 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 < > > > [EMAIL PROTECTED]> wrote: > > > > > > > Hi, all... Does anyone know any way to open custom .pdb files with the > > Cn3D > > > > tool? > > > > > > > > -- > > > > Javier Forment Millet > > > > Instituto de Biolog�a Celular y Molecular de Plantas (IBMCP) CSIC-UPV > > > > Ciudad Polit�cnica de la Innovaci�n (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 > > > > [EMAIL PROTECTED] > > > > > > > > > > > > _______________________________________________ > > > > BBB mailing list > > > > [email protected] > > > > http://www.bioinformatics.org/mailman/listinfo/bbb > > > > > > > > > > > > > > > > -- > > > K. Shameer > > > NCBS - TIFR > > > > > > ========================================= > > > | Indulge | Innovate | Inspire | > > > _______________________________________________ > > > BBB mailing list > > > [email protected] > > > http://www.bioinformatics.org/mailman/listinfo/bbb > > > > > > > > > -- > > Javier Forment Millet > > Instituto de Biolog�a Celular y Molecular de Plantas (IBMCP) CSIC-UPV > > Ciudad Polit�cnica de la Innovaci�n (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 > > [EMAIL PROTECTED] > > > > > > > > _______________________________________________ > > BBB mailing list > > [email protected] > > http://www.bioinformatics.org/mailman/listinfo/bbb > > > > > > > -- > K. Shameer > ------------------------------------------------------------ > Computational Biology Lab, NCBS - TIFR > Molecular Biophysics Unit, IISc > _______________________________________________ > BBB mailing list > [email protected] > http://www.bioinformatics.org/mailman/listinfo/bbb > -- Javier Forment Millet Instituto de Biolog�a Celular y Molecular de Plantas (IBMCP) CSIC-UPV Ciudad Polit�cnica de la Innovaci�n (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 [EMAIL PROTECTED]
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