BOL

First to open and visualize protein structure you use any one of this tools : RASMOL,JMOL,SPDBV,Cn3D,Chimera, DSViewerPro60, PyMOL.

if you want to identify the chain,ring,atoms and specific part of the percular protein molecule then in the different software there is different menu for visulization option. so you can download manual of software that you are using and see the visulization menu. some software like RASMOL,Chimera have a commandline also so you can also identify the atom,chain,ring etc by using command. you can download manual of commands or you can google it.

Thank you.

Hi Bhavana,

There are several software available online for your job. You can find links, which includes free software for 3D molecular visualization. My favourate tool for molecular-graphics, modeling and simulation program powered by PVL (Portable Vector Language).

http://www.science.co.il/Biomedical/Molecular-Graphics-Software.asp

http://www.chembiogrid.info/related/resources/molviztools.html

http://en.wikipedia.org/wiki/List_of_molecular_graphics_systems

Thanks

Hi Bhavana,

There are many software to this work for you. They have cached libraries to describe common bond types. The tag "CONECT" to describe the specific connectivity of exogenous molecules. I recommend you to read about mol format defined here http://www.tripos.com/data/support/mol2.pdf

The BOND block of mol2 or SD files defines which atoms are bonded to which and in what way (single, double, triple, aromatic etc.) In other word most file formats explicitly define connectivity. These CAN be specified in a PDB format file using the CONECT tag, but this is not required for small molecules in protein-ligand complexes.

The VMD can also be useful for you
http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD

Thanks