I have a set of pdb files which I have to seggregate into monomer, dimer (homo+hetero) and protein-nucleic acid. Kindly help with the keyword to look for, I shall write my code accordingly. Thanks in advance.
You can use VMD program (http://www.ks.uiuc.edu/Research/vmd/). It is graphical program for showing structures of proteins and their complexes and manipulating these structures. In addition, you can also save the coordinates of the structures (either complex or monomers) as PDB or other formats.
By complex structure, I think you mean bounded structure.
You can use any visualizer like Chimera, PymoL, Discovery Studio, or even VMD as suggested by Hiqmet Kamberaj.
Moreover, you can even edit your file manually.
Search for MOL_ID, MOLECULE, and CHAIN.
check the MOL_ID for the number of chains, for a file with two proteins, mol_id 1 and mol_id 2 must be there, molecule shows the name of the protein or nucleic acid and chain shows the number of chains of the same molecule.
I think it will be easy using visualisation tools
if you want to do it manually by editing PDB file than:
if you have only two proteins or chains than u can differentiate it using chain id as a identifier...
if you have ligand bounded protein than ligand atoms have HETATM , so you can differentiate using it also...
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