Dear Swapnil, there are many softwares which can be used for  multiple structure superposition . we use  pymol  or  chimera . these are freely available.

Thank you Arjun. I'll try them out.

ccp4: superpose

Dear Swapnil! there are two main approaches for superimposition of protein structures. One is "superposition" which is suitable for closely related structures and another one "structural alignment" which allows superimposition of structures with low identity. Both of them are realised in YASARA View which is free or higher (commercial) YASARA versions. But superposition requires the same molecule naming and residue numbering in YASARA

Try the Least Squares Comparison (Lsq command) in the program "O" (http://xray.bmc.uu.se/alwyn/A-Z_of_O/everything_e-l.html#anchor1340987) which according to my experience gives the best fit of the superposed structures.  

CCP4 supported program : gesamt. This program can superpose the search model with an entire PDB archive (i.e. a directory with all pdb files to align).   

QMOL, Abalone http://www.biomolecular-modeling.com/Abalone/index.html

Swiss PDB viewer.

VMD (http://www.ks.uiuc.edu/Research/vmd/) is very good at it and has a huge number of useful options, so you can always get what you want.

Pymol (http://www.pymol.org) can do that easily as well.

As Bartosz suggested, Pymol can be used, with the command "Super". Also you can try Coot, which has both SSM and Least Squares Superimposition. Or Theseus, that uses maximum likelihood.

You could just use SSM server, no software is required, can be done from any browser. 

http://www.ebi.ac.uk/msd-srv/ssm/cgi-bin/ssmserver

With UCSF Chimera. (https://www.cgl.ucsf.edu/chimera/) you have 3D match alignment   tools.

PyMOl ! nice and easy. No command line, just right menu under A(ctions) - "align to molecule X" and left mouse click

I agree wit most of the answers here, I just add a comment: try a multiple alignement before superpose your structures, it will help you on identifying a core of common/similar residues you can use to feed superposition. In fact with big structures and many loops could be difficult to correct superpose them unless you don't specify a core. For simple superpositions I found good this software (Superpose 1° link), available also as webserver, it allows you multiple superpositions at one time.

If you need to do a complicated jobs with involve also multiple alignments look at the 2° link.

http://wishart.biology.ualberta.ca/SuperPose/

http://www.cgl.ucsf.edu/home/meng/grpmt/structalign.html

thank you guys. I'm trying.

You can use PyMol for superimposing the structures. However it works better with FATCAT server. First get the structure aligned in this server then use PyMol to view it. Hope this works.

I will recommend you a software called MATRAS that was developed by Dr Kawabata. It is available at http://strcomp.protein.osaka-u.ac.jp/matras/index.html , and very fast.

Our lab has moved away from DeepView to routinely use Pymol and Chimera for superimposing protein structures. 

Discovery studio 3.5

As Niyaz Safarov suggested, for quick alignments I teach people to use the graphical interface of PyMOL. One useful addition is the ability to align selections of molecules to other molecules or to other selections. I'll type up some example tutorials here:

Basic:

Using selections:

FATCAT

Hi, I work on several programs. From my experience, Coot makes better superpositions than PyMol. For making pictures I save superimposed pdb files in Coot and work on them in PyMol. Cheers and good luck.

LOOS can do it too, using the iterative alignment algorithm in the program "aligner".

chimera can be used. u can use match command to superimpose domain by domain. or schrodinger is the best tools for superimposing protein structures.

I have used several softs and my suggestion is: 1. Use coot to extract molecular info. Coot makes good fit and you can notice much from these superimpositions. 2. For making pictures use PyMol. However load structures which had been superimposed in Coot and their coordinates were saved in Coot. 

i just used lsqman to superimpose structures. works well and there are options to improve fit using dp. try using that!

How do u superpose two protein complex structures?  I have a structure with a bound ligand and i want to compare with another structure from pdb with slightly different ligand bound at the same place. That is i have two different proteins and two different ligands

You can use coot, POSA, Superpose or FATCAT. 

Thank you everyone for the suggestions. (I hope its not too late for thanking you all)

You can use FATCAT server. Its preety good. Here is the link.

http://fatcat.sanfordburnham.org/fatcat-cgi/cgi/fatcat.pl?-func=pairwise

In pymol

Ligand protein complexes can be superposed in FATCAT. Use the 'download complete structure of protein A on protein B' option and edit pdb file manually. Alternatively, Coot has SSM and LSQ superpose that are quite good. For multi-proteins, you can use POSA or Coot. I have used coot for upto 5 structures. PyMOL is best for figure preparation

for the sequence alignment and a structural superposition, Pymol, is the best by this command "align protein1, protein2 ".

PyMol is a pretty decent option

UCSF Chimera

Phenix has such option

https://phenix-online.org/documentation/reference/superpose_pdbs.html