Well to be honest, I don't think that there is such a thing as "the best" software for visualization, that depends greatly on which one is the software that you feel more comfortable with, and the skills you have to work with it. A simple comparison (i.e. just visual) can easily be done with VMD (http://www.ks.uiuc.edu/Research/vmd/). More complete analysis can be made with pymol (http://www.pymol.org/ ; but you will need to know a bit of how to use it and is not as straight forward) or kinemage (http://kinemage.biochem.duke.edu./).

Most of them can show you the differences, and playing with them, will give you the answers you need. Pymol and Kinemage (not sure about VMD) can also give you stearic clashes between atoms, and you can move them around (using a particular rotamer library), so you can see how different a point mutation might be from the energetic perspective.

All of the above, is assuming you have them already aligned. Pymol have some utilities to align them, but I will trust other more specialized software to align structures, such as MATT, FATCAT, etc...

Hope this is of help.

Well to be honest, I don't think that there is such a thing as "the best" software for visualization, that depends greatly on which one is the software that you feel more comfortable with, and the skills you have to work with it. A simple comparison (i.e. just visual) can easily be done with VMD (http://www.ks.uiuc.edu/Research/vmd/). More complete analysis can be made with pymol (http://www.pymol.org/ ; but you will need to know a bit of how to use it and is not as straight forward) or kinemage (http://kinemage.biochem.duke.edu./).

Most of them can show you the differences, and playing with them, will give you the answers you need. Pymol and Kinemage (not sure about VMD) can also give you stearic clashes between atoms, and you can move them around (using a particular rotamer library), so you can see how different a point mutation might be from the energetic perspective.

All of the above, is assuming you have them already aligned. Pymol have some utilities to align them, but I will trust other more specialized software to align structures, such as MATT, FATCAT, etc...

Hope this is of help.

A very good molecular visualization tool is UCSF Chimera ( http://www.cgl.ucsf.edu/chimera/ ) which is often more powerful than VMD, makes much more beautiful graphics, and it is less cumbersome than PyMol. (VMD is still essential however for analysis of simulation trajectories, and it has the advantage of being much more lightweight). Chimera includes a relatively good and quick structure alignment tool, MatchMaker (which is sequence-based, but makes sense if you have very related proteins), and has other structure alignment options: see http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html

Also, if you want to align structures independently from a visualization software, you could try LOVOALIGN.

Thanks Massimo and Jose!

I originally started playing with Deep View software but I got a bit lost in the tutorials and overall I didn't find it very user-friendly.

I had a look at the software you suggested and I think the range covered pretty much all I want to do: align, superimpose and compare the bits that are different. I will start playing with them and see how I go!

I provide another online server: http://www.ebi.ac.uk/msd-srv/ssm/ssmstart.html.

The EBI-SSM(secondary structure matching) works well when superimpose two 3D protein structures, as they stated one of the function is "pairwise comparison and 3D alignment of protein structures ". Most of of , it is easy to handle.

I use PyMOl and Chimera for such purpose. They both work very well.

I have used CCP4mg and PyMOL for comparing structures. Both handle it well I would say.

pymol software is used.....to compare