There are a large number of tools available for visualising, manipulating and analysing protein structures and models. The list below is by no means complete. Instead it is my attempt to get you started with some of the tools I've used that I think were pretty good. The best tool for you will be determined by what you want to do. Hopefully you can try the options below and discover which ones do what you need.
I am giving the briefest possible outline of each tool as all of them, even the simplest ones, have a large number of features that I don't want to go into here. Also, I am not an expert in any of these tools, so take my descriptions with a large grain of salt!
For a more exhaustive list of tools, visit the RCSB Here
This is a standalone version of the jmol viewer used in the Phyre2 site.
Pros Small and lightweight, good for quickly getting a feel of your structure, under constant development, free and open-source. A good starting point, Jmol was originally based on Rasmol (see below).
Cons Don't expect to do any deep analysis or simulations with it. The README that came with it was useless in figuring out what file to run. Based on java, so you may have troubles depending on your system set-up.
This was one of the first and I still use it a lot.
Pros Fast and simple to use, free and open source for everyone.
Cons Like Jmol above, less functionality than other systems listed here. Getting the right version for recent Mac OS X was a bit of a pain. Pretty old technology.
A very impressive application from UCSF.
Pros A very wide range of functionality, excellent options for fancy images, very well documented and constantly updated.
Cons Not many that I can see, except the range of things you can do is so large it may be daunting at first.
Available here.
A powerful platform but you may have to pay.
Pros Lots of options for rendering, movie making and structure manipulation.
Cons I personally find the layout and syntax of commands counterintuitive but your mileage may vary. Also it seems to only be free for 'teachers and students' and you have to register and see if you count as such a thing - otherwise you pay. A big downside to me.
Get it at www.pymol.org
Good for molecular dynamics work, not particular suited to making publication images easily or examining sequence-structure relationships - but I may be wrong!
Pros Seems to have a lot of functionality for advanced users, especially for molecular dynamics work, cross platform, free.
Cons I find the interface tricky and a bit archaic - for advanced users only I would say.
Get it here
Its surprising Accelerys give this away for free....
Pros Very impressive, easy to use, nice interface with lots of powerful applications. Free to all academic, government and commercial researchers.
Cons Only Windows and Linux (no Mac), need to register for a copy.
Get it here.
This is developed by the SwissModel team and can interact with the Swissmodel server.
Pros Lots of functionality and the dynamic interplay between the visualisation and the web server may be very helpful to some. Freely available to all, just a licence agreement to click. Lots of documentation, actively developed.
Cons Only available for Mac and Windows (no Linux). I personally find the interface a bit confusing, but as with all these things, there is a learning curve.
Get it here.
