VMD

Molecular analysis or biological system visualization may sound like very complicated activities and the truth is they actually are quite complex. Usually, only specialists and those who study biophysics will come across these concepts on a regular basis, but since there are software applications closely related to them, pretty much anyone can get an insight on what this is all about.
VMD is one of the utilities directly involved in handling proteins as well as other types of molecules. You can use it to view the intricate structure of such particles, but those with experience in the above mentioned area will make the most of this tool.
The interface is not at all complicated, only the features it hosts may seem so to the untrained eye. There are lots of resources, most of them online, which can aid you understand the concepts and the functioning of this program, which will be of great help for anyone.
Here are a few molecules that are bundled with VMD, but you can select some of your own using the dedicated 'Molecule File Browser'. There is an option for having the kind of file that was loaded detected automatically and it is advisable to keep it that way, unless you know for a fact that the type presented by the app differs from the actual content of the selected file.
The OpenGL Display window will show you the graphical representation of the molecules you pick and the colors, materials and labels can be customized from the dedicated modules of VMD. Also, the display options can be easily modified so you can choose the desired light, axes or type of background.
Thanks to the impressive array of functions and extensions that are available or can be added inside VMD, this software manages to provide all the necessary tools for anyone involved in the practice or study of biophysics.