Kurt,

I have been recently using PyMol for the same purpose and found it to be a big improvement from RasMol. I would also suggest the use of Swiss PDB viewer for the same purpose. It is also a freeware and has much more features that RasMol. The best software I've used till date is Accelrys Discovery Studio. It is a paid software, however, the visualizer is available for free and is great to use for students at the beginning level of structural biology.

Hi Kurt,

            I regularly use UCSF Chimera for the molecular visualization. It is  user friendly and lots of tools are available for the structural analysis. You can also save the session.  Discovery studio visualizer is also good, but i will suggest Chimera.

As per my experience, PyMol is the best freeware visualization software. After that, Chimera is the best one.

Dear Kurt,

I would recommend you PyMOL, conclusively.

UCSF chimera covers lot of modules as like Pymol. it is freeware and can be used for matching structures, calculating distances between atoms, energy minimization, different type of visulation of structure, like RIBBON, ATOM, SURFACE,etc. Also color labeling can be done easily.Images for high quality can also be rendered. also it is easy to convert files from one format to another by using this tool. I myself used to work with Pymol but rather find Chimera more user friendly and easy to operate even for beginners.

I would highly recommend using UCSF Chimera.

although others programs can be used to perform these tasks like MGL Tools, Avogadro, swiss pdbviewer, jmol etc.

Thank you @Dev, @Vikash, @Shakti, @Alžběta, and @Tanuj for your insights. I do have experience with Pymol, UCSF Chimera, and SwissPDB (and many others) in my research group. I tested Pymol and SwissPDB in a teaching environment once and abandoned it as many students found them too "complicated".

Good to step back, look around, and try new things once in a while. I am re-evaluating current software for teaching purposes, will put Pymol and UCSF Chimera on a shortlist and make another student trial as soon as possible.

Chimera is an excellent tool. Being a beginner in Structural Biology myself, I found it much easier to navigate around and analyze structures.

Thanks @SR. A beginner's insights are very helpful. 

It depends on your teaching objectives and the molecular literacy and computational competence of the student. We use PyMOL to teach biomedical science graduate students from several disciplines to analyze structures and make publication quality figures. We have had several non-structural biology students publish papers with figures that they made independently with PyMOL. I use a teaching spiral approach to progressively introduce more advanced features. It is very easy to overwhelm students with too much information. Chimera is easier to use than PyMOL to do sophisticated structure analyses, so it would be more appropriate for an advanced course protein structure analysis. 

Thanks for your comments @Blaine.

I concur. It is too easy to overwhelm new and inexperienced students. Very important to match the software and educational goals to the ambition and ability of the student. I believe it is more important for new students to "get their feet wet" and experience what can be seen, than make an investment in learning a program that may serve them better in the long run. As you know, once you know one program and have an idea what you want to investigate, learning another program is not so difficult.

I like PyMol because it can gently ease the students into things: they can generate quite sophisticated figures just by using point-and-click interface and presets in the action menu, easing them gradually into the command-line interface to gain more control, which then automatically lead into pml scripting .

I highly recommend 

C.Mura, C.M. McCrimmon, J.Vertrees, M.R. Sawaya “An Introduction to Biomolecular Graphics” PLoS Computational Biology 8 (2010) Vol. 6, pp 1-11  

Thank you for the reply, Kurt!

I agree with you that exposing students to what is possible is valuable if they already have a modest to high levels of molecular literacy. If they do not, the most awe-inspiring tour de force of molecular graphics may go right over their heads if they do not understand what they are seeing.

For beginners with low to modest molecular literacy, I follow Annemaries's go-easy approach. I have been guilty of overwhelming students with too much information in the past. I now lead the students with an interactive PyMOL session through a series of skill-building exercises starting with the control of the viewing port by the mouse. These exercises are peppered with explanations of molecular structure. I start our second class with a review of the basics because many students are not yet hooked enough to have done much self-guided learning and need a reminder of the basics. I give them a pdf with the commands that I use so that they copy and paste these onto the command line of the external GUI as they follow along.  The document also allows them to reproduce the results from class on their own at a later time.

I learned how to use Jmol because a student suggested it.  I now use Jmol to make certain kinds of figures in my research. It has some capabilities that PyMOL lacks.  However, I decided to stick with PyMOL in my teaching because if a student is going to bother to learn how to use a molecular graphics program, they would prefer to invest their time in one that gives publication quality figures with a modest amount of knowledge and skill.

I too have been requiring the reading of Mura et al. 2010 for several years. It contains a goldmine of valuable advice by leading master PyMOL users and developers. That landmark paper was an important gift to the structural biology community.

I prefer chimera.

I would recommend you PyMOL and chimera due to their easily understandable interfaces for students.