Hello!

In my point of view, there is no "top choice". Each software has his own advantage, but I will put 3 softs on my top list : 

•  Pymol : developed now by Schrödinger. A open source and a paid version is available.  The open source is very complete (you have more features for videos in the paid version but it's not really useful because you can script your videos).

Is relativelly easy to use and you can find a lot of tutorial on the web. You also have a great and active wiki (http://www.pymolwiki.org/index.php/Main_Page) where users share their own plugins that you can add easily. The ray casting command is also relatively quick and produce beautiful images. The command line syntax is not hard to understand either.

For a linux or windows installation of the latest source I invite you to see this tutorial on my website (http://http://tubiana.me/how-to-install-and-compile-pymol-windows-linux/). For Mac OS X you can install macPymol (wich is free)

• USCF Chimera : This is completely free and you have a mac version. Chimera support a lot of format (pdb, gro, mol2, but also density map from cryoEM for example). It is well adapted for very big structure like virus capsid and provide tools for symmetry models. You can also find plenty of features to analyse and modify your structure. 

Great pictures and animation are not difficult to do with this software and you can find a lot of examples with a script in the gallery section of the official website (http://www.cgl.ucsf.edu/chimera/).

The command line syntax is a little trickier than Pymol, but with some tries you will get it.

• VMD : Also free and compatible with mac (http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD). If you want to deal with molecular dynamic trajectories, it is the best choice! You can quickly load and display them. You also have some analyse tools adapted for PDB and molecular dynamics and you can find some plugins. It is also well adapted for big structure because it's very memory optimized but the command line and scripting language is in TCL. If you never have programmed before, it can be hard to start with this.

Personally, I use Pymol and chimera to produce images. Pymol to visually analyse a pdb (intereaction between ligand and protein, hydrogen and salt bonds, secondary structures etc...). Chimera to work with my virus capsids and produce videos, and VMD to work with molecular dynamics :-)

Regards,

Thibault.

http://www.pymolwiki.org/index.php/Main_Page

http://tubiana.me/how-to-install-and-compile-pymol-windows-linux/

http://www.cgl.ucsf.edu/chimera/

http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD

i suggest you VMD is good and complete

Any suggested link to download MacPyMol. The one I tried, once installed does not load properly (PyMol application is created, but when clicking on the icon, nothing happens, with no error message). I have Mac OS X Yosemite version 10.10.2. Thanks

The latest version of VMD (1.9.2) has some cool features to produce very nice figures. Check out this Youtube video made by the group who develops VMD. https://www.youtube.com/watch?v=ip7lmmD7Z2k

https://www.youtube.com/watch?v=ip7lmmD7Z2k

pymol and chimera u can use

Hello! can I ask how to run Swiss PDB Viewer in mac? Thank you

Check https://spdbv.unil.ch/ for instructions. Seems non-trivial, as DeepView is 32 bit software.

I can recommend VMD and Discovery Studio Visualizer (Biovia).