FirstGlance in Jmol is the easiest way to look at the 3D structures of proteins, DNA, RNA, and their complexes. It works within a web browser, and was designed to enable the readers of scientific journals to see the main features of newly published 3D models in a few clicks, without installing anything, and in all popular web browsers and computer platforms.
VMD is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure.
From the University of Illinois Urbana-Champaign: VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer.
Custom molecule structures can also be downloaded to the device from any publicly available web server. The location of these structures can either be manually specified in the application, or custom URLs, such as molecules://www.sunsetlakesoftware.com/sites/default/files/neonPump.pdb.gz , can be clicked on within Safari or Mail on the device. This will launch Molecules and have it start downloading the file at that address.
$ Browse protein, DNA, and drug molecules in 3D. The app has a direct link to the Protein Data Bank (PDB) and DrugBank and has a fast and easy to use interface. Touching the molecules via the screen allows you to interact immediately with the 3D structures.