Click S, then cartoon to show the protein's secondary structure in popular cartoon form. Each button contains a submenu with more options. The right side of the Viewer shows the loaded PDB as an object, as well as its command buttons.The protein's structure will appear, probably rendered as simple bonding lines. In this example, a PDB file describing a protein is loaded and its style and color are tweaked.įetch 1 bl8 and you can skip the next step (see Fetch command), as PyMOL will open the file for you. PyMOL is great for casual visualization of biological molecules.
To run any text command, type it in at a PyMOL> command line and hit. But, it's complex, and page upon page of PyMOL documentation cover these commands, so we're going to ignore them as much as possible.Īlthough this guide may include some text commands and links to more advanced documentation, they're purely optional and meant to be informative. Combined with scripting, it is a powerful option for automating tasks and making intricate sets of changes. The PyMOL command line is a great tool that lets the experienced user change all sorts of options that simply don't appear in the point-and-click graphical interface. There is also another command line at the bottom of the Viewer ( PyMOL>). The lower-right corner of the Viewer contains a guide to using the mouse, as well as a powerful selection tool. C - Color: Change the color of atoms and groups.H is the opposite of S and hides unwanted representations. H - Hide: Things that are shown using S accumulate, and don't automatically replace the last view.S - Show: Change the way things appear, eg change to stick or cartoon view.