Rotate the molecule into upright position by clicking and dragging with the left mouse button. Load the DNA molecule that you already studied in PyMOL by typing pymol. The commands are explained in the PyMOL manual. This is the most powerful way to interact with the program, but requires that you are familiar with the logic and syntax of PyMOL commands. For example, you can create dashed lines (a good way to show hydrogen bonds) between oxygens and nearby amide hydrogens in the alpha-helix by using a command "dist (helix and name o), (helix and (name h and neighbor name n)), 2.5". The command line allows you to type in commands that can accomplish almost any of PyMOL's functions.For example, you can select two atoms (first by CTRL-SHIFT/left-clicking, second by CTRL-SHIFT/right-clicking ) and create a covalent by pressing CTRL-T.
Furthermore, you can select and perform specific tasks via mouse and keyboard shortcuts. Your three-button mouse allows you to rotate, move, and zoom in/out by holding down the left, middle, or right button, respectively.
The main reasons of using a program such as PyMOL are affordability and accessibility: as a student you can download an educational version for free, and use it with any computer you have, be it Windows, Mac, or Linux. You will continue mastering this skill today with the help of another molecular visualization program, PyMOL.
But more importantly, you started learning how to think about the properties and functions of biological macromolecules via computer visualization. Welcome back to the molecular visualization tutorial! In the previous session, you became familiar with the Unix operating system, and learned some basic features of the program SYBYL. PyMOL Tutorial: Introduction Chem 110L: Macromolecular Visualization Laboratory Exercise: PyMOL