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. But more importantly, you started learning how to think about the properties and functions of biological macromolecules via computer visualization. You will continue mastering this skill today with the help of another molecular visualization program, PyMOL.
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. A secondary reason is that PyMOL offers a uniquely powerful way to create remarkably stunning images and animations that help to understand molecules under study. PyMOL is not as capable as SYBYL in some areas. For example, it is not designed for building molecules or performing many types of calculations that commercial programs such as SYBYL do.
According to the program's author, Dr. Warren DeLano, PyMOL is a molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations. It can also perform many other valuable tasks (such as editing PDB files) to assist you in your research.
Two unique and valuable features of this program over some other visualization program are the use of the powerful programming language (Python) and an emphasis on high-quality graphics. At the present time the program is still undergoing active development, but it is mature enough to be used for learning and research. During the early development, emphasis was placed on providing functionality, and not on intuitive user interface. As a result, it takes a little time to learn the program. You can interact with the program via four complimentary ways
Open a new Unix shell. Load the DNA molecule that you already studied in PyMOL by typing pymol ../MOL/DNA.pdb and let the program start. Rotate the molecule into upright position by clicking and dragging with the left mouse button. Notice the five columns, labeled | A | S | H | L | C | in the task bar on the right side. These letters stand for Actions, Show, Hide, Label, and Color, respectively. Notice the two rows, labeled all and DNA. You can change the appearence of individual objects, such as DNA using the menu items under these letters. Lets Show the object DNA in Sticks.
Now, lets color each chain uniquely. Notice the green Selecting field near the bottom of the task bar. It says Residues by default, but you want to select chains. Left-click of the field until it says Chains. Now left-click on any atom in one of the chain; notice that the whole chain is selected. Now select a Color such as smudge from greens. Click on any atom in the other chain to select it, and color it firebrick from red. Inspect your work; think if this was a good color combination for distinguishing the two strands of DNA? Once you have decided on best colors, save your image using the Save Image As ... PNG from the File menu. Incorporate this image into your lab report. You can insert PNG image files into your Office documents by selecting Insert -> Picture -> From File ...