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.A - Actions: Rename, duplicate, remove, apply presets (like "ball-and-stick" or "publication"), perform computations.Here are the buttons and some of their options: After each object name is a set of command buttons which control the object. PyMOL can display more than one object at a time, and provides an Object Control Panel to adjust viewing modes, colors, labels, hiding, and just about anything else relating to objects.
The objects that PyMOL renders in 3D are loaded from coordinate files that describe (in great detail) locations of individual atoms in the molecule. In the Viewer, 3D models are displayed, and the user interacts (eg rotates) and manipulates the model. The second window is the PyMOL Viewer, which is where all the magic happens.
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