Editing Practical Pymol for Beginners (section)

==The PyMOL Interface==
When PyMOL is opened, two windows appear. The smaller window (called the "External GUI" in PyMOL documentation) contains the menu bar ('''File''', '''Edit''', '''Help''', '''Display''', etc), shortcut buttons for common commands, and the command line.

[[Image:Viewer_guide.png|right|thumb|The PyMol Viewer Window]]
The second window is the PyMOL Viewer, which is where all the magic happens. In the Viewer, 3D models are displayed, and the user interacts (eg rotates) and manipulates the model. 

The objects that PyMOL renders in 3D are loaded from coordinate files that describe (in great detail) locations of individual atoms in the molecule. 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. After each object name is a set of command buttons which control the object. Here are the buttons and some of their options:
* '''A''' - ''Actions'': Rename, duplicate, remove, apply presets (like "ball-and-stick" or "publication"), perform computations
* '''S''' - ''Show'': Change the way things appear, eg change to stick or cartoon view. 
* '''H''' - ''Hide'': Things that are shown using '''S''' accumulate, and don't automatically replace the last view. '''H''' is the opposite of '''S''' and hides unwanted representations. 
* '''L''' - ''Label'': Label atoms, residues, etc.
* '''C''' - ''Color'': Change the color of atoms and groups. 

The lower-right corner of the Viewer contains a guide to using the mouse, as well as a powerful selection tool. There is also another command line at the bottom of the Viewer ('''PyMOL>''').

===About the command line===
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. It can also be a lot faster. Combined with scripting, it is a powerful option for automating tasks and making intricate sets of changes. 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.

Although this guide may include some text commands and links to more advanced documentation, they're purely optional and meant to be informative. 

To run any text command, type it in at a '''PyMOL>''' command line and hit ''[Enter]''.