# Overview of the Interface

The EZ-Viz graphical user interface (GUI) was devloped as a plugin for Delano Scientific's molecular cisualization program, PyMOL. It features a notebook style design with separate tabs to distinguish one section from another. There are a total of nine tabs with the titles; Welcome, Presets, Settings, Commands, Movies, Information, Advanced, Save, and About. Each individual tab has a series of buttons, menus, and entry fields which the user can employ to manipulate the appearance of their molecule in PyMOL’s viewing window. An additional row of buttons is displayed along the bottom of the EZ-Viz window at all times. These buttons are used primarily for loading files into the PyMOL viewer, accessing the help file, clearing the viewing window, and quitting EZ-Viz.The interface utilizes a PDB file parser that is used to identify the separate structures that exist within the molecule that is currently being viewed. Using this information, the program creates a number of unique objects in PyMOL, such as DNA, RNA and protein that can be individually altered. If a molecule does not contain a certain type of structure, such as DNA, an object will not be created for it.

### The Commands Tab

On this tab you will also find the Chime/PyMOL converter. The converter will allow you to input either Chime or PyMOL commands into and entry field and have the command executed in the PyMOL viewer window.Also, the radio buttons found here allow you to control some of the features of the PyMOL Viewing window. You can turn on stereo viewing for cool 3D images, change the background color to make you image stand out, and even hide the original PyMOLinterface.

### The Settings Tab

Here you will find a series of pre-defined views that you may want to use to view your molecule. Some of the views include a default view that distinguishes alpha helices from beta sheets, a color by chain view, and a ball and stick model. This tab also contains all the buttons you need to select attributes of your molecule (protein, DNA, chains, water molecules, etc.) and change the way they appear in the viewer. You can show and hide molecular representations, such as spheres, mesh, sticks, and surface, as well as change the colors.

### The View Options Tab

This tab gives the you more control over what the representations you're seeing in the viewing window. Some of the features you'll have control over are the size of spheres and sticks, the width and thickness of cartoon, and the ability to make the molecule transparent.

### The Information Tab

This is where you'll find specific information about the molecule you're working with beyond it's PDB ID number. Sequence information for each chain, the molecule's classification, and list of all the hetero atoms found in your molecule are just some of the things you'll find here.

The Button Box

On the bottom of the interface you will see a group of five buttons that are available for yout to use at all times. These buttons are used for some common taks such as loading a PDB file, clearing the viewing wincow and quitting EZ-Viz.

The Movie Tab

This tab features some general movies that can be created with almost any molecule that you bring into PyMOL. There is also a control panel that allows you to control the playback of the movie after its been created.