Another aspect of this interface that drastically reduces the need for command line arguments can be found in this tab. Using a series of buttons and sliders the user has the ability to alter characteristics such as cartoon width, tube width, cartoon type, various transparencies, sphere size, etc.When the update button is clicked, the viewing window will be instantaneously updated. The nature of objects in PyMOL allows users to set different sizes and transparencies for different sections of the molecule. For this reason, there is a label on the bottom of the window telling the user what the current selection is. The current selection, determines what part of the molecule the advanced commands will be applied to.
Cartoon Settings