The Graphics form is the most complicated form in VMD, which could be expected from a visualization program. The details of most of the subjects discussed below are covered in the special topics on selections, drawing methods, and coloring methods. In short, a molecule can have many different representation, also referred to as views. Each view consists of three parts: a selection, a drawing method (also called representation style, and a coloring method. The selection determines which part of the molecule is drawn, the drawing method defines which rendering representation is used, and the coloring method gives the the color of each part of the representation.
There are actually two parts to the graphics form. The Image Controls button brings up the controls used to alter the drawing and coloring methods. The Atom Name Lists button provides access to browsers which display the lists of atom names, residue names, and so forth for the selected molecule.
This form is used to control the appearance of one molecule at a time. The molecule it affects is selected in the `Selected Molecule' chooser at the top of the form. The browser below this chooser lists the views available for the molecule. Each line of the browser shows information about the drawing method, the coloring method, and the selection which completely specify the view. To change the attributes of a given view, click on the view that should be changed. The atom selection for that view will appear in the Atom Selection text area and, if the Image Controls button is pressed, the drawing and coloring method choosers will also change to reflect the current view.
To add a new view of the molecule, enter the selection into the Atom Selection text area (or keep what is there) and press Create New. This adds the view to the currently selected molecule.
To delete a view, select the view in the browser and press the Delete button. Bear in mind that this does not delete the molecule, it only deletes a view of the molecule. (To delete the molecule, use the Mol form.)
The drawing method indicates how the view's selected atoms are displayed in the graphics display window, and the coloring method indicates how to color the displayed atoms. The selected view's drawing and coloring methods are changed via the corresponding chooser. Some of the methods have additional controls which will appear when that particular method (either drawing or coloring) is chosen. The controls for the drawing method are:
Clicking on a field in the value browser will add it to the selection text field. Double clicking a keyword field adds the keyword to the text field. A double click is used so that the single click is available for simple viewing of the possible keyword values.
To clear the selection text for a given view double click on the Clear Changes button. The first (and every odd) click reverts the text to its previous setting, the second (and every even) click clears it completely.
A few details regarding the mechanism for `selections' is in order. For beginners, it is best to use the Atom Name Lists and the Image Controls together in order to generate and organize views. For instance, load a molecule and choose the Atom Name Lists option. If you double click on the name keyword, you will notice that two things happen. First, a listing of values appears to the right of the keyword. Second, the word ``name'' appears in the text selection window. Now if you go ahead and single click on some of the available values, you will notice that they are also printed in the text selection box. In this way you can use the mouse to generate a description of your selection and then hit Apply Changes in order to have that description register with VMD. The moral is, if you want to create a complex description quickly with the mouse:
As a final note, keep in mind that both the Color form and the Molecule form can be accessed from the Graphics form by clicking on the buttons located in the upper corners of the form.
For information about how the Tools work with atom selections, see Tool descriptions.
