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Graphics Form

Figure 4.4: The Graphics form (in Image Controls mode)

Figure 4.5: The Graphics form (in Atom Name Lists mode)

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.)

Image Controls

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:

The Material pulldown menu allows you to select a material for the current drawing representation. There are two pre-defined materials, named "Opaque" and "Transparent". Materials can be created and modified using the Materials Form. Also, when `ColorID' is chosen for the coloring method, a text entry box is shown allowing you to specify the index of a color to use for the selection, which may be a number from 0 to 15.

Atom Name Lists

When the Atom Name Lists button is pressed, two browsers appear in place of the drawing and coloring method controls. These are used to list the available keywords and values for use in choosing atoms for the selected views. The left browser contains a list of the keywords and functions understood by the selection command. If a keyword is selected which can take on a value (for instance, name and index), then the possible names will be displayed in the rightmost browser. The functions can be identified by the ( to the right of the name. After selecting a keyword, the right browser will display all the names associated with the keyword. For example, selecting resname in the left browser will show all the three-letter residue names known for the selected molecule.

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.

Changing Views

In addition to adding or removing views from a molecule, this form is also used to change how an existing view is displayed. After selecting a view for a specific molecule, the form's controls are updated to show the current settings for that view. Changing the settings will automatically change the respective view, and the new format will be shown in the graphics display window. The display will be updated after every change, however, which is sometimes not always desirable (for example, if a number of different aspects need to be changed at once). The Apply Changes Automatically button may be toggled off to change this behavior - if it is turned off, selected changes will only be applied when the Apply Changes button is pressed. Selecting a different view, or pressing the Clear Changes button, before applying the changes will reset the form controls to the current settings of the selected view.

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.

The Tool Selection Button

Next to the Apply Changes button on the Graphics Form is the Tool Selection button. This button allows the tools defined in the Tracker form to affect certain atom selections, rather than simply a single atom or the entire molecule. Only one atom selection, if any, can be assigned to the tools. To make the assignment, click on the desired representation in the browser window so that it is highlighted, then press the Tool Selection button. If you have multiple representations or multiple molecules loaded, the button will be lighted only when the assigned representation is highlighted. To clear the assignment, again highlight the previously assigned representation in the browser window (when it is found, the Tool Selection button should be on) and press the button. Deleting the assigned representation also has the effect of clearing the assignment.

For information about how the Tools work with atom selections, see Tool descriptions.

next up previous contents index
Next: Animate Form Up: Description of each VMD Previous: Files Form   Contents   Index