Draw Style Tab

Figure 4.6: The Graphics form (in Draw Style mode)

Select a molecule for editing using the `Selected Molecule' chooser at the top of the form. The browser below this chooser lists the reps available for the molecule. Each line of the browser summarizes information about the drawing method, the coloring method, and the selection. Below this browser, choosers and a text input filed reflect the current state of the rep, and provide controls for changing the properties of the rep. Each drawing method has specific controls which will appear when it is selected. When the `ColorID' coloring method is selected, 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 16.

Changing a rep.

To change a representation, select it in the representation browser. The atom selection for that rep will appear in the Selected Atoms text area and the controls will update to reflect the current settings. Changing the settings will immediately affect the displayed representation if the Apply Changes Automatically check box is selected. When it is disabled updates will only occur when the Apply button is pressed. Changing the drawing method brings up method-specific controls and defaults. If you go back to the previous draw style, VMD restores any changes that you may have made to the settings. Pressing the Default button will restore the default settings. The display will be updated after every change.

Adding a rep.

To add a new representation of the molecule, enter the selection into the Atom Selection text area (or keep what is there) and press Create New. This adds the representation to the currently selected molecule.

Deleting a rep.

To delete a representation, select the representation in the browser and press the Delete button. Bear in mind that this does not delete the molecule, it only deletes one of its graphical representations.

Hiding a rep.

To hide a rep, double-click its entry in the browser. The text will turn pink to indicate that the rep is hidden. Turn the rep back on by double-clicking again on the same line. Note that hidden reps will still recalculate their geometry if the animation frame changes.

Rep auto-update.

When an atom selection such as water within 3 of protein is made, the atoms in the selection are computed for the current animation frame. When the animation frame changes, the selection is not normally recalculated; thus the displayed atoms may not correspond to those that would be selected if the atom selection were performed for the new animation frame. If the Update Selection Every Frame checkbox is highlighted by clicking on the checkbox, then the atom selection for the current rep will be recalculated every time the animation frame changes.

Selections Tab

Figure 4.7: The Graphics form (in Selections mode)

The Selections tab provides access to browsers which display the lists of atom names, residue names, and so forth for the selected molecule. When the Selections tab is pressed, several browsers appear in place of the drawing and coloring method controls. These are used to list the available keywords, macros, and values for use in selecting atoms for the associated representation. The top browser lists singlewords and macros such as all, water, and hydrophobic. The botton 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 bottom-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. Press Apply to actually change the atom selection for the current rep. Press Reset to restore the atom selection to its original value.

The Selections tab also shows the atom selection macros that have been defined. These macros let you define a commonly used atom selection as a single word so that it can be inserted into a rep more conveniently. Atom selection macros can currently be defined only through the Tcl or Python text interfaces; see these sections for details.

Smoothing Tab

The Smoothing tab is used to control the application of a per-representation windowed-averaging smoothing function. This simple smoothing feature can be used to eliminate much of the thermal noise inherent in a molecular dynamics trajectory so that one can more easily see structural changes occuring over a wider time scale. The window size parameter controls how many timesteps are averaged together to produce a the coordinates which are actually used to display the representation. One important consideration when using the trajectory smoothing feature is that VMD does not take periodic boundary conditions into consideration when smoothing trajectory coordinates, so any atoms which wrap around within the span of the window will cause erratic motions in the displayed representation. This can be avoided by unwrapping trajectory coordinates prior to loading into VMD or by using atom selections to eliminate atoms which wrap around.